Search tips
Search criteria 


Logo of oliMary Ann Liebert, Inc.Mary Ann Liebert, Inc.JournalsSearchAlerts
Oligonucleotides. 2011 April; 21(2): 55–75.
PMCID: PMC3078494

Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential


Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential.


Development of nucleic acid-based therapies for treatment of inherited diseases provides potential avenues for mitigating, if not eliminating, genetic disease-associated pathologies by correcting the underlying genetic mutations. Most nucleic acid-based therapies now in clinical trials involve the use of therapeutic transgene vectors that complement the missing or abnormal protein with a wild-type version of the defective protein. The complementing transgene is typically a cDNA or minigene with nonnative (heterologous) promoters, polyA sites, and other regulatory sequences inserted into a viral or plasmid delivery vector (Colosimo et al., 2000). This approach has several well-described problems. Transgene delivery vectors are usually incorporated randomly into cellular genomes and can lead to unpredictable transgene expression and gene silencing and transform cells to cancer (Cavazzana-Calvo et al., 2004; Cereseto and Giacca, 2004; BAUM, 2007; BUSHMAN, 2007; Cavazzana-Calvo and Fischer, 2007; Hackett et al., 2007; Pike-Overzet et al., 2007b). Although transgene-based therapies have had some success in treating monogenic disorders, it might be a case wherein the side effects mitigate the therapeutic potential of the treatment (Cavazzana-Calvo et al., 2001; Cavazzana-Calvo and Fischer, 2007; Pike-Overzet et al., 2007a; Thornhill et al., 2008).

The ultimate goal of gene therapy for inherited diseases is the correction of genomic mutations responsible for disease pathology. The ideal approach would leave the endogenous gene structure intact and maintain the natural linkage between the coding sequences and native regulatory sequences. Classical gene targeting strategies have been used successfully for over 20 years to engineer mouse models of disease and, more recently, for genetically modifying genes in mammalian somatic cells (CAPECCHI, 1989, 1994, 2000). However, one significant limitation of classical gene targeting is the inefficiency of the process, with only 10−6 to 10−7 transfected cells facilitating homologous recombination (HR) between the gene targeting vector and the chromosomal target. This may, in part, be due to the presence of nonnative DNA, drug selection, and DNA sequences that undermine the stability of the homologous pairing process. Further, drug selection genes typically contained in classical targeting vectors require subsequent cellular manipulations for their removal and often leave behind genetic footprints of nonnative DNA sequences. The developments in oligo/polynucleotide gene targeting strategies and in the use of recombinant nucleases that introduce site-specific double-strand breaks (DSBs) to enhance the frequency of HR are the focus of this review (Fig. 1).

FIG. 1.
Sequence-specific gene modification. Modification of a specific chromosomal locus (star) in cells may be performed using DNA with the normal wild-type sequence to correct a mutation or mutant sequences to introduce a mutation. The modifying DNA may be ...

For over two decades there have been efforts to develop alternative gene therapy strategies that focus on gene targeting, that is, sequence-specific modification of endogenous mutant sequences without the limitations associated with classical gene targeting or transgene approaches (BOGGS, 1990; VEGA, 1991; WALDMAN, 1992; Porter and Dallman, 1997; GRUENERT, 1998, 1999; Yanez and Porter, 1998; Lai and Lien, 1999; Richardson et al., 2001; Vasquez et al., 2001b; Wu et al., 2001; Vasquez and Glazer, 2002; Gruenert et al., 2003; Igoucheva et al., 2004; Kuan and Glazer, 2004). The approaches discussed use oligonucleotide (25–200 nucleotides or bp in length) or polynucleotide (>200 nucleotides or bp in length) sequences to induce sequence-specific modifications of native genomic targets. Several of these strategies have shown promise in terms of both the cell-type versatility and the apparent efficiencies of gene modification that can be achieved. Each strategy can be defined in terms of the oligo- or polynucleotides used to affect the homologous exchange and include polynucleotide small DNA fragments (SDFs), triplex-forming oligonucleotides (TFOs), and single-stranded oligodeoxynucleotides (ssODNs/SSOs) (Table 1).

Table 1.
Oligo/Polynucleotide Gene Targeting Approaches

Chimeric RNA/DNA oligonucleotides (RDOs) are another class of oligonucleotides that have been used for gene targeting and have shown to achieve correction efficiencies up to 50% (Kren et al., 1999b). However, the reproducibility of the studies has been limited in mammalian systems (Zhang et al., 1998; de Semir et al., 2002; TAUBES, 2002a, 2002b). There are numerous speculations about the mechanism underlying RDO-mediated exchange (Kren et al., 1999a; Gamper et al., 2000a; Richardson et al., 2001; Andersen et al., 2002), and it has been suggested that the limited reproducibility of previous studies in multiple independent laboratories is related to the synthesis of the RDOs. Although this system may have applications for sequence-specific gene modification and repair, the difficulty in reproducibly achieving high levels of homologous exchange in multiple laboratories makes it less attractive as a potential therapy (Diaz-Font et al., 2003; Manzano et al., 2003) and will therefore not be discussed in detail.

The oligo/polynucleotide gene targeting strategies using SDFs, TFOs, and SSOs have shown promise and may provide new paradigms for therapeutically manipulating the genome of individuals with inherited diseases or generating animal models for disease (Gruenert et al., 2003; Aarts et al., 2006, 2009; Goncz et al., 2006; Maurisse et al., 2006a; Andrieu-Soler et al., 2007; Murphy et al., 2007; Todaro et al., 2007; Sangiuolo et al., 2008; Zou et al., 2009). Thus, an understanding of the nuances of the application of these systems, their analysis and the potential mechanisms that underlie their efficacy is critical to their development as a viable therapy.

Oligo/Polynucleotide Gene Modification Strategies

Therapeutic oligo/polynucleotides generally carry a limited number (between 1 and 5) of modifying bases within a segment of DNA that is otherwise homologous to the target sequences. While more base mismatches may be used, their effect on efficacy needs to be tested empirically for each oligo/polynucleotide construct. The oligo/polynucleotide-mediated homologous exchange process relies on the endogenous cellular machinery to affect an exchange between the exogenous nucleotide sequences and the endogenous target sequences (Tables 24). This enzymatically driven “genetic surgery” both maintains the integrity of the gene and will minimize permanent regional chromatin remodeling that could change gene expression patterns (Cavazzana-Calvo et al., 2004; Cereseto and Giacca, 2004; Evans-Galea et al., 2007). The cellular machinery involved in oligo/polynucleotide homologous exchanges is not well defined for human cells. Extrapolating from what is know about classical HR pathways in bacteria and yeast, it is likely that DNA repair (particularly nucleotide excision repair, NER) and replication genes and pathways play a primary role the process of sequence-specific modification (Table 2 and Fig. 2). However, the actual mechanisms that underlie oligo/polynucleotide-mediated modification require further elucidation and are the subject of numerous studies (Swagemakers et al., 1998; HABER, 1999; Yanez and Porter, 1999, 2002; Taniguchi et al., 2002; Vasquez et al., 2002; GRUENERT, 2003; Gruenert et al., 2003; Villemure et al., 2003; Shivji and Venkitaraman, 2004; Yang et al., 2004; Igoucheva et al., 2006a; Sleeth et al., 2007; Zhang et al., 2007).

Table 2.
DNA Repair Genes and Pathways
Table 4.
Chromosomal Gene Targeting: Heterologous Gene
FIG. 2.
DNA repair pathways. There are 5 primary DNA repair processes that respond to sequence and/or structural changes in the DNA. Single-stranded DNA damage is generally repaired using the complementary strand as a template. Single-base damage generally engages ...

It has been difficult to gain insight into similarities and differences in the mechanisms underlying the various oligo/polynucleotide gene targeting approaches, because of the variability in the exogenous DNA, the genetic target, the cell systems employed, and the approaches used to analyze the efficiency of homologous exchange. Since there are multiple DNA repair and replication pathways (Fig. 2 and Table 2) that depend not only on the type of DNA modification, but also on the cell type and the stage of the cell cycle (eg, HR is likely involved in S-phase repair), it is difficult to generalize about the involvement of specific mechanisms in the homologous exchange process for an individual strategy. The situation becomes even more complicated when the exogenous modifying/therapeutic DNA (referred to as “therapeutic DNA” from this point forward) is either single-stranded DNA (ssDNA) or double-stranded DNA, is of varying lengths, and/or contains a variable number of mismatches, modifications of the bases, sugars, 5′ or 3′ ends, or the backbone; placed in different regions and sequence contexts within the therapeutic DNA (Jain et al., 2008). A number of studies have begun to investigate potential pathways for specific gene targeting approaches and have shed some light on the involvement of general pathway and enzymatic features of a given approach (Kucherlapati et al., 1985; KUCHERLAPATI, 1987; GRUENERT, 1998, 2003; Yanez and Porter, 1999; Datta et al., 2001; Vasquez et al., 2001b; Igoucheva et al., 2004, 2006a; Terunuma et al., 2004; Ferrara and Kmiec, 2006; Goncz et al., 2006; Knauert et al., 2006; Radecke et al., 2006b) (Table 2). Understanding the role that these pathways play in modulating oligo/polynucleotide-based sequence modification will be critical for development and optimization of therapeutic efficacy and assessing potential adverse outcomes.

ssODN/SSO targeting

ssODN/SSOs (for the purposes of this review, SSOs will be used) are <200 bp in length. SSOs are comprised of a single mismatch to the target sequence that is generally in the middle of the molecule (Fig. 3). SSOs were initially evaluated using plasmids carrying reporter genes (Campbell et al., 1989) or in the targeting of the HPRT1 gene in lymphoblasts (Hunger-Bertling et al., 1990; Kenner et al., 2002, 2004; Hegele et al., 2008; Wuepping et al., 2009). Although SSOs have been synthesized with phosphorothioate backbones (Gamper et al., 2000b), 2′-O-methyl uracil (Igoucheva et al., 2001) or with 5′ or 3′ thymidine clamps (Hegele et al., 2008) to inhibit degradation, they have also been used without modification to facilitate homologous exchange.

FIG. 3.
Oligo/polynucleotide homologous exchange. (A) Triplex-forming oligonucleotide (TFO)-mediated recombination. TFOs have a bipartite structure that contains sequences that are favorable for triple helix formation (black) and donor DNA sequences homologous ...

Analysis of cellular responses after transfection with either SSOs or plasmids indicated that a greater number of genes involved in DNA repair, cell cycle arrest, and apoptosis were upregulated after transfection with a plasmid when compared with transfection of SSOs (Igoucheva et al., 2006a). Thus, the frequency of genomic correction was ~5-fold higher when the SSOs were cotransfected with an unrelated plasmid when compared with transfection with the correcting SSO alone. These studies clearly suggest that cellular DNA repair processes influence SSO-mediated, sequence-specific modification of genomic DNA.

One repair pathway, mismatch repair (MMR), appears to suppress SSO-mediated targeting of genomic DNA, but not episomal gene targeting through MSH2 (Dekker et al., 2003; Aarts et al., 2006). Studies evaluating MMR showed that SSOs were effective in correcting mutations in reporter genes that had been introduced into msh2 −/− cells, but not in wild-type cells, unless the expression of MSH2 was transiently inhibited by RNA interference. However, when the target was episomal, SSO-mediated modification was observed in both the wild-type and msh2 −/− mouse embryo fibroblasts, whereas it was reduced in CHO cells defective in NER (Igoucheva et al., 2006a).

Studies targeting different reporter genes generally indicate that there is a higher efficiency of correction with the antisense, nontranscribed SSO target (Igoucheva et al., 2001; Nickerson and Colledge, 2003; Pierce et al., 2003; Olsen et al., 2005b; Yin et al., 2005). When comparing the efficiency of correction in CHO cells carrying a single integrated lacZ, the clone with higher lacZ mRNA expression had a relatively greater gene targeting efficiency for the transcribed sense than the untranscribed antisense SSOs compared with a clone that had lower level of expression (Igoucheva et al., 2003). This study suggests that transcription may be a factor in the correction process. However, one might also view this result in the context of chromatin accessibility. As the lacZ transgenes in the individual clones are likely integrated in different regions of the genome, their chromosomal environment is different in terms of gene expression. There are data to suggest that the antisense SSOs are more effective at facilitating homologous exchange than their sense counterparts; however, there is also evidence that there are no strand-associated differences in SSO-mediated targeting (Dekker et al., 2003). Whether these contradictory findings reflect differences in the cells used in the targeting studies requires further analysis.

