TY - JOUR
T1 - Stacking interactions and DNA intercalation
AU - Li, Shen
AU - Cooper, Valentino R.
AU - Thonhauser, T.
AU - Lundqvist, Bengt I.
AU - Langreth, David C.
PY - 2009/8/13
Y1 - 2009/8/13
N2 - The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.
AB - The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.
UR - http://www.scopus.com/inward/record.url?scp=68649106697&partnerID=8YFLogxK
U2 - 10.1021/jp905765c
DO - 10.1021/jp905765c
M3 - Article
AN - SCOPUS:68649106697
SN - 1520-6106
VL - 113
SP - 11166
EP - 11172
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 32
ER -