B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Balaeff, A; Craig, SL; Beratan, DN

Published Date

  • September 2011

Published In

Volume / Issue

  • 115 / 34

Start / End Page

  • 9377 - 9391

PubMed ID

  • 21598926

Pubmed Central ID

  • PMC3615717

Electronic International Standard Serial Number (EISSN)

  • 1520-5215

International Standard Serial Number (ISSN)

  • 1089-5639

Digital Object Identifier (DOI)

  • 10.1021/jp110871g


  • eng