In addition to the implications that DNA repair pathways are involved in modulating SSO-mediated gene modification, higher efficiencies of modification were also observed for cells stalled in S-phase (Brachman and Kmiec, 2005; Olsen et al., 2005a; Wu et al., 2005), indicating that DNA replication and/or the chromatin structure may also be involved. In this context, there is a possibility that an SSO can be incorporated into the genome as Okazaki fragment during replication (GRUENERT, 1998; Wu et al., 2005; Radecke et al., 2006b). Several studies showed physical incorporation of an SSO into the genome (Radecke et al., 2006b; Hegele et al., 2008) and also indicated that in the presence of DSBs, SSOs appear to act as a template and are not incorporated (Radecke et al., 2006a). This suggests that the mechanism for incorporation of the SSO into the genome may not involve the HR or the nonhomologous end joining (NHEJ) pathways that are activated by DSBs (Thompson and Schild, 1999).

Small fragment homologous replacement/SDF

Small fragment homologous replacement (SFHR) modification is distinct from SSO-mediated modification in that the SDF polynucleotides used in SFHR (generally between 200 and 2000 bp/nt in length) are larger than the SSOs and are either individual ssDNA, complementary ssDNA, or double-stranded DNA. The term “polynucleotides,” rather than oligonucleotides, will be used to designate SDFs.

SFHR effectively relies on (1) an SDF, carrying a single or multiple base alterations, finding its sequence homolog (genomic or episomal), and (2) the cellular enzymatic pathways that facilitate homologous exchange between target sequences and the SDF. Although there has been speculation about the mechanism(s) that underlie SFHR (GRUENERT, 1998, 1999, 2003; Gruenert et al., 2003), there is still only limited knowledge of the cellular factors that influence SFHR (Fig. 3).

SFHR has been shown to occur in a variety of cell types both in vitro and in vivo, targeting a number of different genes related to inherited diseases (Table 3). Previous studies have demonstrated SFHR-mediated modification of genes associated with sickle cell disease (Goncz et al., 2006) and β-thalassemia (Colosimo et al., 2007) (β-globin), cystic fibrosis (CFTR) (Kunzelmann et al., 1996; Goncz et al., 1998, 2001, 2002; Sangiuolo et al., 2002, 2008), Duchene's muscular dystrophy (dystrophin) (Kapsa et al., 2001, 2002; Todaro et al., 2007), severe combined immune deficiency (DNA-dependent kinase catalytic subunit) (Zayed et al., 2006), alpha-1 antitrypsin deficiency (alpha-1 antitrypsin) (McNab et al., 2007), spinal muscular atrophy (survival motor neuron-1) (Sangiuolo et al., 2005), and Lesch-Nyhan syndrome (hypoxanthine-guanine phosphoribosyl transferase, HPRT) (Bedayat et al., 2010).

Table 3.
Extrachromosomal Gene Targeting

Although most corrections are single base substitutions, studies with the CFTR concentrated on the most common mutation, a 3-bp deletion in human CFTR exon 10 resulting in a phenylalanine deletion at codon 508 (ΔF508) (CONSORTIUM, 1990; Tsui et al., 2010). Approximately 1% of immortalized CF airway epithelial cells homozygous for the ΔF508 mutation have been functionally and/or genotypically corrected following transfection with an SDF that reinserts the 3 deleted bases (Kunzelmann et al., 1996; Bruscia et al., 2002; Sangiuolo et al., 2002). A ΔF508, 3-bp deletion mutation was also introduced into primary human airway epithelial cells in vitro (Goncz et al., 1998), mouse airway epithelium in vivo (Goncz et al., 2001), and in mouse embryonic stem cells (Sangiuolo et al., 2008). Studies using the SDF-transfected mouse embryonic stem cells indicated that at least 12% of the CFTR mRNA transcript was ΔF508 and that there was a significant reduction in cAMP-dependent chloride efflux.

Thus far there have been only a limited number of studies that have explored the mechanisms that underlie SFHR-mediated modification. One study, using an episomal target, evaluated how components of different DNA repair pathways influence SDF-mediated episomal repair (Fig. 2 and Table 2) (Morrison and Wagner, 1996). This study indicated that cells defective in genes encoding for Ku80 (NHEJ), Mlh-1 (MMR), xeroderma pigmentosum complementation group C (NER), ataxia telangiectasia mutated (DNA damage response/repair, cell cycle regulation), or ADP-ribosyl transferase (base excision repair) show no differences in their ability to undergo homologous replacement when compared with normal controls. The study evaluated correction of an episomal target within 48 hours of transfection, thereby suggesting that episomal homologous exchange mediated by a double-strand SDF is not affected by each of these pathways independently. Although this study and that evaluating SFHR in a DNA-dependent kinase catalytic subunit knockout mouse cells (Zayed et al., 2006) suggest that SFHR is independent of the NHEJ pathway, the role of the HR repair pathway needs to be confirmed. In addition, the possibility that components from both the NHEJ and HR repair pathways, acting in concert, may influence episomal homologous exchange cannot be ruled out.

Studies with hRad51, a key element in HR, indicate that hRad51 overexpression will slightly enhance (up to 3-fold higher) homologous replacement in an episomal target (Yanez and Porter, 1999; Thorpe et al., 2002), but will not significantly improve the frequency of homologous exchange in genomic DNA (Yanez and Porter, 2002). Evaluating an episomal target provides some insight into the process of polynucleotide-mediated homologous exchange, whereas episomal gene targeting and genomic gene targeting appear to be mechanistically distinct. This is consistent with the findings of studies using SSOs indicating that there are differences between episomal targeting and targeting in chromatin (Igoucheva et al., 2001, 2006a, 2008; Olsen et al., 2005a; Ferrara and Kmiec, 2006; Radecke et al., 2006a, 2006b; Murphy et al., 2007). Whether there are elements of each type of homologous exchange that overlap is clearly an area open to further investigation.

Another study evaluating genomic homologous exchange mediated by an SDF used a severe combined immune-deficient mouse defective in the DNA-dependent kinase catalytic subunit (DNA-PKCS), a component of the NHEJ repair pathway. This study indicated that SDFs could mediate homologous exchange at the DNA-PKCS locus (Zayed et al., 2006). Taken further, one would expect an increase in homologous replacement as the cells are forced to rely on the HR machinery because of the defect in the NHEJ pathway. It therefore appears that the NHEJ pathways do not play a substantive role in the SFHR/polynucleotide-mediated homologous exchange process.

TFO-mediated targeting

TFOs are ssODNs/SSOs, generally 10–40 nt in length, that bind to specific regions in duplex DNA as a third strand to form a triple helix. These triple helices, originally described >50 years ago (Felsenfeld and Rich, 1957), were formed at polypurine or polypyrimidine regions of DNA bound via Hoogsteen hydrogen bonds to TFOs (Kallenbach et al., 1976). Because of their high binding affinity, TFOs have been used to manipulate genes and gene function, for example, for sequence-specific induced mutagenesis in plasmids (Wang and Glazer, 1995) or mice (Vasquez et al., 2001a) or for enhanced intrachromosomal recombination (Luo et al., 2000; Datta and Glazer, 2001) (Fig. 3). TFOs have also been used successfully for gene targeting by tethering an SDF to a TFO directed to the proximity of the sequence to be modified. These studies showed correction of an episomal reporter gene that had been transfected into mammalian cells (Chan et al., 1999; Maurisse et al., 2002). In addition, TFO-mediated correction of adenosine deaminase-deficient human lymphocytes and p53 mutant human glioblastoma cells has been demonstrated (Culver et al., 1999).

Studies evaluating the enzymatic pathways that may underlie the TFO-mediated homologous exchange indicate that NER is involved (Wang et al., 1996; Duval-Valentin et al., 1998; Christensen et al., 2008) (Fig. 2). These studies indicated that sequence-specific mutagenesis or intramolecular episomal HR was not detectable in cells deficient in the xeroderma pigmentosum group A (XPA) gene, whereas XPA cells complemented with the wild-type XPA cDNA or naive wild-type cells were able to facilitate the HR (Faruqi et al., 1996; Wang et al., 1996; Datta et al., 2001; Vasquez et al., 2002; Simon et al., 2008; Lonkar et al., 2009). TFO-induced mutagenesis was also not detected in cells deficient in the Cockayne's syndrome group B gene that is involved in the transcription-coupled NER pathway (Wang et al., 1996). In addition, there appear to be other repair pathways involved in TFO-mediated homologous exchange that can be enhanced in the presence of DSBs (Vasquez and Glazer, 2002; Villemure et al., 2003; Chin et al., 2007; Zhang et al., 2007; Chin and Glazer, 2009).

As sequences rich in polypurine and polypyrimidine often occur in the human genome (Goni et al., 2004), this sequence specificity also limits the ability of TFOs to target any DNA lesion. One approach to overcome this limitation has been to develop TFOs that have modified nucleotides such as locked nucleic acid or peptide nucleic acid residues to increase the affinity of the TFO for specific target sequences (Simon et al., 2008). Another approach has been linkage of the TFO to psoralens that bind to DNA upon UV light irradiation and both anchor the TFO to its target site and also stimulate DNA repair (Gruenert and Cleaver, 1985; Luo et al., 2000; Vasquez et al., 2001a; Broitman et al., 2003; Varganov et al., 2007; Liu et al., 2009b). Although the use of psoralens might be useful in a laboratory setting, it may not meet safety standards because of its ability to enhance DNA damage and potentiate carcinogenesis (Pathak et al., 1959; Pathak and Joshi, 1984; Gruenert et al., 1985; Tamaro et al., 1986). The UVA irradiation requirement for psoralens to form covalent linkage to the DNA is only feasible in skin or ex vivo through the use of a 2-photon laser (Vasquez and Legerski, 2010). Further, the UVA irradiation component of psoralen addition presents additional problems because of the production of reactive oxygen species (YOUNG, 1986; Carraro and Pathak, 1988; Moller et al., 1995; Viola et al., 2008).

Optimizing Gene Targeting

Optimization of the efficiency of oligo/polynucleotide-driven homologous exchange is a critical component for achieving therapeutic efficacy. As most of the oligo/polynucleotide-based approaches appear to involve elements of DNA repair and/or DNA replication (Biggerstaff et al., 1993; KUNKEL, 1995; GRUENERT, 1998, 2003; JIRICNY, 1998; Yanez and Porter, 1998; HABER, 1999; Ng and Baker, 1999; Bode et al., 2000; CAPECCHI, 2000; Ray and Langer, 2002; Saintigny and Lopez, 2002; Thompson and Schild, 2002; HELLEDAY, 2003; Wang and James Shen, 2004; Durant and Nickoloff, 2005; Wu et al., 2005; Bugreev et al., 2007; Cuozzo et al., 2007; Sleeth et al., 2007; Li and Heyer, 2008; Waldman et al., 2008), there are specific enzymatic mechanisms that can be investigated. It will be important to develop assay systems that can be readily used to quantify homologous exchange in the context of particular repair or replication mechanisms. There are a number of gene and cell systems that have already been developed, including the HPRT gene (Doetschman et al., 1987; Hunger-Bertling et al., 1990; Valancius and Smithies, 1991; Kenner et al., 2002; Hendrie et al., 2003; Ohbayashi et al., 2005; Pierce and Jasin, 2005; Hinz et al., 2006; Bedayat et al., 2010), green fluorescent protein (GFP) (Thorpe et al., 2002; Radecke et al., 2004; Olsen et al., 2005a; Tsuchiya et al., 2005c; Vasileva et al., 2006; Sakamoto et al., 2007; Kamiya et al., 2008), neomycin resistance (G418) (Song et al., 1985; Campbell et al., 1989; Manivasakam et al., 2001; Hendrie et al., 2003; Murphy et al., 2007), zeocin resistance (Colosimo et al., 2001), and β-galactocidase (Nickerson and Colledge, 2003). Although the reporter/selectable marker gene systems are often used, the HPRT system represents a gene in its natural genomic context and may more accurately reflect homologous exchange at other genomic loci. However, if these analytical endpoints are to be instructive with regard to specific DNA repair and replication mechanisms, it will be necessary to evaluate these endpoints under conditions where specific enzymatic components of a given pathway are incapacitated or activated. This can be either done in cell systems that are defective in specific DNA repair and/or replication enzymes, in cells where specific enzyme components are repressed, or in systems where specific pathways are activated.

Although some of these approaches have been pursued in particular cell systems where there is a genetic defect in an aspect of DNA repair or replication, there is still a great deal of ambiguity about which pathways predominate for any given oligo/polynucleotide base approach. Studies with TFOs have already demonstrated that there is a correlation between the XPA gene and the TFO targeting (Datta et al., 2001; Vasquez et al., 2002; Simon et al., 2008; Lonkar et al., 2009), and studies with SSOs suggest that MMR is involved (Whitehouse et al., 1996; Yin et al., 2005; Liu et al., 2009a; Olsen et al., 2009). On the other hand, SDFs appear to be DNA replication dependent and do not involve the NHEJ pathways (Morrison and Wagner, 1996; GRUENERT, 1998, 2003; Goncz et al., 2006; Zayed et al., 2006). There is still the issue of episomal vs. chromatin targeting that needs to be resolved, before there can be any accurate association between a specific pathway and a specific oligonucleotide strategy.

