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Title: Stacking interactions and DNA intercalation

Abstract

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. 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.

Authors:
 [1];  [2];  [3];  [4];  [5]
  1. Fred Hutchinson Cancer Research Center
  2. ORNL
  3. Wake Forest University, Winston-Salem, NC
  4. Chalmers University of Technology, Sweden
  5. Rutgers University
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
963922
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Physical Chemistry B; Journal Volume: 113; Journal Issue: 32
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CONFIGURATION; DNA; ELECTRON CORRELATION; FUNCTIONALS; POTENTIAL ENERGY; PROFLAVINE; TORQUE

Citation Formats

Li, Dr. Shen, Cooper, Valentino R, Thonhauser, Prof. Timo, Lundqvist, Prof. Bengt I., and Langreth, David C. Stacking interactions and DNA intercalation. United States: N. p., 2009. Web. doi:10.1021/jp905765c.
Li, Dr. Shen, Cooper, Valentino R, Thonhauser, Prof. Timo, Lundqvist, Prof. Bengt I., & Langreth, David C. Stacking interactions and DNA intercalation. United States. doi:10.1021/jp905765c.
Li, Dr. Shen, Cooper, Valentino R, Thonhauser, Prof. Timo, Lundqvist, Prof. Bengt I., and Langreth, David C. Thu . "Stacking interactions and DNA intercalation". United States. doi:10.1021/jp905765c.
@article{osti_963922,
title = {Stacking interactions and DNA intercalation},
author = {Li, Dr. Shen and Cooper, Valentino R and Thonhauser, Prof. Timo and Lundqvist, Prof. Bengt I. and Langreth, David C.},
abstractNote = {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. 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.},
doi = {10.1021/jp905765c},
journal = {Journal of Physical Chemistry B},
number = 32,
volume = 113,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}