Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.
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.
Cubero
Elena
E
Molecular Modeling & Bioinformatic Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
Abrescia
Nicola G A
NG
Subirana
Juan A
JA
Luque
F Javier
FJ
Orozco
Modesto
M
D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D012996:Solutions; D014867:Water; D011067:Poly dA-dT; D004247:DNA