One potential avenue for optimizing the efficiency of homologous exchange is through the introduction of DSBs (Thompson and Schild, 2002; Golding et al., 2004; Nickoloff and Brenneman, 2004; Radecke et al., 2006a; Engels et al., 2007; Zhang et al., 2007). Although DSBs can be cytotoxic and mutagenic, cells have the capacity to repair such lesions through either NHEJ or HR (THOMPSON, 1991; JEGGO, 1998; Johnson and Jasin, 2001; Sonoda et al., 2001; Tamulevicius et al., 2007). DSBs can be induced through physical or chemical DNA damaging agents that either directly or indirectly generate lesions in the DNA. The random nature of physically or chemically induced DSBs make these approaches more challenging when developing a therapeutic regimen to correct pathological mutations (Li and Heyer, 2008). To circumvent the issue of random DSBs throughout the genome, strategies have been developed using rare cutting, sequence-specific endonucleases (Rouet et al., 1994; Choulika et al., 1995; Smih et al., 1995; Cohen-Tannoudji et al., 1998; Elliott et al., 1998; Johnson and Jasin, 2001; Cabaniols and Paques, 2008; Grizot et al., 2009, 2010), chimeric endonucleases with sequence-specific zinc finger motifs (Kim and Chandrasegaran, 1994; Kim et al., 1997; Chandrasegaran and SMITH, 1999; Smith et al., 1999; Bibikova et al., 2001, 2003; Porteus and Baltimore, 2003), and TFOs conjugated with125I (Mezhevaya et al., 1999; Sedelnikova et al., 2000) or pyrene (Benfield et al., 2008) to introduce DSBs at defined genomic loci.

The most studied rare-cutting endonuclease, I-SceI, is derived from yeast and has an 18-bp recognition site. As this 18-bp recognition sequence is not found in mammalian cells, the target DNA (whether episomal or genomic) must be modified to contain the unique recognition sequence before DSBs can be introduced (Choulika et al., 1994, 1995; Rouet et al., 1994; Smih et al., 1995; Sargent et al., 1997; Cohen-Tannoudji et al., 1998; Kim et al., 2001; Willers et al., 2001; Akyuz et al., 2002; Nickoloff and Brenneman, 2004; Saleh-Gohari and Helleday, 2004; Puttini et al., 2005; Radecke et al., 2006a). Numerous studies have clearly demonstrated that, when compared with uncleaved DNA or DNA that does not contain the recognition sequence, the frequency of homologous exchange is significantly increased when the target DNA containing the I-SceI recognition sequence is cleaved (Smih et al., 1995; Liang et al., 1998; Moynahan et al., 1999; Johnson and Jasin, 2001). A primary drawback in using I-SceI cleavage for generating DSBs in mammalian DNA is that there are no endogenous I-SceI recognition sequences in mammalian cells. The 18-bp recognition sequence must always be introduced into the cells near the target site to have a maximum effect. There is also a relationship between the cut site and the distance from the target site that shows a significant decrease as the distance from the target sequence increases, falling to 0% conversion after ~500 bp in one model system (Elliott et al., 1998).

The development of chimeric zinc finger nucleases (ZFNs) has provided an alternative to the I-SceI endonuclease to generate sequence-specific DSBs (Kim and Chandrasegaran, 1994; Kim et al., 1996; Porteus and Baltimore, 2003; CARROLL, 2004). These chimeric endonucleases are comprised of a customized sequence-specific zinc-finger domain linked to nonspecific nucleases for targeted cleavage (Kim et al., 1997; Chandrasegaran and SMITH, 1999; Bibikova et al., 2001; Porteus and Carroll, 2005). ZFNs have been successfully used to enhance targeted gene replacement by a donor plasmid in Drosophila (Bibikova et al., 2002, 2003; Carroll et al., 2008; Bozas et al., 2009) and human cells (Porteus and Baltimore, 2003; Alwin et al., 2005; Urnov et al., 2005; Potts et al., 2006; Lombardo et al., 2007; Pruett-Miller et al., 2008; Mittelman et al., 2009; Zou et al., 2009). The donor plasmid contains sequences essentially homologous to the endogenous target, with the exception of the bases to be modified in a bacterial plasmid backbone. One study has demonstrated that a ZFN/donor plasmid-mediated approach could correct a one-base frameshift mutation in the IL2RG gene in human erythroleukemia K562 cells and also demonstrated the expression of IL2RG mRNA and protein after correction (Urnov et al., 2005). In addition, ZFNs have been shown to enhance the correction of a mutant EGFP integrated in HEK293 cells by SSOs (Olsen et al., 2009) and SDFs (H. Parsi and D.C. Gruenert, unpublished data).

Although the endonuclease and ZFN strategies have a certain appeal for enhancing homologous exchange, they are similar to other cDNA-based gene therapies, in that they involve introduction of a therapeutic cDNA into cells to facilitate gene modification. There is the potential of eliciting an immune response to the ZFN protein because it is a foreign protein; however, this may be somewhat mitigated ex vivo. Moreover, it is possible that the ZFNs will cut at sites other than the ZF-directed site (Porteus and Carroll, 2005; CARROLL, 2008; Radecke et al., 2010). This nonspecific offsite cutting would generate multiple DSBs that could affect the karyotypic and genetic stability of the target cell. Clearly, these limitations will affect the therapeutic potential of any approach that relies on the introduction of DSBs. It will therefore be paramount to evaluate these aspects of enzymatically induced DSBs in cell systems that are directly relevant to the cells targeted by any given therapeutic strategy rather than surrogate cell lines.


The enhancement of oligonucleotide-mediated modification requires evaluation of multiple parameters that might influence efficacy or the assessment of efficacy. These include, but are not limited to, the genetic target to be modified, the degree of homology associated with the size and character of the therapeutic DNA, the cell type, the mode of transfection, the enzymatic pathways involved, and the method of assessing homologous exchange. Several studies have shown that even when the transfection efficiency between different cell types is similar, the efficiency of targeting can be quite different. One study indicated that, although the efficiency of transfecting a plasmid or oligonucleotide into CHO-K1 and HEK239 cells was the same (~80%), the efficiency of episomal gene correction varies from 29% for CHO-K1 cells to <2 × 10−3 for HEK293 cells (Igoucheva et al., 2006b). Another study also evaluating episomal targeting for the same pair of cells and the same target gene (lacZ) indicated an efficiency of 0.44% for the CHO-K1 cells and 2.6% for the HEK293T cells (Nickerson and Colledge, 2003). Although on the surface it appears that the studies are similar, there are significant differences that may provide some insight into factors that are significant for a particular gene modification method. The above studies were carried out with SSOs that were of different sizes, 45 nt (Igoucheva et al., 2006b) vs. 35 nt (Nickerson and Colledge, 2003). Although this 10 nt difference is small, it represents a significant fraction of the SSO length and may reflect the importance of length in SSO targeting. Alternatively, this difference may be a function of the proportion of cells in S-phase or the transfection method. Further, an examination of the sequences, that is, base composition, could be important in establishing reproducibility. Along those lines, one study indicated that a TA repeat at the 5′ end of an SSO is more effective at facilitating homologous exchange (Wuepping et al., 2009). Sequence is particularly important for TFO recognition and sequence-specific modification (Fox and Brown, 2005).

Other approaches using TFOs or SDFs also require close scrutiny of the transfection conditions for oligo/polynucleotide introduction, cell type, composition, and target. There appears to be a relationship between the SDF size and the targeting efficiency. However, there is only limited data in this regard. Preliminary studies in HEK293 cells indicate that smaller SDFs, within a range from ~200 to 500 bases, are more effective at targeting an integrated GFP (H. Parsi and D.C. Gruenert, unpublished observations). As indicated for the SSOs, there is also a distinct difference between the modification of a genomic or an episomal target. The reasons for this difference are not well defined; however, a previous study evaluating the induction of genes by a plasmid vs. an oligonucleotide suggests that the quantity of repair and replication genes transcribed after the introduction of a plasmid is significantly greater than those induced by an oligonucleotide alone (Igoucheva et al., 2006b). Therefore, the plasmid introduced during a study evaluating episomal targeting would likely activate multiple pathways relevant to the oligo/polynucleotide modification of the plasmid and thereby facilitate episomal targeting. Moreover, the episomal copy number (especially with replicating plasmids) is generally greater than that of the genomic target and further enhances the potential of detecting a targeting event.

Another consideration involves the assessment of the homologous exchange (Fig. 4). In the event that a phenotypic readout is not possible, as with correction of an allele where there is no chemical or physical means to facilitate enrichment of the modified cells, it becomes necessary to devise screening protocols that can identify modifications in the DNA and RNA. The most obvious assessment strategy is polymerase chain reaction (PCR) and reverse transcription–PCR analysis. Although, on the surface, PCR appears straightforward, there are important experimental design features that must be implemented to avoid aberrant or misleading results (Zhang et al., 1998; De Semir and Aran, 2003, 2006; Gruenert et al., 2004; Maurisse et al., 2006a). In particular, assessment of genomic DNA modification requires that the DNA be gel purified, especially at early time points following the transfection, to eliminate spurious amplification due to the presence of unincorporated oligo/polynucleotide (Maurisse et al., 2006b). The assessment of modification at the transcriptional level requires that the RNA samples be treated with DNase to avoid any contribution to the reverse transcription–PCR by residual oligo/polynucleotide (Goncz et al., 1998, 2001; Maurisse et al., 2006b). Analysis of the genomic DNA is generally more of a screening, whereas analysis of the RNA can be confirmatory under the appropriate conditions, for example, DNase treatment and a unique silent mutation present in the modifying oligo/polynucleotide that results in introduction of an restriction fragment length polymorphism. Clearly, a phenotypic functional readout is the most definitive indication that a homologous exchange has occurred.

FIG. 4.
Potential pathways for dsSDF-mediated homologous exchange: SDF repair of chromosomal DSBs. DSBs [eg, nuclease-induced (yellow) as well as replication anomalies and damage caused by physical or chemical agents] can activate intracellular exonucleases to ...

If oligo/polynucleotide-based gene modification strategies are to have therapeutic applications, the degree of random integration must be measured. The finding that the random integration of recombinant retrovirus led to adverse affects such as leukemia in the cDNA-based severe combined immune deficient-X1 clinical trials is an indication that insertional mutagenesis can compromise therapeutic efficacy (Cavazzana-Calvo et al., 2004; Williams and Baum, 2004; Evans-Galea et al., 2007). Given this observation, it appears that random integration of cDNA with its associated regulatory elements can significantly affect the surrounding chromatin and gene expression profile. Although it is possible that a randomly integrated oligo/polynucleotide may result in detrimental insertional mutagenesis, the potential will be minimized because of the lack of regulatory elements directly associated with the therapeutic DNA. In studies evaluating a clonal population of cells modified by HPRT-specific SDFs, random integration was not apparent (Bedayat et al., 2010). However, the potential for random integration needs to be thoroughly evaluated. This can be achieved through direct sequencing, inverse PCR, assessment of adverse effects in animal models, and/or transfection of sequences not found in the genomic DNA that are of similar size. Ultimately, before any oligo/polynucleotide-based approach can be used clinically, the extent of random integration needs to be assessed in terms of risks vs. potential benefit.


The prospect of a genetic therapy that will “surgically” correct a disease-causing mutation in an endogenous gene is not only appealing but also represents the ultimate goal for gene therapy. The possibility of treating the myriad of genetic disorders by correcting specific genomic sequences and maintaining the integrity of the genetic structure is clearly very enticing. However, evaluation of the therapeutic potential of oligo/polynucleotide-based gene modification remains in its infancy and additional mechanistic studies are required to gain insight into the weaknesses and strengths of the different approaches, as well as how they might be optimized to maximize therapeutic efficacy without adverse effects.

It will be critical to determine whether the introduction of large quantities of DNA will lead to apoptosis (GRUENERT, 2003; Gruenert et al., 2003; Liu et al., 2009a; Olsen et al., 2009). There are dosage and threshold issues that need to be clarified to determine whether the dose of the oligo/polynucleotide required to achieve maximal modification induces significant apoptosis undermining therapeutic efficacy by decreasing the number of corrected cells.

The safe clinical application of the cDNA/donor plasmid-based ZFN (CARROLL, 2004; Alwin et al., 2005; Porteus and Carroll, 2005; Urnov et al., 2005) or the meganuclease (Cabaniols and Paques, 2008; Grizot et al., 2009, 2010) gene targeting approaches also requires careful assessment of offsite DSBs (CARROLL, 2008; Bozas et al., 2009). Minimizing the number of extraneous DSBs will be critical to ensure that genomic integrity is maintained and does not lead to karyotypic instability and/or neoplasia (Griffin and Thacker, 2004; Acilan et al., 2007; Mittelman et al., 2009). Recent studies using reengineered FokI nucleases may be one means to address this limitation (Kandavelou et al., 2009; Ramalingam et al., 2010).

