Conformational control of TT dimerization in DNA conjugates. A molecular dynamics study

Martin McCullagh, Mahesh Hariharan, Frederick D. Lewis, Dimitra Markovitsi, Thierry Douki, George C Schatz

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

The paper presents quantum yield results for the [2+2] and 6-4 photodimerization of TT steps in several DNA structures, including hairpins where the context dependence of the photodimerization yield is determined, and it develops a theoretical model that correctly describes the trends in dimerization yield with DNA structure. The DNA conjugates considered include dT20, dA20dT20, and three alkane-linked hairpins that contain a single TT step. The theoretical modeling of the [2+2] process is based on CASSCF electronic structure calculations for ethylene + ethylene, which show that photoexcitation of low-lying excited states leads to potential surfaces that correlate without significant barriers to a conical intersection with the ground state surface at geometries close to the dimer structure. The primary constraint on dimerization is the distance d between the two double bonds, and it is found that d <3.52 Å leads to quantum yield trends that match the observed trends within a factor of 3. Constraints on the dihedral angle between the two double bonds are not as important, and although it is possible to generate better dimerization yield predictions for some structures by including these constraints, the best overall picture is obtained with no constraint. For 6-4 dimerization, a distance g <2.87 Å and no constraint on dihedral angle provide an accurate description of the yield.

Original languageEnglish
Pages (from-to)5215-5221
Number of pages7
JournalJournal of Physical Chemistry B
Volume114
Issue number15
DOIs
Publication statusPublished - Apr 22 2010

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Dimerization
dimerization
Molecular dynamics
DNA
deoxyribonucleic acid
molecular dynamics
Quantum yield
Dihedral angle
Ethylene
trends
Alkanes
dihedral angle
Photoexcitation
Surface potential
ethylene
Excited states
Dimers
Paraffins
Ground state
Electronic structure

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Conformational control of TT dimerization in DNA conjugates. A molecular dynamics study. / McCullagh, Martin; Hariharan, Mahesh; Lewis, Frederick D.; Markovitsi, Dimitra; Douki, Thierry; Schatz, George C.

In: Journal of Physical Chemistry B, Vol. 114, No. 15, 22.04.2010, p. 5215-5221.

Research output: Contribution to journalArticle

McCullagh, Martin ; Hariharan, Mahesh ; Lewis, Frederick D. ; Markovitsi, Dimitra ; Douki, Thierry ; Schatz, George C. / Conformational control of TT dimerization in DNA conjugates. A molecular dynamics study. In: Journal of Physical Chemistry B. 2010 ; Vol. 114, No. 15. pp. 5215-5221.
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