Search tips
Search criteria

Results 1-25 (61)

Clipboard (0)

Select a Filter Below

Year of Publication
1.  Introducing Artificial DNA: PNA & XNA 
PMCID: PMC3109443  PMID: 21687520
2.  RNA topology 
Artificial DNA, PNA & XNA  2013;4(2):35-36.
A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.
PMCID: PMC3771995  PMID: 23603781
3.  Digitizing humanity 
Artificial DNA, PNA & XNA  2013;4(2):37-38.
The application of ex vivo synthetic DNA as a high capacity information storage medium is well documented. Herein, we consider the potential for synthetic DNA to be incorporated as part of the human genome; providing a definitive, accessible, in vivo database of patient history.
PMCID: PMC3771996  PMID: 23912716
synthetic DNA; diagnostics; information; storage; identification
4.  In vitro selection of BNA (LNA) aptamers 
Artificial DNA, PNA & XNA  2013;4(2):39-48.
Recently, we achieved the first in vitro selection of 2′-O,4′-C-methylene bridged/locked nucleic acid (2′,4′-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2′-O,4′-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5′-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5′-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.
PMCID: PMC3771997  PMID: 24044051
2′,4′-BNA/LNA; KODDNA polymerase; Bridged (locked) nucleic acid aptamer; Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX); Xeno-nucleic acid (XNA)
5.  Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5 
Artificial DNA, PNA & XNA  2013;4(2):49-57.
The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of Chemokine Receptor 5 (CCR5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.
PMCID: PMC3771998  PMID: 23954968
CCR5; PEG; PNA; antisense; nanoparticle; γPNA
6.  Rapid genotyping using pyrene−perylene locked nucleic acid complexes 
Artificial DNA, PNA & XNA  2013;4(2):58-68.
We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene−perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2′-amino group of 2′-amino-LNA in position 4 allows for the first time to efficiently utilize dipole−dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene−perylene FRET pairs, e.g., in imaging and clinical diagnostics.
PMCID: PMC3771999  PMID: 24044052
oligonucleotide; LNA; pyrene; perylene; fluorescence; FRET; SNP
7.  Bending of short DNA helices 
Artificial DNA, PNA & XNA  2013;4(1):1-3.
In their recent Science paper, Vafabakhsh and Ha claim that DNA duplexes at the range of 100 bp experience anomalous flexibility, much greater than the flexibility of large DNA molecules.1 However, careful reevaluation of their data leads to the conclusion that the presented data do not warrant the authors’ claim.
PMCID: PMC3654724  PMID: 23406786
DNA bending flexibility; DNA minicircles; DNA sticky ends; DNA extreme bendability; single-molecule data
8.  Di-heterometalation of thiol-functionalized peptide nucleic acids 
Artificial DNA, PNA & XNA  2013;4(1):11-18.
As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium(II) polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru(II)-polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone (H-a-a-g-t-c-t-g-c-linker-cys-NH2) has been performed by standard peptide coupling method. As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 (H-gly-a-a-g-t-c-t-g-c-linker-cys-NH2) and PNA2 (C1-a-a-g-t-c-t-g-c-linker-cys-NH2) to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed. The synthesized ruthenium(II)-cymantrenyl PNA oligomers have been characterized by mass spectrometry (ESI-MS) and IR spectroscopy. The distinct Mn-CO vibrational IR stretches, between 1,924–2,074 cm−1, have been used as markers to confirm the presence of cymantrenyl units in the PNA sequences and the purity of the HPLC-purified PNA thioethers assessed using LC-MS.
PMCID: PMC3654725  PMID: 23422249
peptide nucleic acids; hetero-metalation; ruthenium; cymantrene; thioether; organometallics
9.  Fluorescent triplex-forming DNA oligonucleotides labeled with a thiazole orange dimer unit 
Artificial DNA, PNA & XNA  2013;4(1):19-27.
Fluorescent probes for the detection of a double-stranded DNA were prepared by labeling a triplex-forming DNA oligonucleotide with a thiazole orange (TO) dimer unit. They belong to ECHO (exciton-controlled hybridization-sensitive fluorescent oligonucleotide) probes which we have previously reported. The excitonic interaction between the two TO molecules was expected to effectively suppress the background fluorescence of the probes. The applicability of the ECHO probes for the detection of double-stranded DNA was confirmed by examining the thermal stability and photophysical and kinetic properties of the DNA triplexes formed by the ECHO probes.
PMCID: PMC3654726  PMID: 23445822
DNA; duplex; triplex; fluorescence; probe; thiazole orange; excitonic interaction
10.  A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates 
Artificial DNA, PNA & XNA  2013;4(1):4-10.