As is the case with any new therapy, it will be necessary to appropriately evaluate underlying mechanisms and how they relate to efficiency, efficacy, and safety. The potential candidate pathways and enzymes and the studies investigating aspects of individual approaches outlined in Tables 25 represent a partial list of an ongoing effort to gain a better understanding of the mechanisms involved and the therapeutic potential of individual approaches. Although Tables 35 are extensive, they are not comprehensive and are intended to highlight representative studies that have provided insight into both the phenomenology and the mechanisms involved and lay the foundation for future studies that will help determine how a given oligo/polynucleotide-based strategy can be most effectively applied. It may be that there is not one approach that will predominate, but rather that each approach has specific applications where it will be the most effective and/or that a given gene targeting strategy complements another therapeutic strategy. Whatever the case, the oligo/polynucleotide-based strategies offer the potential for exciting alternatives that have limited other genetic therapy approaches.

Table 5.
Chromosomal Gene Targeting: Endogenous Gene


The authors thank Drs. Hooman Parsi, Hamid Emamekhoo, Rosalie Maurisse, and David DeSemir for their input and for sharing their data, as well as Drs. Karen Vasquez and James Cleaver for their reading of the manuscript and constructive comments. This overview has been supported by NIH grants (GM075111 and GM075111-04S1) and Pennsylvania Cystic Fibrosis, Inc.

Author Disclosure Statement

No competing financial interests exist.


