@article {213,
	title = {Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex},
	journal = {Journal of the American Chemical Society},
	volume = {125},
	year = {2003},
	month = {2003/11/26/},
	pages = {14603 - 14612},
	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.},
	keywords = {DNA/chemistry; Models, Molecular; Nucleic Acid Conformation; Poly dA-dT/chemistry; Solutions; Thermodynamics; Water/chemistry},
	author = {Cubero,E. and Abrescia,N. G. and Subirana,J. A. and F. J. Luque and M. Orozco}
}