The synthesis of an azide containing PNA monomer is described. The monomer was incorporated into two PNA sequences for the purpose of synthesizing an intercalating fluorophore-labeled PNA and a metal binding hairpin using a solid phase copper catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Click chemistry was performed using 2-ethynylfluorene or 1-ethynylpyrene to add a fluorophore to the PNA, which were tested for their ability to recognize an abasic site on a DNA target. A PNA hairpin possessing azide monomers at each termini was synthesized and reacted with 2-ethynylpyridine to form a hairpin that is stabilized by Ni2+.
PMCID: PMC3654728  PMID: 23422048
click chemistry; pyrene; fluorene; metal-binding; hairpin; on-resin; Huisgen cycloaddition
11.  Enhanced splice correction by 3′, 5′-serinol and 2′-(ω-O-methylserinol) guarded OMe-RNA/DNA mixmers in cells 
Artificial DNA, PNA & XNA  2013;4(3):77-83.
Development of artificial nucleic acids for therapeutic applications warrants that the oligomers be endowed with high specificity, enzymatic stability and with no/reduced off-target effects. The balance between strength of the duplex with target RNA and enzyme stability is therefore the key factor for the designed modification. The chiral serinol derivative combines the attributes of amino- and methoxy- substitution when at 2′- position and at 3′- and 5′- ends, effectively balancing the duplex stability and resistance to hydrolytic enzymes. The biological effect seen is the remarkable improvement in splice correction by the steric blocking antisense oligonucleotide with just 4 modified units, i.e ~20% substitution with R-aminomethoxypropyloxy (R-AMP)-thymidine within the 2′-OMe 18mer sequence.
PMCID: PMC3962517  PMID: 24300385
splice correction; steric-blocking; antisense; oligonucleotides
12.  Templating effect in DNA proximity ligation enables use of non-bioorthogonal chemistry in biological fluids 
Artificial DNA, PNA & XNA  2012;3(3):123-128.
Here we describe the first example of selective reductive amination in biological fluids using split aptamer proximity ligation (StAPL). Utilizing the cocaine split aptamer, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of target concentrations in buffer, human blood serum and artificial urine medium. We explore the substrate binding preferences of the split aptamer and find that the cinchona alkaloids quinine and quinidine bind to the aptamer with higher affinity than cocaine. This increased affinity leads to improved detection limits for these small-molecule targets. We also demonstrate that linker length and hydrophobicity impact the efficiency of split aptamer ligation. The ability to carry out selective chemical transformations using non-bioorthogonal chemistry in media where competing reactive groups are present highlights the power of the increased effective molarity provided by DNA assembly. Obviating the need for bioorthogonal chemistry would dramatically expand the repertoire of chemical transformations available for use in templated reactions such as proximity ligation assays, in turn enabling the development of novel methods for biomolecule detection.
PMCID: PMC3581511  PMID: 23370267
DNA; reductive amination; split aptamer; templated reaction; bioorthogonal
13.  Nucleic acid sensing by an orthogonal reporter system based on homo-DNA 
Artificial DNA, PNA & XNA  2013;4(1):28-33.
We have developed an assay for single strand DNA or RNA detection which is based on the homo-DNA templated Staudinger reduction of the profluorophore rhodamine-azide. The assay is based on a three component system, consisting of a homo-DNA/DNA hybrid probe, a set of homo-DNA reporter strands and the target DNA or RNA. We present two different formats of the assay (Omega probe and linear probe) in which the linear probe was found to perform best with catalytic turnover of the reporter strands (TON: 8) and a match/mismatch discrimination of up to 19. The advantage of this system is that the reporting (homo-DNA) and sensing (DNA) domain are decoupled from each other since the two pairing systems are bioorthogonal. This allows independent optimization of either domain which may lead to higher selectivity in in vivo imaging.
PMCID: PMC3654727  PMID: 23507698
homo-DNA; Staudinger reaction; RNA diagnostics; fluorescence sensing; oligonucleotides
14.  DNA display of PNA-tagged ligands 
Artificial DNA, PNA & XNA  2012;3(3):105-108.
Over the past decade, several technologies have emerged to access nucleic acid-tagged libraries and select the fittest compound within such libraries. This perspective focuses on recent development with PNA-tagged small molecules displayed on DNA templates for screening purposes and to probe the optimal geometry in multivalent interactions.
PMCID: PMC3581508  PMID: 22871882
DNA display; PNA-encoded synthesis; cooperative binding; inhibitor; multivalent interaction; screen
15.  To DNA, all information is equal 
Artificial DNA, PNA & XNA  2012;3(3):109-111.