  • AARTS M. DEKKER M. DEKKER R. DE VRIES S. VAN DER WAL A. WIELDERS E. RIELE H.T. Gene modification in embryonic stem cells by single-stranded DNA oligonucleotides. Methods Mol. Biol. 2009;530:79–99. [PubMed]
  • AARTS M. DEKKER M. DE VRIES S. VAN DER WAL A. TE RIELE H. Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells. Nucleic Acids Res. 2006;34:e147. [PubMed]
  • AARTS M. TE RIELE H. Parameters of oligonucleotide-mediated gene modification in mouse ES cells. J. Cell. Mol. Med. 2010a;14:1657–1667. [PubMed]
  • AARTS M. TE RIELE H. Subtle gene modification in mouse ES cells: evidence for incorporation of unmodified oligonucleotides without induction of DNA damage. Nucleic Acids Res. 2010b;38:6956–6967. [PMC free article] [PubMed]
  • ACILAN C. POTTER D.M. SAUNDERS W.S. DNA repair pathways involved in anaphase bridge formation. Genes Chromosomes Cancer. 2007;46:522–531. [PubMed]
  • AKYUZ N. BOEHDEN G.S. SUSSE S. RIMEK A. PREUSS U. SCHEIDTMANN K.H. WIESMULLER L. DNA substrate dependence of p53-mediated regulation of double-strand break repair. Mol. Cell. Biol. 2002;22:6306–6317. [PMC free article] [PubMed]
  • ALAM M.R. MAJUMDAR A. THAZHATHVEETIL A.K. LIU S.T. LIU J.L. PURI N. CUENOUD B. SASAKI S. MILLER P.S. SEIDMAN M.M. Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo. Biochemistry. 2007;46:10222–10233. [PubMed]
  • ALEXEEV V. IGOUCHEVA O. YOON K. Simultaneous targeted alteration of the tyrosinase and c-kit genes by single-stranded oligonucleotides. Gene Ther. 2002;9:1667–1675. [PubMed]
  • ALWIN S. GERE M.B. GUHL E. EFFERTZ K. BARBAS C.F., 3rd SEGAL D.J. WEITZMAN M.D. CATHOMEN T. Custom zinc-finger nucleases for use in human cells. Mol. Ther. 2005;12:610–617. [PubMed]
  • ANDERSEN M.S. SORENSEN C.B. BOLUND L. JENSEN T.G. Mechanisms underlying targeted gene correction using chimeric RNA/DNA and single-stranded DNA oligonucleotides. J. Mol. Med. 2002;80:770–781. [PubMed]
  • ANDRIEU-SOLER C. HALHAL M. BOATRIGHT J.H. PADOVE S.A. NICKERSON J.M. STODULKOVA E. STEWART R.E. CIAVATTA V.T. DOAT M. JEANNY J.C., et al. Single-stranded oligonucleotide-mediated in vivo gene repair in the rd1 retina. Mol. Vis. 2007;13:692–706. [PMC free article] [PubMed]
  • BAUM C. Insertional mutagenesis in gene therapy and stem cell biology. Curr. Opin. Hematol. 2007;14:337–342. [PubMed]
  • BEDAYAT B. ABDOLMOHAMADI A. YE L. MAURISSE R. PARSI H. SCHWARZ J. EMAMEKHOO H. NICKLAS J.A. O'NEILL J.P. GRUENERT D.C. Sequence-specific correction of genomic hypoxanthine-Guanine phosphoribosyl transferase mutations in lymphoblasts by small fragment homologous replacement. Oligonucleotides. 2010;20:7–16. [PMC free article] [PubMed]
  • BELOUSOV E.S. AFONINA I.A. KUTYAVIN I.V. GALL A.A. REED M.W. GAMPER H.B. WYDRO R.M. MEYER R.B. Triplex targeting of a native gene in permeabilized intact cells: covalent modification of the gene for the chemokine receptor CCR5. Nucleic Acids Res. 1998;26:1324–1328. [PMC free article] [PubMed]
  • BENFIELD A.P. MACLEOD M.C. LIU Y. WU Q. WENSEL T.G. VASQUEZ K.M. Targeted generation of DNA strand breaks using pyrene-conjugated triplex-forming oligonucleotides. Biochemistry. 2008;47:6279–6288. [PMC free article] [PubMed]
  • BERTLING W.M. GAREIS M. PASPALEEVA V. ZIMMER A. KREUTER J. NURNBERG E. HARRER P. Use of liposomes, viral capsids, and nanoparticles as DNA carriers. Biotechnol. Appl. Biochem. 1991;13:390–405. [PubMed]
  • BERTONI C. RUSTAGI A. RANDO T.A. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Nucleic Acids Res. 2009;37:7468–7482. [PMC free article] [PubMed]
  • BESCH R. GIOVANNANGELI C. KAMMERBAUER C. DEGITZ K. Specific inhibition of ICAM-1 expression mediated by gene targeting with Triplex-forming oligonucleotides. J. Biol. Chem. 2002;277:32473–32479. [PubMed]
  • BIBIKOVA M. BEUMER K. TRAUTMAN J.K. CARROLL D. Enhancing gene targeting with designed zinc finger nucleases. Science. 2003;300:764. [PubMed]
  • BIBIKOVA M. CARROLL D. SEGAL D.J. TRAUTMAN J.K. SMITH J. KIM Y.G. CHANDRASEGARAN S. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 2001;21:289–297. [PMC free article] [PubMed]
  • BIBIKOVA M. GOLIC M. GOLIC K.G. CARROLL D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics. 2002;161:1169–1175. [PubMed]
  • BIGGERSTAFF M. SZYMKOWSKI D.E. WOOD R.D. Co-correction of the ERCC1, ERCC4 and xeroderma pigmentosum group F DNA repair defects in vitro. EMBO J. 1993;12:3685–3692. [PubMed]
  • BODE J. BENHAM C. ERNST E. KNOPP A. MARSCHALEK R. STRICK R. STRISSEL P. Fatal connections: when DNA ends meet on the nuclear matrix. J. Cell. Biochem. Suppl. 2000;(Suppl 35):3–22. [PubMed]
  • BOGGS S.S. Targeted gene modification for gene therapy of stem cells. Int. J. Cell. Cloning. 1990;8:80–96. [PubMed]
  • BONNER M. KMIEC E.B. DNA breakage associated with targeted gene alteration directed by DNA oligonucleotides. Mutat. Res. 2009;669:85–94. [PMC free article] [PubMed]
  • BOZAS A. BEUMER K.J. TRAUTMAN J.K. CARROLL D. Genetic analysis of zinc-finger nuclease-induced gene targeting in Drosophila. Genetics. 2009;182:641–651. [PubMed]
  • BRACHMAN E.E. KMIEC E.B. DNA replication and transcription direct a DNA strand bias in the process of targeted gene repair in mammalian cells. J. Cell. Sci. 2004;117:3867–3874. [PubMed]
  • BRACHMAN E.E. KMIEC E.B. Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks. DNA Repair (Amst). 2005;4:445–457. [PubMed]
  • BROITMAN S.L. AMOSOVA O. FRESCO J.R. Repairing the Sickle Cell mutation. III. Effect of irradiation wavelength on the specificity and type of photoproduct formed by a 3′-terminal psoralen on a third strand directed to the mutant base pair. Nucleic Acids Res. 2003;31:4682–4688. [PMC free article] [PubMed]
  • BRUSCIA E. SANGIUOLO F. SINIBALDI P. GONCZ K.K. NOVELLI G. GRUENERT D.C. Isolation of CF cell lines corrected at DeltaF508-CFTR locus by SFHR-mediated targeting. Gene Ther. 2002;9:683–685. [PubMed]
  • BUGREEV D.V. YU X. EGELMAN E.H. MAZIN A.V. Novel pro- and anti-recombination activities of the Bloom's syndrome helicase. Genes Dev. 2007;21:3085–3094. [PubMed]
  • BUSHMAN F.D. Retroviral integration and human gene therapy. J. Clin. Invest. 2007;117:2083–2086. [PMC free article] [PubMed]
  • CABANIOLS J.P. PAQUES F. Robust cell line development using meganucleases. Methods Mol. Biol. 2008;435:31–45. [PubMed]
  • CAMPBELL C.R. KEOWN W. LOWE L. KIRSCHLING D. KUCHERLAPATI R. Homologous recombination involving small single-stranded oligonucleotides in human cells. New Biol. 1989;1:223–227. [PubMed]
  • CAPECCHI M.R. Altering the genome by homologous recombination. Science. 1989;244:1288–1292. [PubMed]
  • CAPECCHI M.R. Targeted gene replacement. Sci. Am. 1994;270:52–59. [PubMed]
  • CAPECCHI M.R. How close are we to implementing gene targeting in animals other than the mouse? Proc. Natl. Acad. Sci. U. S. A. 2000;97:956–957. [PubMed]
  • CARRARO C. PATHAK M.A. Studies on the nature of in vitro and in vivo photosensitization reactions by psoralens and porphyrins. J. Invest. Dermatol. 1988;90:267–275. [PubMed]
  • CARROLL D. Using nucleases to stimulate homologous recombination. Methods Mol. Biol. 2004;262:195–207. [PubMed]
  • CARROLL D. Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther. 2008;15:1463–1468. [PMC free article] [PubMed]
  • CARROLL D. BEUMER K.J. MORTON J.J. BOZAS A. TRAUTMAN J.K. Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases. Methods Mol. Biol. 2008;435:63–77. [PubMed]
  • CAVAZZANA-CALVO M. FISCHER A. Gene therapy for severe combined immunodeficiency: are we there yet? J. Clin. Invest. 2007;117:1456–1465. [PMC free article] [PubMed]
  • CAVAZZANA-CALVO M. HACEIN-BEY S. YATES F. DE VILLARTAY J.P. LE DEIST F. FISCHER A. Gene therapy of severe combined immunodeficiencies. J. Gene Med. 2001;3:201–206. [PubMed]
  • CAVAZZANA-CALVO M. THRASHER A. MAVILIO F. The future of gene therapy. Nature. 2004;427:779–781. [PubMed]
  • CERESETO A. GIACCA M. Integration site selection by retroviruses. AIDS Rev. 2004;6:13–21. [PubMed]
  • CHAN P.P. LIN M. FARUQI A.F. POWELL J. SEIDMAN M.M. GLAZER P.M. Targeted correction of an episomal gene in mammalian cells by a short DNA fragment tethered to a triplex-forming oligonucleotide. J. Biol. Chem. 1999;274:11541–11548. [PubMed]
  • CHANDRASEGARAN S. SMITH J. Chimeric restriction enzymes: what is next? Biol. Chem. 1999;380:841–848. [PubMed]
  • CHIN J.Y. GLAZER P.M. Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol. Carcinog. 2009;48:389–399. [PMC free article] [PubMed]
  • CHIN J.Y. SCHLEIFMAN E.B. GLAZER P.M. Repair and recombination induced by triple helix DNA. Front Biosci. 2007;12:4288–4297. [PubMed]
  • CHOULIKA A. PERRIN A. DUJON B. NICOLAS J.F. The yeast I-Sce I meganuclease induces site-directed chromosomal recombination in mammalian cells. C. R. Acad. Sci. III. 1994;317:1013–1019. [PubMed]
  • CHOULIKA A. PERRIN A. DUJON B. NICOLAS J.F. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 1995;15:1968–1973. [PMC free article] [PubMed]
  • CHRISTENSEN L.A. WANG H. VAN HOUTEN B. VASQUEZ K.M. Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease. Nucleic Acids Res. 2008;36:7136–7145. [PMC free article] [PubMed]
  • COHEN-TANNOUDJI M. ROBINE S. CHOULIKA A. PINTO D. EL MARJOU F. BABINET C. LOUVARD D. JAISSER F. I-SceI-induced gene replacement at a natural locus in embryonic stem cells. Mol. Cell. Biol. 1998;18:1444–1448. [PMC free article] [PubMed]
  • COLOSIMO A. GONCZ K.K. HOLMES A.R. KUNZELMANN K. NOVELLI G. MALONE R.W. BENNETT M.J. GRUENERT D.C. Transfer and expression of foreign genes in mammalian cells. Biotechniques. 2000;29:314–318. 320–322, 324 passim. [PubMed]
  • COLOSIMO A. GONCZ K.K. NOVELLI G. DALLAPICCOLA B. GRUENERT D.C. Targeted correction of a defective selectable marker gene in human epithelial cells by small DNA fragments. Mol. Ther. 2001;3:178–185. [PubMed]
  • COLOSIMO A. GUIDA V. ANTONUCCI I. BONFINI T. STUPPIA L. DALLAPICCOLA B. Sequence-specific modification of a beta-thalassemia locus by small DNA fragments in human erythroid progenitor cells. Haematologica. 2007;92:129–130. [PubMed]
  • CONSORTIUM T.C.F.G.A. World-wide survey of ΔF508 mutation—report from Cystic Fibrosis Genetic Analysis Consortium. Am J Hum Genet. 1990;47:354–357. [PubMed]
  • CULVER K.W. HSIEH W.T. HUYEN Y. CHEN V. LIU J. KHRIPINE Y. KHORLIN A. Correction of chromosomal point mutations in human cells with bifunctional oligonucleotides. Nat. Biotechnol. 1999;17:989–993. [PubMed]
  • CUOZZO C. PORCELLINI A. ANGRISANO T. MORANO A. LEE B. DI PARDO A. MESSINA S. IULIANO R. FUSCO A. SANTILLO M.R., et al. DNA damage, homology-directed repair, and DNA methylation. PLoS Genet. 2007;3:e110. [PubMed]
  • DATTA H.J. CHAN P.P. VASQUEZ K.M. GUPTA R.C. GLAZER P.M. Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51. J. Biol. Chem. 2001;276:18018–18023. [PubMed]
  • DATTA H.J. GLAZER P.M. Intracellular generation of single-stranded DNA for chromosomal triplex formation and induced recombination. Nucleic Acids Res. 2001;29:5140–5147. [PMC free article] [PubMed]
  • DEKKER M. BROUWERS C. TE RIELE H. Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides. Nucleic Acids Res. 2003;31:e27. [PMC free article] [PubMed]
  • DE SEMIR D. ARAN J.M. Misleading gene conversion frequencies due to a PCR artifact using small fragment homologous replacement. Oligonucleotides. 2003;13:261–269. [PubMed]
  • DE SEMIR D. ARAN J.M. Targeted gene repair: the ups and downs of a promising gene therapy approach. Curr. Gene Ther. 2006;6:481–504. [PubMed]
  • DE SEMIR D. AVINYO A. LARRIBA S. NUNES V. CASALS T. ESTIVILL X. ARAN J.M. Quantitative assessment of chimeraplast stability in biological fluids by polyacrylamide gel electrophoresis and laser-assisted fluorescence analysis. Pharm. Res. 2002;19:914–918. [PubMed]
  • DIAZ-FONT A. CORMAND B. CHABAS A. VILAGELIU L. GRINBERG D. Unsuccessful chimeraplast strategy for the correction of a mutation causing Gaucher disease. Blood Cells Mol. Dis. 2003;31:183–186. [PubMed]
  • DOETSCHMAN T. GREGG R.G. MAEDA N. HOOPER M.L. MELTON D.W. THOMPSON S. SMITHIES O. Targeted correction of a mutant HPRT gene in mouse embryonic stem cells. Nature. 1987;330:576–578. [PubMed]
  • DURANT S.T. NICKOLOFF J.A. Good timing in the cell cycle for precise DNA repair by BRCA1. Cell Cycle. 2005;4:1216–1222. [PubMed]
