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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. 2009. "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 = 2009,
month = 1
}
  • Stacking fault tetrahedra (SFTs) are formed under irradiation in fcc metals and alloys. The high number density of SFTs observed suggests that they should contribute to radiation-induced hardening and, therefore, be taken into account when estimating mechanical property changes of irradiated materials. The key issue in this is to describe the interaction between a moving dislocation and an individual SFT, which is distinguished by a small physical size of the order of {approx}1-10 nm. We have performed atomistic simulations of edge and screw dislocations interacting with SFTs of different sizes at different temperatures and strain rates. Five possible interaction outcomesmore » have been identified, involving either partial absorption, or shearing or restoration of SFTs. The mechanisms that give rise to these processes are described and their dependence on interaction parameters, such as SFT size, dislocation-SFT geometry, temperature and stress/strain rate are determined. Mechanisms that help to explain the formation of defect-free channels cleared by gliding dislocations, as observed experimentally, are also discussed. Hardening due to the various mechanisms and their dependence on loading conditions will be presented in a following paper (Part II).« less
  • A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is muchmore » smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization of the h-bonded dimers results in barrierless (or nearly barrierless) protontransfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions.« less
  • The collapse of stacking-fault tetrahedra (SFT) by gliding dislocations was observed in in situ straining experiments in a transmission electron microscope (TEM). A stacking-fault tetrahedron was collapsed by intersection with a gliding perfect dislocation: only the base portion divided by the gliding plane of the dislocation annihilated, while the apex portion remained intact. As a result of analysis on evolution of atom configuration induced by intersection with perfect dislocation in SFT, it was found that an unusual atom configuration inevitably appeared in one of the ledges formed on stacking-fault planes, which is traditionally called I-ledge: the atoms on adjacent (111)more » planes were overlapping each other. The overlapping configuration provides a strong repulsive force, being a conceivable driving force to induce a chain reaction of atom displacements that collapses the SFT base portion.« less
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