Information storage capabilities are key in most aspects of society and the requirement for storage capacity is rapidly expanding. In principle, DNA could be a high-density medium for information storage. Church and coworkers recently demonstrated how binary data can be encoded, stored in, and retrieved from a library of oligonucleotides, increasing by several orders of magnitude the amount and density of manmade information stored in DNA to date. The technology remains in its infancy and important hurdles have yet to be overcome in order to realize its potential. However, DNA may be particularly useful as a storage-medium over long time-scales (centuries), because data-access is compatible with any large-scale DNA-sequencing and -synthesis technology.
PMCID: PMC3581509  PMID: 23104084
DNA; information storage in DNA; bit; byte; binary encoding
16.  Peptide nucleic acids in materials science 
Artificial DNA, PNA & XNA  2012;3(3):112-122.
This review highlights the recent methods to prepare PNA-based materials through a combination of self-assembly and self-organization processes. The use of these methods allows easy and versatile preparation of structured hybrid materials showing specific recognition properties and unique physicochemical properties at the nano- and micro-scale levels displaying potential applications in several directions, ranging from sensors and microarrays to nanostructured devices for biochips.
PMCID: PMC3581510  PMID: 22925824
PNA; monolayers; nanoparticles; self-assembly; self-organisation; materials; surfaces; sensors; microarrays; biochips; DNA-PNA duplexes; hybridization
17.  Letter from the Editors 
Artificial DNA, PNA & XNA  2012;3(2):29-30.
We are happy to publish this special issue dedicated to Prof. Rosangela Marchelli. This issue not only celebrates her long-standing scientific activity on occasion of her significant anniversary, but it is meant to recognize her contribution to Bioorganic Chemistry in the field of Artificial DNA, and in particular of Peptide Nucleic Acids.
PMCID: PMC3429528  PMID: 22777061
18.  Helix control in polymers 
Artificial DNA, PNA & XNA  2012;3(2):31-44.
The helix is a critical conformation exhibited by biological macromolecules and plays a key role in fundamental biological processes. Biological helical polymers exist in a single helical sense arising from the chiral effect of their primary units—for example, DNA and proteins adopt predominantly a right-handed helix conformation in response to the asymmetric conformational propensity of D-sugars and L-amino acids, respectively. In using these homochiral systems, nature blocks our observations of some fascinating aspects of the cooperativity in helical systems, although when useful for a specific purpose, “wrong” enantiomers may be incorporated in specific places. In synthetic helical systems, on the contrary, incorporation of non-racemic chirality is an additional burden, and the findings discussed in this review show that this burden may be considerably alleviated by taking advantage of the amplification of chirality, in which small chiral influences lead to large consequences. Peptide nucleic acid (PNA), which is a non-chiral synthetic DNA mimic, shows a cooperative response to a small chiral effect induced by a chiral amino acid, which is limited, however, due to the highly flexible nature of this oligomeric chimera. The lack of internal stereochemical bias is an important factor which makes PNA an ideal system to understand some cooperative features that are not directly accessible from DNA.
PMCID: PMC3429529  PMID: 22772039
helix control; chiral amplification; cooperativity; helical polymers; PNA
19.  Artificial DNA and surface plasmon resonance 
Artificial DNA, PNA & XNA  2012;3(2):45-244.
The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years.
Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows forbetter exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.
PMCID: PMC3429530  PMID: 22821257
DNAzyme; LNA; PNA; SPR; aptamer; biosensors
20.  PNA bearing 5-azidomethyluracil 
Artificial DNA, PNA & XNA  2012;3(2):53-62.
Fmoc- and Boc-protected modified monomers bearing 5-azidomethyluracil nucleobase were synthesized. Four different solid-phase synthetic strategies were tested in order to evaluate the application of this series of monomers for the solid-phase synthesis of modified PNA. The azide was used as masked amine for the introduction of amide-linked functional groups, allowing the production of a library of compounds starting from a single modified monomer. The azide function was also exploited as reactive group for the modification of PNA in solution via azide-alkyne click cycloaddition.
PMCID: PMC3429531  PMID: 22772040
modified uracil; peptide nucleic acids; PNA; solid-phase modification; click reaction; orthogonal protection
21.  Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays 
Artificial DNA, PNA & XNA  2012;3(2):63-72.
PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes.
PMCID: PMC3429532  PMID: 22772038
PNA; olive oil; hazelnut oil; SNP; cultivar identification; DNA fingerprinting
22.  Introduction of multiphosphonate ligand to peptide nucleic acid for metal ion conjugation 
Artificial DNA, PNA & XNA  2012;3(2):73-79.