  • DUVAL-VALENTIN G. TAKASUGI M. HELENE C. SAGE E. Triple helix-directed psoralen crosslinks are recognized by Uvr(A)BC excinuclease. J. Mol. Biol. 1998;278:815–825. [PubMed]
  • ELLIOTT B. RICHARDSON C. WINDERBAUM J. NICKOLOFF J.A. JASIN M. Gene conversion tracts from double-strand break repair in mammalian cells. Mol. Cell. Biol. 1998;18:93–101. [PMC free article] [PubMed]
  • ENGELS W.R. JOHNSON-SCHLITZ D. FLORES C. WHITE L. PRESTON C.R. A third link connecting aging with double strand break repair. Cell Cycle. 2007;6:131–135. [PubMed]
  • EVANS-GALEA M.V. WIELGOSZ M.M. HANAWA H. SRIVASTAVA D.K. NIENHUIS A.W. Suppression of clonal dominance in cultured human lymphoid cells by addition of the cHS4 insulator to a lentiviral vector. Mol. Ther. 2007;15:801–809. [PubMed]
  • FAN W. YOON K. In vivo alteration of the keratin 17 gene in hair follicles by oligonucleotide-directed gene targeting. Exp. Dermatol. 2003;12:832–842. [PubMed]
  • FARUQI A.F. DATTA H.J. CARROLL D. SEIDMAN M.M. GLAZER P.M. Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway. Mol. Cell. Biol. 2000;20:990–1000. [PMC free article] [PubMed]
  • FARUQI A.F. SEIDMAN M.M. SEGAL D.J. CARROLL D. GLAZER P.M. Recombinaiton induced by triple-helix-targeted DNA damage in mammalian cells. Mol. Cell. Biol. 1996;16:6820–6828. [PMC free article] [PubMed]
  • FELSENFELD G. RICH A. Studies on the formation of two- and three-stranded polyribonucleotides. Biochim. Biophys. Acta. 1957;26:457–468. [PubMed]
  • FERRARA L. KMIEC E.B. Targeted gene repair activates Chk1 and Chk2 and stalls replication in corrected cells. DNA Repair (Amst). 2006;5:422–431. [PubMed]
  • FOX K.R. BROWN T. An extra dimension in nucleic acid sequence recognition. Q. Rev. Biophys. 2005;38:311–320. [PubMed]
  • GAMPER H.B., Jr. COLE-STRAUSS A. METZ R. PAREKH H. KUMAR R. KMIEC E.B. A plausible mechanism for gene correction by chimeric oligonucleotides. Biochemistry. 2000a;39:5808–5816. [PubMed]
  • GAMPER H.B. PAREKH H. RICE M.C. BRUNER M. YOUKEY H. KMIEC E.B. The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts. Nucleic Acids Res. 2000b;28:4332–4339. [PMC free article] [PubMed]
  • GOLDING S.E. ROSENBERG E. KHALIL A. MCEWEN A. HOLMES M. NEILL S. POVIRK L.F. VALERIE K. Double strand break repair by homologous recombination is regulated by cell cycle-independent signaling via ATM in human glioma cells. J. Biol. Chem. 2004;279:15402–15410. [PubMed]
  • GONCZ K.K. COLOSIMO A. DALLAPICCOLA B. GAGNE L. HONG K. NOVELLI G. PAPAHADJOPOULOS D. SAWA T. SCHREIER H. WIENER-KRONISH J., et al. Expression of DeltaF508 CFTR in normal mouse lung after site-specific modification of CFTR sequences by SFHR. Gene Ther. 2001;8:961–965. [PubMed]
  • GONCZ K.K. KUNZELMANN K. XU Z. GRUENERT D.C. Targeted replacement of normal and mutant CFTR sequences in human airway epithelial cells using DNA fragments. Hum. Mol. Genet. 1998;7:1913–1919. [PubMed]
  • GONCZ K.K. PROKOPISHYN N.L. ABDOLMOHAMMADI A. BEDAYAT B. MAURISSE R. DAVIS B.R. GRUENERT D.C. Small fragment homologous replacement-mediated modification of genomic beta-globin sequences in human hematopoietic stem/progenitor cells. Oligonucleotides. 2006;16:213–224. [PubMed]
  • GONCZ K.K. PROKOPISHYN N.L. CHOW B.L. DAVIS B.R. GRUENERT D.C. Application of SFHR to gene therapy of monogenic disorders. Gene Ther. 2002;9:691–694. [PubMed]
  • GONI J.R. DE LA CRUZ X. OROZCO M. Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Res. 2004;32:354–360. [PMC free article] [PubMed]
  • GRIFFIN C.S. THACKER J. The role of homologous recombination repair in the formation of chromosome aberrations. Cytogenet. Genome Res. 2004;104:21–27. [PubMed]
  • GRIZOT S. EPINAT J.C. THOMAS S. DUCLERT A. ROLLAND S. PAQUES F. DUCHATEAU P. Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucleic Acids Res. 2010;38:2006–2018. [PMC free article] [PubMed]
  • GRIZOT S. SMITH J. DABOUSSI F. PRIETO J. REDONDO P. MERINO N. VILLATE M. THOMAS S. LEMAIRE L. MONTOYA G., et al. Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease. Nucleic Acids Res. 2009;37:5405–5419. [PMC free article] [PubMed]
  • GRUENERT D.C. Gene Correction with small DNA fragments. Curr. Res. Mol. Ther. 1998;1:607–613.
  • GRUENERT D.C. Opportunities and challenges in targeting genes for therapy. Gene Ther. 1999;6:1347–1348. [PubMed]
  • GRUENERT D.C. Genomic medicine: development of DNA a therapeutic drug for sequence-specific modification of genomic DNA. Discov. Med. 2003;3:58–60. [PubMed]
  • GRUENERT D.C. ASHWOOD-SMITH M. MITCHELL R.H. CLEAVER J.E. Induction of DNA-DNA cross-link formation in human cells by various psoralen derivatives. Cancer Res. 1985;45:5394–5398. [PubMed]
  • GRUENERT D.C. BRUSCIA E. NOVELLI G. COLOSIMO A. DALLAPICCOLA B. SANGIUOLO F. GONCZ K.K. Sequence-specific modification of genomic DNA by small DNA fragments. J. Clin. Invest. 2003;112:637–641. [PMC free article] [PubMed]
  • GRUENERT D.C. CLEAVER J.E. Repair of psoralen-induced cross-links and monoadducts in normal and repair-deficient human fibroblasts. Cancer Res. 1985;45:5399–5404. [PubMed]
  • GRUENERT D.C. KUNZELMANN K. NOVELLI G. COLOSIMO A. KAPSA R. BRUSCIA E. Oligonucleotide-based gene targeting approaches. Oligonucleotides. 2004;14:157–158. author reply 158–160. [PubMed]
  • HABER J.E. DNA recombination: the replication connection. Trends Biochem. Sci. 1999;24:271–275. [PubMed]
  • HACKETT C.S. GEURTS A.M. HACKETT P.B. Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy. Genome Biol. 2007;8(Suppl 1):S12. [PMC free article] [PubMed]
  • HAVRE P.A. GLAZER P.M. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide. J. Virol. 1993;67:7324–7331. [PMC free article] [PubMed]
  • HAVRE P.A. GUNTHER E.J. GASPARRO F.P. GLAZER P.M. Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen. Proc. Natl. Acad. Sci. U. S. A. 1993;90:7879–7883. [PubMed]
  • HEGELE H. WUEPPING M. REF C. KENNER O. KAUFMANN D. Simultaneous targeted exchange of two nucleotides by single-stranded oligonucleotides clusters within a region of about fourteen nucleotides. BMC Mol. Biol. 2008;9:14. [PMC free article] [PubMed]
  • HELLEDAY T. Pathways for mitotic homologous recombination in mammalian cells. Mutat. Res. 2003;532:103–115. [PubMed]
  • HENDRIE P.C. HIRATA R.K. RUSSELL D.W. Chromosomal integration and homologous gene targeting by replication-incompetent vectors based on the autonomous parvovirus minute virus of mice. J. Virol. 2003;77:13136–13145. [PMC free article] [PubMed]
  • HINZ J.M. TEBBS R.S. WILSON P.F. NHAM P.B. SALAZAR E.P. NAGASAWA H. URBIN S.S. BEDFORD J.S. THOMPSON L.H. Repression of mutagenesis by Rad51D-mediated homologous recombination. Nucleic Acids Res. 2006;34:1358–1368. [PMC free article] [PubMed]
  • HUNGER-BERTLING K. HARRER P. BERTLING W. Short DNA fragments induce site specific recombination in mammalian cells. Mol. Cell. Biochem. 1990;92:107–116. [PubMed]
  • IGOUCHEVA O. ALEXEEV V. ANNI H. RUBIN E. Oligonucleotide-mediated gene targeting in human hepatocytes: implications of mismatch repair. Oligonucleotides. 2008;18:111–122. [PMC free article] [PubMed]
  • IGOUCHEVA O. ALEXEEV V. PRYCE M. YOON K. Transcription affects formation and processing of intermediates in oligonucleotide-mediated gene alteration. Nucleic Acids Res. 2003;31:2659–2670. [PMC free article] [PubMed]
  • IGOUCHEVA O. ALEXEEV V. SCHARER O. YOON K. Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides. 2006a;16:94–104. [PubMed]
  • IGOUCHEVA O. ALEXEEV V. YOON K. Targeted gene correction by small single-stranded oligonucleotides in mammalian cells. Gene Ther. 2001;8:391–399. [PubMed]
  • IGOUCHEVA O. ALEXEEV V. YOON K. Oligonucleotide-directed mutagenesis and targeted gene correction: a mechanistic point of view. Curr. Mol. Med. 2004;4:445–463. [PubMed]
  • IGOUCHEVA O. ALEXEEV V. YOON K. Differential cellular responses to exogenous DNA in mammalian cells and its effect on oligonucleotide-directed gene modification. Gene Ther. 2006b;13:266–275. [PubMed]
  • JAIN A. WANG G. VASQUEZ K.M. DNA triple helices: biological consequences and therapeutic potential. Biochimie. 2008;90:1117–1130. [PMC free article] [PubMed]
  • JEGGO P.A. Identification of genes involved in repair of DNA double-strand breaks in mammalian cells. Radiat. Res. 1998;150:S80–S91. [PubMed]
  • JIRICNY J. Eukaryotic mismatch repair: an update. Mutat. Res. 1998;409:107–121. [PubMed]
  • JOHNSON R.D. JASIN M. Double-strand-break-induced homologous recombination in mammalian cells. Biochem. Soc. Trans. 2001;29:196–201. [PubMed]
  • KALISH J.M. GLAZER P.M. Targeted genome modification via triple helix formation. Ann. N. Y. Acad. Sci. 2005;1058:151–161. [PubMed]
  • KALISH J.M. SEIDMAN M.M. WEEKS D.L. GLAZER P.M. Triplex-induced recombination and repair in the pyrimidine motif. Nucleic Acids Res. 2005;33:3492–3502. [PMC free article] [PubMed]
  • KALLENBACH N.R. DANIEL W.E., Jr. KAMINKER M.A. Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs. Biochemistry. 1976;15:1218–1224. [PubMed]
  • KAMIYA H. UCHIYAMA M. NAKATSU Y. TSUZUKI T. HARASHIMA H. Effects of target sequence and sense versus anti-sense strands on gene correction with single-stranded DNA fragments. J. Biochem. 2008;144:431–436. [PubMed]
  • KANDAVELOU K. RAMALINGAM S. LONDON V. MANI M. WU J. ALEXEEV V. CIVIN C.I. CHANDRASEGARAN S. Targeted manipulation of mammalian genomes using designed zinc finger nucleases. Biochem. Biophys. Res. Commun. 2009;388:56–61. [PMC free article] [PubMed]
  • KAPSA R. QUIGLEY A. LYNCH G.S. STEEPER K. KORNBERG A.J. GREGOREVIC P. AUSTIN L. BYRNE E. In vivo and in vitro correction of the mdx dystrophin gene nonsense mutation by short-fragment homologous replacement. Hum. Gene Ther. 2001;12:629–642. [PubMed]
  • KAPSA R.M. QUIGLEY A.F. VADOLAS J. STEEPER K. IOANNOU P.A. BYRNE E. KORNBERG A.J. Targeted gene correction in the mdx mouse using short DNA fragments: towards application with bone marrow-derived cells for autologous remodeling of dystrophic muscle. Gene Ther. 2002;9:695–699. [PubMed]
  • KENNER O. KNEISEL A. KLINGLER J. BARTELT B. SPEIT G. VOGEL W. KAUFMANN D. Targeted gene correction of hprt mutations by 45 base single-stranded oligonucleotides. Biochem. Biophys. Res. Commun. 2002;299:787–792. [PubMed]
  • KENNER O. LUTOMSKA A. SPEIT G. VOGEL W. KAUFMANN D. Concurrent targeted exchange of three bases in mammalian hprt by oligonucleotides. Biochem. Biophys. Res. Commun. 2004;321:1017–1023. [PubMed]
  • KIM K.H. NIELSEN P.E. GLAZER P.M. Site-specific gene modification by PNAs conjugated to psoralen. Biochemistry. 2006;45:314–323. [PubMed]
  • KIM P.M. ALLEN C. WAGENER B.M. SHEN Z. NICKOLOFF J.A. Overexpression of human RAD51 and RAD52 reduces double-strand break-induced homologous recombination in mammalian cells. Nucleic Acids Res. 2001;29:4352–4360. [PMC free article] [PubMed]
  • KIM Y.G. CHA J. CHANDRASEGARAN S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. U. S. A. 1996;93:1156–1160. [PubMed]
  • KIM Y.G. CHANDRASEGARAN S. Chimeric restriction endonuclease. Proc. Natl. Acad. Sci. U. S. A. 1994;91:883–887. [PubMed]
  • KIM Y.G. SHI Y. BERG J.M. CHANDRASEGARAN S. Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions. Gene. 1997;203:43–49. [PubMed]
  • KNAUERT M.P. KALISH J.M. HEGAN D.C. GLAZER P.M. Triplex-stimulated intermolecular recombination at a single-copy genomic target. Mol. Ther. 2006;14:392–400. [PubMed]
  • KNAUERT M.P. LLOYD J.A. ROGERS F.A. DATTA H.J. BENNETT M.L. WEEKS D.L. GLAZER P.M. Distance and affinity dependence of triplex-induced recombination. Biochemistry. 2005;44:3856–3864. [PubMed]
  • KREN B.T. METZ R. KUMAR R. STEER C.J. Gene repair using chimeric RNA/DNA oligonucleotides. Semin. Liver Dis. 1999a;19:93–104. [PubMed]
  • KREN B.T. PARASHAR B. BANDYOPADHYAY P. CHOWDHURY N.R. CHOWDHURY J.R. STEER C.J. Correction of the UDP-glucuronosyltransferase gene defect in the gunn rat model of crigler-najjar syndrome type I with a chimeric oligonucleotide. Proc. Natl. Acad. Sci. U. S. A. 1999b;96:10349–10354. [PubMed]
  • KUAN J.Y. GLAZER P.M. Targeted gene modification using triplex-forming oligonucleotides. Methods Mol. Biol. 2004;262:173–194. [PubMed]
  • KUCHERLAPATI R. Gene replacement by homologous recombination in mammalian cells. Somat. Cell. Mol. Genet. 1987;13:447–449. [PubMed]
