title: B-DNA structure and stability: the role of hydrogen bonding, π-π stacking interactions, twist-angle, and solvation.
abstract: We have computationally investigated the structure and stability of B-DNA. To this end, we have analyzed the bonding in a series of 47 stacks consisting of two base pairs, in which the base pairs cover the full range of natural Watson-Crick pairs, mismatched pairs, and artificial DNA base pairs. Our analyses provide detailed insight into the role and relative importance of the various types of interactions, such as, hydrogen bonding, π-π stacking interactions, and solvation/desolvation. Furthermore, we have analyzed the functionality of the twist-angle on the stability of the structure. Interestingly, we can show that all stacked base pairs benefit from a stabilization by 6 to 12 kcal mol(-1) if stacked base pairs are twisted from 0° to 36°, that is, if they are mutually rotated from a congruent superposition to the mutually twisted stacking configuration that occurs in B-DNA. This holds especially for stacked AT pairs but also for other stacked base pairs, including GC. The electronic mechanism behind this preference for a twisted arrangement depends on the base pairs involved. We also show that so-called "diagonal interactions" (or cross terms) in the stacked base pairs are crucial for understanding the stability of B-DNA, in particular, in GC-rich sequences.
authors.affiliation: Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University Amsterdam, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands. C. FonsecaGuerra@vu.nl.
authors.forename: Jordi
authors.initials: J
authors.lastname: Poater
authors.forename: Marcel
authors.initials: M
authors.lastname: Swart
authors.forename: F Matthias
authors.initials: FM
authors.lastname: Bickelhaupt
authors.forename: Célia
authors.initials: C
authors.lastname: Fonseca Guerra
mesh_terms: D020029:Base Pairing; D059371:DNA, B-Form / Q000737:chemistry*; D004583:Electrons; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D059371:DNA, B-Form; D012997:Solvents