Peptide nucleic acid (PNA) is one of the most widely used synthetic DNA analogs. Conjugation of functional molecules to PNA is very effective to further widen its potential applications. For this purpose, here we report the synthesis of several ligand monomers and introduced them to PNA. These ligand-modified PNAs attract cerium ion and are useful for site-selective DNA hydrolysis. It should be noted that these ligands on PNA are also effective even under the conditions of invasion complex.
PMCID: PMC3429533  PMID: 22772037
cerium; DNA; hydrolysis; ligand; metal ion; peptide nucleic acid
23.  Peptide nucleic acids tagged with four lysine residues for amperometric genosensors 
Artificial DNA, PNA & XNA  2012;3(2):80-87.
A homothymine PNA decamer bearing four lysine residues has been synthesized as a probe for the development of amperometric sensors. On one hand, the four amino groups introduced make this derivative nine times more soluble than the corresponding homothymine PNA decamer and, on the other hand, allow the stable anchoring of this molecule on Au nanostructured surface through the terminal -NH2 moieties. In particular, XPS and electrochemical investigations performed with hexylamine, as a model molecule, indicate that the stable deposition of primary amine derivatives on such a nanostructured surface is possible and involves the free electron doublet on the nitrogen atom. This finding indicates that this PNA derivative is suitable to act as the probe molecule for the development of amperometric sensors.
Thanks to the molecular probe chosen and to the use of a nanostructured surface as the substrate for the sensor assembly, the device proposed makes possible the selective recognition of the target oligonucleotide sequence with very high sensitivity.
PMCID: PMC3429534  PMID: 22772036
DNA recognition; PNA; amperometric genosensors; nanostructured surfaces; amine deposition
24.  Targeting pre-miRNA by Peptide Nucleic Acids 
Artificial DNA, PNA & XNA  2012;3(2):88-96.
PNAs conjugated to carrier peptides have been employed for the targeting of miRNA precursor, with the aim to develop molecules able to interfere in the pre-miRNA processing. The capability of the molecules to bind pre-miRNA has been tested in vitro by fluorescence assayes on Thiazole Orange labeled molecules and in vivo, in K562 cells, evaluating the amount of miRNA produced after treatment of cells with two amounts of PNAs.
PMCID: PMC3429535  PMID: 22699795
FACS; fluorescence; miR-210; PNA; pre-miR; thiazole orange
25.  Effects of decoy molecules targeting NF-kappaB transcription factors in Cystic fibrosis IB3–1 cells 
Artificial DNA, PNA & XNA  2012;3(2):97-296.
One of the clinical features of cystic fibrosis (CF) is a deep inflammatory process, which is characterized by production and release of cytokines and chemokines, among which interleukin 8 (IL-8) represents one of the most important. Accordingly, there is a growing interest in developing therapies against CF to reduce the excessive inflammatory response in the airways of CF patients. Since transcription factor NF-kappaB plays a critical role in IL-8 expression, the transcription factor decoy (TFD) strategy might be of interest. In order to demonstrate that TFD against NF-kappaB interferes with the NF-kappaB pathway we proved, by chromatin immunoprecipitation (ChIP) that treatment with TFD oligodeoxyribonucleotides of cystic fibrosis IB3–1 cells infected with Pseudomonas aeruginosa leads to a decrease occupancy of the Il-8 gene promoter by NF-kappaB factors. In order to develop more stable therapeutic molecules, peptide nucleic acids (PNAs) based agents were considered. In this respect PNA-DNA-PNA (PDP) chimeras are molecules of great interest from several points of view: (1) they can be complexed with liposomes and microspheres; (2) they are resistant to DNases, serum and cytoplasmic extracts; (3) they are potent decoy molecules. By using electrophoretic mobility shift assay and RT-PCR analysis we have demonstrated that (1) the effects of PDP/PDP NF-kappaB decoy chimera on accumulation of pro-inflammatory mRNAs in P.aeruginosa infected IB3–1 cells reproduce that of decoy oligonucleotides; in particular (2) the PDP/PDP chimera is a strong inhibitor of IL-8 gene expression; (3) the effect of PDP/PDP chimeras, unlike those of ODN-based decoys, are observed even in the absence of protection with lipofectamine. These informations are of great impact, in our opinion, for the development of stable molecules to be used in non-viral gene therapy of cystic fibrosis.
PMCID: PMC3429536  PMID: 22772035
NF-kappaB; transcription factor decoy; inflammation; Peptide Nucleic Acids; PNA-DNA chimeras

Results 1-25 (61)