  • KUCHERLAPATI R. SPENCER J. MOORE P. Homologous recombination catalyzed by human cell extracts. Mol. Cell. Biol. 1985;5:714–720. [PMC free article] [PubMed]
  • KUNKEL T.A. DNA-mismatch repair. The intricacies of eukaryotic spell-checking. Curr. Biol. 1995;5:1091–1094. [PubMed]
  • KUNZELMANN K. LEGENDRE J.Y. KNOELL D.L. ESCOBAR L.C. XU Z. GRUENERT D.C. Gene targeting of CFTR DNA in CF epithelial cells. Gene Ther. 1996;3:859–867. [PubMed]
  • LAI L.W. LIEN Y.H. Homologous recombination based gene therapy. Exp. Nephrol. 1999;7:11–14. [PubMed]
  • LECLERC X. DANOS O. SCHERMAN D. KICHLER A. A comparison of synthetic oligodeoxynucleotides, DNA fragments and AAV-1 for targeted episomal and chromosomal gene repair. BMC Biotechnol. 2009;9:35. [PMC free article] [PubMed]
  • LI X. HEYER W.D. Homologous recombination in DNA repair and DNA damage tolerance. Cell. Res. 2008;18:99–113. [PMC free article] [PubMed]
  • LIANG F. HAN M. ROMANIENKO P.J. JASIN M. Homology-directed repair is a major double-strand break repair pathway in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 1998;95:5172–5177. [PubMed]
  • LIU C. WANG Z. HUEN M.S. LU L.Y. LIU D.P. HUANG J.D. Cell death caused by single-stranded oligodeoxynucleotides-mediated targeted genomic sequence modification. Oligonucleotides. 2009a;19:281–286. [PubMed]
  • LIU Y. NAIRN R.S. VASQUEZ K.M. Processing of triplex-directed psoralen DNA interstrand crosslinks by recombination mechanisms. Nucleic Acids Res. 2008;36:4680–4688. [PMC free article] [PubMed]
  • LIU Y. NAIRN R.S. VASQUEZ K.M. Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells. Nucleic Acids Res. 2009b;37:6378–6388. [PMC free article] [PubMed]
  • LOMBARDO A. GENOVESE P. BEAUSEJOUR C.M. COLLEONI S. LEE Y.L. KIM K.A. ANDO D. URNOV F.D. GALLI C. GREGORY P.D., et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat. Biotechnol. 2007;25:1298–1306. [PubMed]
  • LONKAR P. KIM K.H. KUAN J.Y. CHIN J.Y. ROGERS F.A. KNAUERT M.P. KOLE R. NIELSEN P.E. GLAZER P.M. Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids. Nucleic Acids Res. 2009;37:3635–3644. [PMC free article] [PubMed]
  • LUO Z. MACRIS M.A. FARUQI A.F. GLAZER P.M. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells. Proc. Natl. Acad. Sci. U. S. A. 2000;97:9003–9008. [PubMed]
  • MAJUMDAR A. MUNIANDY P.A. LIU J. LIU J.L. LIU S.T. CUENOUD B. SEIDMAN M.M. Targeted gene knock in and sequence modulation mediated by a psoralen-linked triplex-forming oligonucleotide. J. Biol. Chem. 2008;283:11244–11252. [PMC free article] [PubMed]
  • MAJUMDAR A. PURI N. CUENOUD B. NATT F. MARTIN P. KHORLIN A. DYATKINA N. GEORGE A.J. MILLER P.S. SEIDMAN M.M. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide. J. Biol. Chem. 2003a;278:11072–11077. [PubMed]
  • MAJUMDAR A. PURI N. MCCOLLUM N. RICHARDS S. CUENOUD B. MILLER P. SEIDMAN M.M. Gene targeting by triple helix-forming oligonucleotides. Ann. N. Y. Acad. Sci. 2003b;1002:141–153. [PubMed]
  • MANIVASAKAM P. AUBRECHT J. SIDHOM S. SCHIESTL R.H. Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells. Nucleic Acids Res. 2001;29:4826–4833. [PMC free article] [PubMed]
  • MANZANO A. MOHRI Z. SPERBER G. OGRIS M. GRAHAM I. DICKSON G. OWEN J.S. Failure to generate atheroprotective apolipoprotein AI phenotypes using synthetic RNA/DNA oligonucleotides (chimeraplasts) J. Gene Med. 2003;5:795–802. [PubMed]
  • MAURISSE R. CHEUNG J. WIDDICOMBE J. GRUENERT D.C. Modification of the pig CFTR gene mediated by small fragment homologous replacement. Ann. N. Y. Acad. Sci. 2006a;1082:120–123. [PubMed]
  • MAURISSE R. FEUGEAS J.P. BIET E. KUZNIAK I. LEBOULCH P. DUTREIX M. SUN J.S. A new method (GOREC) for directed mutagenesis and gene repair by homologous recombination. Gene Ther. 2002;9:703–707. [PubMed]
  • MAURISSE R. FICHOU Y. DE SEMIR D. CHEUNG J. FEREC C. GRUENERT D.C. Gel purification of genomic DNA removes contaminating small DNA fragments interfering with polymerase chain reaction analysis of small fragment homologous replacement. Oligonucleotides. 2006b;16:375–386. [PubMed]
  • MCNAB G.L. AHMAD A. MISTRY D. STOCKLEY R.A. Modification of gene expression and increase in alpha1-antitrypsin (alpha1-AT) secretion after homologous recombination in alpha1-AT-deficient monocytes. Hum. Gene Ther. 2007;18:1171–1177. [PubMed]
  • MEZHEVAYA K. WINTERS T.A. NEUMANN R.D. Gene targeted DNA double-strand break induction by (125)I-labeled triplex-forming oligonucleotides is highly mutagenic following repair in human cells. Nucleic Acids Res. 1999;27:4282–4290. [PMC free article] [PubMed]
  • MITTELMAN D. MOYE C. MORTON J. SYKOUDIS K. LIN Y. CARROLL D. WILSON J.H. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells. Proc. Natl. Acad. Sci. U. S. A. 2009;106:9607–9612. [PubMed]
  • MOLLER M. STOPPER H. HARING M. SCHLEGER Y. EPE B. ADAM W. SAHA-MOLLER C.R. Genotoxicity induced by furocoumarin hydroperoxides in mammalian cells upon UVA irradiation. Biochem. Biophys. Res. Commun. 1995;216:693–701. [PubMed]
  • MORRISON C. WAGNER E. Extrachromosomal recombination occurs efficiently in cells defective in various DNA repair systems. Nucleic Acids Res. 1996;24:2053–2058. [PMC free article] [PubMed]
  • MOYNAHAN M.E. CHIU J.W. KOLLER B.H. JASIN M. Brca1 controls homology-directed DNA repair. Mol. Cell. 1999;4:511–518. [PubMed]
  • MURPHY B.R. MOAYEDPARDAZI H.S. GEWIRTZ A.M. DIAMOND S.L. PIERCE E.A. Delivery and mechanistic considerations for the production of knock-in mice by single-stranded oligonucleotide gene targeting. Gene Ther. 2007;14:304–315. [PubMed]
  • NG P. BAKER M.D. Mechanisms of double-strand-break repair during gene targeting in mammalian cells. Genetics. 1999;151:1127–1141. [PubMed]
  • NICKERSON H.D. COLLEDGE W.H. A comparison of gene repair strategies in cell culture using a lacZ reporter system. Gene Ther. 2003;10:1584–1591. [PubMed]
  • NICKOLOFF J.A. BRENNEMAN M.A. Analysis of recombinational repair of DNA double-strand breaks in mammalian cells with I-SceI nuclease. Methods Mol. Biol. 2004;262:35–52. [PubMed]
  • OHBAYASHI F. BALAMOTIS M.A. KISHIMOTO A. AIZAWA E. DIAZ A. HASTY P. GRAHAM F.L. CASKEY C.T. MITANI K. Correction of chromosomal mutation and random integration in embryonic stem cells with helper-dependent adenoviral vectors. Proc. Natl. Acad. Sci. U. S. A. 2005;102:13628–13633. [PubMed]
  • OLSEN P.A. RANDOL M. KRAUSS S. Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides. Gene Ther. 2005a;12:546–551. [PubMed]
  • OLSEN P.A. RANDOL M. LUNA L. BROWN T. KRAUSS S. Genomic sequence correction by single-stranded DNA oligonucleotides: role of DNA synthesis and chemical modifications of the oligonucleotide ends. J. Gene Med. 2005b;7:1534–1544. [PubMed]
  • OLSEN P.A. SOLHAUG A. BOOTH J.A. GELAZAUSKAITE M. KRAUSS S. Cellular responses to targeted genomic sequence modification using single-stranded oligonucleotides and zinc-finger nucleases. DNA Repair (Amst). 2009;8:298–308. [PubMed]
  • PATHAK M.A. DANIELS F. HOPKINS C.E. FITZPATRICK T.B. Ultra-violet carcinogenesis in albino and pigmented mice receiving furocoumarins: psoralen and 8-methoxypsoralen. Nature. 1959;183:728–730. [PubMed]
  • PATHAK M.A. JOSHI P.C. Production of active oxygen species (1O2 and O2-.) by psoralens and ultraviolet radiation (320–400 nm. Biochim. Biophys. Acta. 1984;798:115–126. [PubMed]
  • PIERCE A.J. JASIN M. Measuring recombination proficiency in mouse embryonic stem cells. Methods Mol. Biol. 2005;291:373–384. [PubMed]
  • PIERCE E.A. LIU Q. IGOUCHEVA O. OMARRUDIN R. MA H. DIAMOND S.L. YOON K. Oligonucleotide-directed single-base DNA alterations in mouse embryonic stem cells. Gene Ther. 2003;10:24–33. [PubMed]
  • PIKE-OVERZET K. DE RIDDER D. WEERKAMP F. BAERT M.R. VERSTEGEN M.M. BRUGMAN M.H. HOWE S.J. REINDERS M.J. THRASHER A.J. WAGEMAKER G., et al. Ectopic retroviral expression of LMO2, but not IL2Rgamma, blocks human T-cell development from CD34+ cells: implications for leukemogenesis in gene therapy. Leukemia. 2007a;21:754–763. [PubMed]
  • PIKE-OVERZET K. VAN DER BURG M. WAGEMAKER G. VAN DONGEN J.J. STAAL F.J. New insights and unresolved issues regarding insertional mutagenesis in X-linked SCID gene therapy. Mol. Ther. 2007b;15:1910–1916. [PubMed]
  • PORTER A.C. DALLMAN M.J. Gene targeting: techniques and applications to transplantation. Transplantation. 1997;64:1227–1235. [PubMed]
  • PORTEUS M.H. BALTIMORE D. Chimeric nucleases stimulate gene targeting in human cells. Science. 2003;300:763. [PubMed]
  • PORTEUS M.H. CARROLL D. Gene targeting using zinc finger nucleases. Nat. Biotechnol. 2005;23:967–973. [PubMed]
  • POTTS P.R. PORTEUS M.H. YU H. Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks. EMBO J. 2006;25:3377–3388. [PubMed]
  • PRUETT-MILLER S.M. CONNELLY J.P. MAEDER M.L. JOUNG J.K. PORTEUS M.H. Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol. Ther. 2008;16:707–717. [PubMed]
  • PURI N. MAJUMDAR A. CUENOUD B. NATT F. MARTIN P. BOYD A. MILLER P.S. SEIDMAN M.M. Targeted gene knockout by 2′-O-aminoethyl modified triplex forming oligonucleotides. J. Biol. Chem. 2001;276:28991–28998. [PubMed]
  • PURI N. MAJUMDAR A. CUENOUD B. NATT F. MARTIN P. BOYD A. MILLER P.S. SEIDMAN M.M. Minimum number of 2′-O-(2-aminoethyl) residues required for gene knockout activity by triple helix forming oligonucleotides. Biochemistry. 2002;41:7716–7724. [PubMed]
  • PUTTINI S. OUVRARD-PASCAUD A. PALAIS G. BEGGAH A.T. GASCARD P. COHEN-TANNOUDJI M. BABINET C. BLOT-CHABAUD M. JAISSER F. Development of a targeted transgenesis strategy in highly differentiated cells: a powerful tool for functional genomic analysis. J. Biotechnol. 2005;116:145–151. [PubMed]
  • RADECKE F. PETER I. RADECKE S. GELLHAUS K. SCHWARZ K. CATHOMEN T. Targeted chromosomal gene modification in human cells by single-stranded oligodeoxynucleotides in the presence of a DNA double-strand break. Mol. Ther. 2006a;14:798–808. [PubMed]
  • RADECKE F. RADECKE S. SCHWARZ K. Unmodified oligodeoxynucleotides require single-strandedness to induce targeted repair of a chromosomal EGFP gene. J. Gene Med. 2004;6:1257–1271. [PubMed]
  • RADECKE S. RADECKE F. CATHOMEN T. SCHWARZ K. Zinc-finger nuclease-induced gene repair with oligodeoxynucleotides: wanted and unwanted target locus modifications. Mol. Ther. 2010;18:743–753. [PubMed]
  • RADECKE S. RADECKE F. PETER I. SCHWARZ K. Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus. J. Gene Med. 2006b;8:217–228. [PubMed]
  • RAMALINGAM S. KANDAVELOU K. RAJENDERAN R. CHANDRASEGARAN S. Creating designed zinc-finger nucleases with minimal cytotoxicity. J. Mol. Biol. 2011;405:630–641. [PMC free article] [PubMed]
  • RAY A. LANGER M. Homologous recombination: ends as the means. Trends Plant Sci. 2002;7:435–440. [PubMed]
  • RICHARDS S. LIU S.T. MAJUMDAR A. LIU J.L. NAIRN R.S. BERNIER M. MAHER V. SEIDMAN M.M. Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways. Nucleic Acids Res. 2005;33:5382–5393. [PMC free article] [PubMed]
  • RICHARDSON P.D. KREN B.T. STEER C.J. Targeted gene correction strategies. Curr. Opin. Mol. Ther. 2001;3:327–337. [PubMed]
  • ROUET P. SMIH F. JASIN M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol. 1994;14:8096–8106. [PMC free article] [PubMed]
  • SAINTIGNY Y. LOPEZ B.S. Homologous recombination induced by replication inhibition, is stimulated by expression of mutant p53. Oncogene. 2002;21:488–492. [PubMed]
  • SAKAMOTO S. IIJIMA K. MOCHIZUKI D. NAKAMURA K. TESHIGAWARA K. KOBAYASHI J. MATSUURA S. TAUCHI H. KOMATSU K. Homologous recombination repair is regulated by domains at the N- and C-terminus of NBS1 and is dissociated with ATM functions. Oncogene. 2007;26:6002–6009. [PubMed]
  • SALEH-GOHARI N. HELLEDAY T. Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells. Nucleic Acids Res. 2004;32:3683–3688. [PMC free article] [PubMed]
  • SANDOR Z. BREDBERG A. Triple helix directed psoralen adducts induce a low frequency of recombination in an SV40 shuttle vector. Biochim. Biophys. Acta. 1995;1263:235–240. [PubMed]
  • SANGIUOLO F. BRUSCIA E. SERAFINO A. NARDONE A.M. BONIFAZI E. LAIS M. GRUENERT D.C. NOVELLI G. In vitro correction of cystic fibrosis epithelial cell lines by small fragment homologous replacement (SFHR) technique. BMC Med. Genet. 2002;3:8. [PMC free article] [PubMed]
