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J Am Chem Soc. 2003 Nov 26;125(47):14603-12.

Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.

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  • 1Molecular Modeling & Bioinformatic Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.


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.

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