ArticleThe journal of physical chemistry. A2011
B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics.
Article in The journal of physical chemistry. A, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed, 28 citations in OpenAlex.
- Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion.bioRxiv : the preprint server for biology · 2026Article
- Precise Mechanochemical Scission of DNA Guided by Secondary Structures.Journal of the American Chemical Society · 2026Article
- The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA.Nucleic acids research · 2020Article
- Charge splitters and charge transport junctions based on guanine quadruplexes.Nature nanotechnology · 2018Article
- Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.Nanotechnology · 2014Article
- The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.Journal of the Royal Society, Interface · 2014Article
- Effects of cytosine hydroxymethylation on DNA strand separation.Biophysical journal · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force-extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π-π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.