  • SANGIUOLO F. FILARETO A. SPITALIERI P. SCALDAFERRI M.L. MANGO R. BRUSCIA E. CITRO G. BRUNETTI E. DE FELICI M. NOVELLI G. In vitro restoration of functional SMN protein in human trophoblast cells affected by spinal muscular atrophy by small fragment homologous replacement. Hum. Gene Ther. 2005;16:869–880. [PubMed]
  • SANGIUOLO F. SCALDAFERRI M.L. FILARETO A. SPITALIERI P. GUERRA L. FAVIA M. CAROPPO R. MANGO R. BRUSCIA E. GRUENERT D.C., et al. Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR) Front Biosci. 2008;13:2989–2999. [PubMed]
  • SARGENT R.G. BRENNEMAN M.A. WILSON J.H. Repair of site-specific double-strand breaks in a mammalian chromosome by homologous and illegitimate recombination. Mol. Cell. Biol. 1997;17:267–277. [PMC free article] [PubMed]
  • SEDELNIKOVA O.A. PANYUTIN I.G. LUU A.N. REED M.W. LICHT T. GOTTESMAN M.M. NEUMANN R.D. Targeting the human mdr1 gene by 125I-labeled triplex-forming oligonucleotides. Antisense Nucleic Acid Drug Dev. 2000;10:443–452. [PubMed]
  • SHIVJI M.K. VENKITARAMAN A.R. DNA recombination, chromosomal stability and carcinogenesis: insights into the role of BRCA2. DNA Repair (Amst). 2004;3:835–843. [PubMed]
  • SIMON P. CANNATA F. CONCORDET J.P. GIOVANNANGELI C. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie. 2008;90:1109–1116. [PubMed]
  • SLEETH K.M. SORENSEN C.S. ISSAEVA N. DZIEGIELEWSKI J. BARTEK J. HELLEDAY T. RPA mediates recombination repair during replication stress and is displaced from DNA by checkpoint signalling in human cells. J. Mol. Biol. 2007;373:38–47. [PubMed]
  • SMIH F. ROUET P. ROMANIENKO P.J. JASIN M. Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res. 1995;23:5012–5019. [PMC free article] [PubMed]
  • SMITH J. BERG J.M. CHANDRASEGARAN S. A detailed study of the substrate specificity of a chimeric restriction enzyme. Nucleic Acids Res. 1999;27:674–681. [PMC free article] [PubMed]
  • SONG K.Y. CHEKURI L. RAUTH S. EHRLICH S. KUCHERLAPATI R. Effect of double-strand breaks on homologous recombination in mammalian cells and extracts. Mol. Cell. Biol. 1985;5:3331–3336. [PMC free article] [PubMed]
  • SONODA E. TAKATA M. YAMASHITA Y.M. MORRISON C. TAKEDA S. Homologous DNA recombination in vertebrate cells. Proc. Natl. Acad. Sci. U. S. A. 2001;98:8388–8394. [PubMed]
  • SWAGEMAKERS S.M. ESSERS J. DE WIT J. HOEIJMAKERS J.H. KANAAR R. The human RAD54 recombinational DNA repair protein is a double-stranded DNA-dependent ATPase. J. Biol. Chem. 1998;273:28292–28297. [PubMed]
  • TAMARO M. GASTALDI S. CARLASSARE F. BABUDRI N. PANI B. Genotoxic activity of some water-soluble derivatives of 5-methoxypsoralen and 8-methoxypsoralen. Carcinogenesis. 1986;7:605–609. [PubMed]
  • TAMULEVICIUS P. WANG M. ILIAKIS G. Homology-directed repair is required for the development of radioresistance during S phase: interplay between double-strand break repair and checkpoint response. Radiat. Res. 2007;167:1–11. [PubMed]
  • TANIGUCHI T. GARCIA-HIGUERA I. ANDREASSEN P.R. GREGORY R.C. GROMPE M. D'ANDREA A.D. S-phase-specific interaction of the Fanconi anemia protein, FANCD2, with BRCA1 and RAD51. Blood. 2002;100:2414–2420. [PubMed]
  • TAUBES G. Gene therapy. Pioneering papers under the microscope. Science. 2002a;298:2118–2119. [PubMed]
  • TAUBES G. Gene therapy. The strange case of chimeraplasty. Science. 2002b;298:2116–2120. [PubMed]
  • TERUNUMA A. YE J. EMMERT S. KHAN S.G. KRAEMER K.H. VOGEL J.C. Ultraviolet light selection assay to optimize oligonucleotide correction of mutations in endogenous xeroderma pigmentosum genes. Gene Ther. 2004;11:1729–1734. [PubMed]
  • THOMPSON L.H. Properties and applications of human DNA repair genes. Mutat. Res. 1991;247:213–219. [PubMed]
  • THOMPSON L.H. SCHILD D. The contribution of homologous recombination in preserving genome integrity in mammalian cells. Biochimie. 1999;81:87–105. [PubMed]
  • THOMPSON L.H. SCHILD D. Recombinational DNA repair and human disease. Mutat. Res. 2002;509:49–78. [PubMed]
  • THORNHILL S.I. SCHAMBACH A. HOWE S.J. ULAGANATHAN M. GRASSMAN E. WILLIAMS D. SCHIEDLMEIER B. SEBIRE N.J. GASPAR H.B. KINNON C., et al. Self-inactivating gammaretroviral vectors for gene therapy of X-linked severe combined immunodeficiency. Mol. Ther. 2008;16:590–598. [PubMed]
  • THORPE P.H. STEVENSON B.J. PORTEOUS D.J. Functional correction of episomal mutations with short DNA fragments and RNA-DNA oligonucleotides. J. Gene Med. 2002;4:195–204. [PubMed]
  • TODARO M. QUIGLEY A. KITA M. CHIN J. LOWES K. KORNBERG A.J. COOK M.J. KAPSA R. Effective detection of corrected dystrophin loci in mdx mouse myogenic precursors. Hum. Mutat. 2007;28:816–823. [PubMed]
  • TSUCHIYA H. HARASHIMA H. KAMIYA H. Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment. Biochem. Biophys. Res. Commun. 2005a;336:1194–1200. [PubMed]
  • TSUCHIYA H. HARASHIMA H. KAMIYA H. Increased SFHR gene correction efficiency with sense single-stranded DNA. J. Gene Med. 2005b;7:486–493. [PubMed]
  • TSUCHIYA H. SAWAMURA T. UCHIYAMA M. HARASHIMA H. KAMIYA H. Conversion of nucleotide sequence with single-stranded DNA fragment prepared from phagemid DNA. Nucleic Acids Symp. Ser. (Oxf). 2005c;49:93–94. [PubMed]
  • TSUCHIYA H. UCHIYAMA M. HARA K. NAKATSU Y. TSUZUKI T. INOUE H. HARASHIMA H. KAMIYA H. Improved gene correction efficiency with a tailed duplex DNA fragment. Biochemistry. 2008;47:8754–8759. [PubMed]
  • TSUI L.-C., et al. Cystic fibrosis mutation database. 2010.
  • URNOV F.D. MILLER J.C. LEE Y.L. BEAUSEJOUR C.M. ROCK J.M. AUGUSTUS S. JAMIESON A.C. PORTEUS M.H. GREGORY P.D. HOLMES M.C. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature. 2005;435:646–651. [PubMed]
  • VALANCIUS V. SMITHIES O. Double-strand gap repair in a mammalian gene targeting reaction. Mol. Cell. Biol. 1991;11:4389–4397. [PMC free article] [PubMed]
  • VARGANOV Y. AMOSOVA O. FRESCO J.R. Third strand-mediated psoralen-induced correction of the sickle cell mutation on a plasmid transfected into COS-7 cells. Gene Ther. 2007;14:173–179. [PubMed]
  • VASILEVA A. LINDEN R.M. JESSBERGER R. Homologous recombination is required for AAV-mediated gene targeting. Nucleic Acids Res. 2006;34:3345–3360. [PMC free article] [PubMed]
  • VASQUEZ K.M. CHRISTENSEN J. LI L. FINCH R.A. GLAZER P.M. Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions. Proc. Natl. Acad. Sci. U. S. A. 2002;99:5848–5853. [PubMed]
  • VASQUEZ K.M. DAGLE J.M. WEEKS D.L. GLAZER P.M. Chromosome targeting at short polypurine sites by cationic triplex-forming oligonucleotides. J. Biol. Chem. 2001a;276:38536–38541. [PubMed]
  • VASQUEZ K.M. GLAZER P.M. Triplex-forming oligonucleotides: principles and applications. Q. Rev. Biophys. 2002;35:89–107. [PubMed]
  • VASQUEZ K.M. LEGERSKI R.J. DNA interstrand crosslinks: repair, cell signaling, and therapeutic implications. Environ. Mol. Mutagen. 2010;51:491–492. [PubMed]
  • VASQUEZ K.M. MARBURGER K. INTODY Z. WILSON J.H. Manipulating the mammalian genome by homologous recombination. Proc. Natl. Acad. Sci. U. S. A. 2001b;98:8403–8410. [PubMed]
  • VASQUEZ K.M. NARAYANAN L. GLAZER P.M. Specific mutations induced by triplex-forming oligonucleotides in mice. Science. 2000;290:530–533. [PubMed]
  • VASQUEZ K.M. WANG G. HAVRE P.A. GLAZER P.M. Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res. 1999;27:1176–1181. [PMC free article] [PubMed]
  • VEGA M.A. Prospects for homologous recombination in human gene therapy. Hum. Genet. 1991;87:245–253. [PubMed]
  • VILLEMURE J.F. ABAJI C. COUSINEAU I. BELMAAZA A. MSH2-deficient human cells exhibit a defect in the accurate termination of homology-directed repair of DNA double-strand breaks. Cancer Res. 2003;63:3334–3339. [PubMed]
  • VIOLA G. VEDALDI D. DALL'ACQUA F. FORTUNATO E. BASSO G. BIANCHI N. ZUCCATO C. BORGATTI M. LAMPRONTI I. GAMBARI R. Induction of gamma-globin mRNA, erythroid differentiation and apoptosis in UVA-irradiated human erythroid cells in the presence of furocumarin derivatives. Biochem. Pharmacol. 2008;75:810–825. [PubMed]
  • WALDMAN A.S. Targeted homologous recombination in mammalian cells. Crit. Rev. Oncol. Hematol. 1992;12:49–64. [PubMed]
  • WALDMAN B.C. WANG Y. KILARU K. YANG Z. BHASIN A. WYATT M.D. WALDMAN A.S. Induction of intrachromosomal homologous recombination in human cells by raltitrexed, an inhibitor of thymidylate synthase. DNA Repair (Amst). 2008;7:1624–1635. [PMC free article] [PubMed]
  • WANG G. GLAZER P.M. Altered repair of targeted psoralen photoadducts in the context of an oligonucleotide-mediated triple helix. J. Biol. Chem. 1995;270:22595–22601. [PubMed]
  • WANG G. SEIDMAN M.M. GLAZER P.M. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science. 1996;271:802–805. [PubMed]
  • WANG K.Y. JAMES SHEN C.K. DNA methyltransferase Dnmt1 and mismatch repair. Oncogene. 2004;23:7898–7902. [PubMed]
  • WHITEHOUSE A. TAYLOR G.R. DEEBLE J. PHILLIPS S.E. MEREDITH D.M. MARKHAM A.F. A carboxy terminal domain of the hMSH-2 gene product is sufficient for binding specific mismatched oligonucleotides. Biochem. Biophys. Res. Commun. 1996;225:289–295. [PubMed]
  • WILLERS H. MCCARTHY E.E. HUBBE P. DAHM-DAPHI J. POWELL S.N. Homologous recombination in extrachromosomal plasmid substrates is not suppressed by p53. Carcinogenesis. 2001;22:1757–1763. [PubMed]
  • WILLIAMS D. BAUM C. Gene therapy needs both trials and new strategies. Nature. 2004;429:129. [PubMed]
  • WU X.S. LIU D.P. LIANG C.C. Prospects of chimeric RNA-DNA oligonucleotides in gene therapy. J. Biomed. Sci. 2001;8:439–445. [PubMed]
  • WU X.S. XIN L. YIN W.X. SHANG X.Y. LU L. WATT R.M. CHEAH K.S. HUANG J.D. LIU D.P. LIANG C.C. Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression. Proc. Natl. Acad. Sci. U. S. A. 2005;102:2508–2513. [PubMed]
  • WUEPPING M. KENNER O. HEGELE H. SCHWANDT S. KAUFMANN D. Higher efficiency of thymine-adenine clamp-modified single-stranded oligonucleotides in targeted nucleotide sequence correction is not correlated with lower intracellular degradation. Hum. Gene Ther. 2009;20:283–287. [PubMed]
  • YANEZ R.J. PORTER A.C. Therapeutic gene targeting. Gene Ther. 1998;5:149–159. [PubMed]
  • YANEZ R.J. PORTER A.C. Gene targeting is enhanced in human cells overexpressing hRAD51. Gene Ther. 1999;6:1282–1290. [PubMed]
  • YANEZ R.J. PORTER A.C. Differential effects of Rad52p overexpression on gene targeting and extrachromosomal homologous recombination in a human cell line. Nucleic Acids Res. 2002;30:740–748. [PMC free article] [PubMed]
  • YANG Q. ZHANG R. WANG X.W. LINKE S.P. SENGUPTA S. HICKSON I.D. PEDRAZZI G. PERRERA C. STAGLJAR I. LITTMAN S.J., et al. The mismatch DNA repair heterodimer, hMSH2/6, regulates BLM helicase. Oncogene. 2004;23:3749–3756. [PubMed]
  • YIN W. KREN B.T. STEER C.J. Site-specific base changes in the coding or promoter region of the human beta- and gamma-globin genes by single-stranded oligonucleotides. Biochem. J. 2005;390:253–261. [PubMed]
  • YOUNG A.R. Aspects of psoralen phototumorigenesis with emphasis on the possible role of tumour promotion. Biochimie. 1986;68:885–889. [PubMed]
  • ZAYED H. MCIVOR R.S. WIEST D.L. BLAZAR B.R. In vitro functional correction of the mutation responsible for murine severe combined immune deficiency by small fragment homologous replacement. Hum. Gene Ther. 2006;17:158–166. [PubMed]
  • ZHANG N. LIU X. LI L. LEGERSKI R. Double-strand breaks induce homologous recombinational repair of interstrand cross-links via cooperation of MSH2, ERCC1-XPF, REV3, and the Fanconi anemia pathway. DNA Repair (Amst). 2007;6:1670–1678. [PMC free article] [PubMed]
  • ZHANG Z. ERIKSSON M. FALK G. GRAFF C. PRESNELL S.C. READ M.S. NICHOLS T.C. BLOMBACK M. ANVRET M. Failure to achieve gene conversion with chimeric circular oligonucleotides: potentially misleading PCR artifacts observed. Antisense Nucleic Acid Drug Dev. 1998;8:531–536. [PubMed]
  • ZIMMER A. GRUSS P. Production of chimaeric mice containing embryonic stem (ES) cells carrying a homoeobox Hox 1.1 allele mutated by homologous recombination. Nature. 1989;338:150–153. [PubMed]
  • ZOU J. MAEDER M.L. MALI P. PRUETT-MILLER S.M. THIBODEAU-BEGANNY S. CHOU B.K. CHEN G. YE Z. PARK I.H. DALEY G.Q., et al. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell. 2009;5:97–110. [PMC free article] [PubMed]

Articles from Oligonucleotides are provided here courtesy of Mary Ann Liebert, Inc.