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1.  Introducing Artificial DNA: PNA & XNA 
doi:10.4161/adna.1.1.12932
PMCID: PMC3109443  PMID: 21687520
2.  Artificial DNA structures 
doi:10.4161/adna.2.2.17085
PMCID: PMC3166487  PMID: 21912724
3.  Sensitive detection of nucleic acids by PNA hybridization directed co-localization of fluorescent beads 
Artificial DNA, PNA & XNA  2011;2(2):60-66.
We have designed a pair of biotinylated peptide nucleic acid (PNA) probes targeting two sequences in 18S rRNA (from the parasite Trypanosoma brucei) at a distance of 191 nt (corresponding to maximum distance of ca. 60 nm) from each other. The PNA probes were individually bound to (strept)avidin-coated fluorescent beads, differing in size and color [green beads (1 µm) and red beads (5.9 µm)], thereby allowing distinct detection of each PNA probe by conventional fluorescence microscopy. These two PNA beads showed easily detectable co-localization when simultaneously hybridizing to a target nucleic acid. The assay detected the parasite 18S rRNA down to 1.6 fmol while there was no such co-localization visible with human 18S rRNA not containing the PNA targets. Furthermore, the assay showed positive detection with 1.6 ng of total RNA (corresponding to RNA from ca. 300 parasites). Upon further optimization this method may provide a new tool for a diagnosis of Human African Trypanosomiasis (HAT) and it may more generally have applications within diagnostics for (neglected) infectious diseases.
doi:10.4161/adna.2.2.16562
PMCID: PMC3166491  PMID: 21912728
diagnostics; fluorescence microscopy; fluorescent bead; PNA; ribosomal RNA; Trypanosome
4.  Natural Arsenate DNA? 
Artificial DNA, PNA & XNA  2011;2(1):4-5.
The recent paper by Wolfe-Simon et al.1 reporting a bacterial strain, which is able to grow in high concentrations of arsenate, apparently in the absence of phosphate, and claims that in this strain arsenate is substituting for phosphate, e.g. in nucleic acids (Figure 1), was highly profiled, attracted broad attention, and almost immediately resulted in heavy scientific criticism (see e.g. 2–7).
doi:10.4161/adna.2.1.15657
PMCID: PMC3116578  PMID: 21686246
Arsenate; DNA; evolution; origin of life; bacteria
5.  Targeted gene correction using psoralen, chlorambucil and camptothecin conjugates of triplex forming peptide nucleic acid (PNA) 
Artificial DNA, PNA & XNA  2011;2(1):23-32.
Gene correction activation effects of a small series of triplex forming peptide nucleic acid (PNA) covalently conjugated to the DNA interacting ligands psoralen, chlorambucil and camptothecin targeted proximal to a stop codon mutation in an EGFP reporter gene were studied. A 15-mer homopyrimidine PNA conjugated to the topoisomerase I inhibitor camptothecin was found to increase the frequency of repair domain mediated gene correctional events of the EGFP reporter in an in vitro HeLa cell nuclear extract assay, whereas PNA psoralen or chlorambucil conjugates both of which form covalent and also interstrand crosslinked adducts with dsDNA dramatically decreased the frequency of targeted repair/correction. The PNA conjugates were also studied in mammalian cell lines upon transfection of PNA bound EGFP reporter vector and scoring repair of the EGFP gene by FACS analysis of functional EGFP expression. Consistent with the extract experiments, treatment with adduct forming PNA conjugates (psoralen and chlorambucil) resulted in a decrease in background correction frequencies in transiently transfected cells, whereas unmodified PNA or the PNA-camptothecin conjugate had little or no effect. These results suggest that simple triplex forming PNAs have little effect on proximal gene correctional events whereas PNA conjugates capable of forming DNA adducts and interstrand crosslinks are strong inhibitors. Most interestingly the PNA conjugated to the topoisomerase inhibitor, camptothecin enhanced repair in nuclear extract. Thus the effects and use of camptothecin conjugates in gene targeted repair merit further studies.
doi:10.4161/adna.2.1.15553
PMCID: PMC3116579  PMID: 21686249
PNA; triplex; gene correction; repair; DNA modification
6.  A novel pseudo-complementary PNA G-C base pair 
Artificial DNA, PNA & XNA  2011;2(1):33-37.
Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting of the unnatural nucleobases n6-methoxy-2,6-diaminopurine (previously described in a DNA context) and N4-benzoylcytosine is now presented for design of pseudo-complementary PNA oligomers (pcPNAs).
doi:10.4161/adna.2.1.15554
PMCID: PMC3116581  PMID: 21686250
DNA recognition; hybridization; nucleobases; synthesis; PNA
7.  Natural - synthetic - artificial! 
Artificial DNA, PNA & XNA  2010;1(1):58-59.
The terms “natural,” “synthetic” and “artificial” are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.
doi:10.4161/adna.1.1.12934
PMCID: PMC3109441  PMID: 21687528
synthetic chromosomes; synthetic cells; artificial cells; artificial life

Results 1-7 (7)