Stacking interactions and the twist of DNA.
The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.
Cooper
Valentino R
VR
Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854-8019, USA. vcooper@physics.rutgers.edu <vcooper@physics.rutgers.edu>
Thonhauser
Timo
T
Puzder
Aaron
A
Schröder
Elsebeth
E
Lundqvist
Bengt I
BI
Langreth
David C
DC
D000596:Amino Acids / Q000737:chemistry*; D001482:Base Composition; D020029:Base Pairing; D001671:Biochemistry / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D011743:Pyrimidines / Q000737:chemistry; D012984:Software; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry
D000596:Amino Acids; D011743:Pyrimidines; D004247:DNA; D013941:Thymine