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1.  “Artifactual” arsenate DNA 
Artificial DNA, PNA & XNA  2012;3(1):1-2.
The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA1 arose much skepticism, primarily due to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present evidence that the identification of arsenate DNA was artifactual.
doi:10.4161/adna.19672
PMCID: PMC3368811  PMID: 22679526
arsenate; bacteria; DNA; genetic material; life
2.  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.
doi:10.4161/adna.23892
PMCID: PMC3654724  PMID: 23406786
DNA bending flexibility; DNA minicircles; DNA sticky ends; DNA extreme bendability; single-molecule data
3.  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.
doi:10.4161/adna.22671
PMCID: PMC3581509  PMID: 23104084
DNA; information storage in DNA; bit; byte; binary encoding
4.  A DNA nanocapsule with aptamer-controlled open-closure function for targeted delivery 
Artificial DNA, PNA & XNA  2012;3(1):3-4.
A DNA capsule fitted with aptamer controlled target sensing has been “woven” using a 7308-base single-stranded DNA “thread” and 196 staple oligonucleotides. The capsule enables logic-gated molecular cargo delivery to targeted cell surfaces.
doi:10.4161/adna.19843
PMCID: PMC3368814  PMID: 22679527
aptamer; delivery; DNA origami; nanocapsule; nanoscience
5.  RNA-DNA sequence differences spell genetic code ambiguities 
Artificial DNA, PNA & XNA  2011;2(3):69-70.
A recent paper in Science by Li et al. 20111 reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized. 
PMCID: PMC3324336  PMID: 22567189
gene expression; RNA editing; RNA-DNA differences; transcription; transcriptome
6.  A ribozyme transcribed by a ribozyme 
Artificial DNA, PNA & XNA  2011;2(2):40-42.
Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carriers and catalysts would lend support to such a scenario. A pivotal component of this system would be an RNA dependent RNA polymerase ribozyme capable of replicating its own RNA gene. Recent work from the Holliger group at the Laboratory for Molecular Biology in Cambridge has provided synthetic ribozymes1 that just might foreshadow the future engineering of such self-replicative systems.
doi:10.4161/adna.2.2.16852
PMCID: PMC3166488  PMID: 21912725
ribozyme; RNA dependent RNA polymerase; In vitro evolution; RNA engineering; transcription
7.  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
8.  DNA breathes Hoogsteen 
Artificial DNA, PNA & XNA  2011;2(1):1-3.
A recent claim is discussed that Watson-Crick pairs in the naked duplex DNA spontaneously flip into Hoogsteen pairs under ordinary conditions. The claim is considered within the historical retrospective and is put into the broader context of DNA biophysics.
doi:10.4161/adna.2.1.15509
PMCID: PMC3116583  PMID: 21686245
duplex DNA breathing; hoogsteen base pairs; DNA structure; DNA motility
9.  Evolution of synthetic polymers 
Artificial DNA, PNA & XNA  2010;1(2):61-63.
A strategy for the enrichment of a DNA template that encodes a functionalized PNA oligomer is discussed. The method relies on iterated cycles of chemical translation (of the template into PNA), selection (for function), and amplification (of the survivors). Potential restrictions and future perspectives are considered.
doi:10.4161/adna.1.2.13501
PMCID: PMC3116572  PMID: 21686238
chemical evolution; selection; enrichment; DNA template
10.  Adding mRNA to the list of spatially organized components in bacteria 
Artificial DNA, PNA & XNA  2010;1(2):66-67.
Using LNA in situ hybridization, select mRNAs have been shown to be spatially confined to their chromosomal loci in two distantly related bacterial organisms. Translating ribosomes are diffusion limited by mRNA association.
doi:10.4161/adna.1.2.14150
PMCID: PMC3116576  PMID: 21686240
mRNA spatial distribution; locked nucleic acid (LNA); fluorescence in situ hybridization (FISH)
11.  Small RNAs hit a new target 
Artificial DNA, PNA & XNA  2010;1(2):64-65.
The University of Texas researchers have recently discovered that small synthetic RNAs (sRNAs) that are complementary to sequences located 3′-outside of genes can efficiently modulate gene expression. These new findings significantly expand the transcription-regulatory potential of sRNAs, and they also may provide useful leads for other artificial nucleobase oligomers to target sequences beyond the 3′ termini of mRNA.
doi:10.4161/adna.1.2.13945
PMCID: PMC3116577  PMID: 21686239
small RNAs; 3′ non-coding transcripts; gene expression modulation; DNA looping; peptide nucleic acid (PNA)
12.  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 1-12 (12)