Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.
Title | Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. |
Publication Type | Journal Article |
Year of Publication | 2003 |
Authors | Cubero, Elena, Abrescia Nicola G. A., Subirana Juan A., F Luque Javier, and Orozco Modesto |
Journal | J Am Chem Soc |
Volume | 125 |
Pagination | 14603-12 |
Date Published | 2003 Nov 26 |
ISSN | 0002-7863 |
Keywords | DNA, Models, Molecular, Nucleic Acid Conformation, Poly dA-dT, Solutions, Thermodynamics, Water |
Abstract | The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. The structure, which was found to be stable in all of the simulations, has many similarities with the standard Watson-Crick duplex in terms of general structure, flexibility, and molecular recognition patterns. Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved. |
DOI | 10.1021/ja035918f |