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1.  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.
doi:10.4161/adna.25786
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)
2.  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.
doi:10.4161/adna.21941
PMCID: PMC3581510  PMID: 22925824
PNA; monolayers; nanoparticles; self-assembly; self-organisation; materials; surfaces; sensors; microarrays; biochips; DNA-PNA duplexes; hybridization
3.  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.
doi:10.4161/adna.20572
PMCID: PMC3429529  PMID: 22772039
helix control; chiral amplification; cooperativity; helical polymers; PNA
4.  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.
doi:10.4161/adna.21383
PMCID: PMC3429530  PMID: 22821257
DNAzyme; LNA; PNA; SPR; aptamer; biosensors
5.  Antisense mediated exon skipping therapy for duchenne muscular dystrophy (DMD) 
Artificial DNA, PNA & XNA  2011;2(1):6-15.
Duchenne Muscular Dystrophy (DMD) is a lethal disease caused by mutations in the dystrophin gene (DMD) that result in the absence of essential muscle protein dystrophin. Among many different approaches for DMD treatment, exon skipping, mediated by antisense oligonucleotides, is one of the most promising methods for restoration of dystrophin expression. This approach has been tested extensively targeting different exons in numerous models both in vitro and in vivo. During the past 10 years, there has been a considerable progress by using DMD animal models involving three types of antisense oligonucleotides (2′-O-methyl phosphorothioate (2OME-PS), phosphorodiamidate morpholino oligomer (PMO)) and peptide nucleic acid (PNA).
doi:10.4161/adna.2.1.15425
PMCID: PMC3116580  PMID: 21686247
antisense; DMD; exon skipping; in vivo; splicing modulation; therapy
6.  Mega-cloning and the advent of synthetic genomes 
Artificial DNA, PNA & XNA  2010;1(1):54-57.
Molecular biology owes its prominent role in the biological sciences to the tools of recombinant DNA. While the foundations of recombinant DNA were laid in the 1970s with the discovery of type II restriction endonucleases,1,2 development of robust sequencing technology3 and pioneering work on gene synthesis,4,5 it was not until the turn of the new millennium before the first complete synthetic viral genomes saw the light of day including that of hepatitis C,6 poliovirus,7 and bacteriophage PhiX174.8 Recombinant DNA has come of age as entire cellular genomes are sequenced and stored as digitized information. So what's next? One novel branch of recombinant DNA, referred to as synthetic genomics,9 is occupied with (re)construction of entire cellular genomes from virtual sequence information and using chemical components. Here we look at the most recent developments in such de novo construction. For a broader and more extensive review on genome engineering, the reader is referred to the excellent paper by Carr and Church.10
doi:10.4161/adna.1.1.12935
PMCID: PMC3109442  PMID: 21687527
synthetic genomics; recombinant DNA; genome transplantation; whole-genome assembly; synthetic chromosome

Results 1-6 (6)