Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins

Sameer Patwardhan, Stefano Tonzani, Frederick D. Lewis, Laurens D A Siebbeles, George C Schatz, Ferdinand C. Grozema

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.

Original languageEnglish
Pages (from-to)11447-11458
Number of pages12
JournalJournal of Physical Chemistry B
Volume116
Issue number37
DOIs
Publication statusPublished - Sep 20 2012

Fingerprint

dynamic structural analysis
Structural dynamics
Excited states
DNA
deoxyribonucleic acid
excitation
DNA sequences
Dichroism
Excitons
dichroism
Molecular dynamics
excitons
disorders
molecular dynamics
Computer simulation
electronics
simulation

ASJC Scopus subject areas

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

Cite this

Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins. / Patwardhan, Sameer; Tonzani, Stefano; Lewis, Frederick D.; Siebbeles, Laurens D A; Schatz, George C; Grozema, Ferdinand C.

In: Journal of Physical Chemistry B, Vol. 116, No. 37, 20.09.2012, p. 11447-11458.

Research output: Contribution to journalArticle

Patwardhan, Sameer ; Tonzani, Stefano ; Lewis, Frederick D. ; Siebbeles, Laurens D A ; Schatz, George C ; Grozema, Ferdinand C. / Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins. In: Journal of Physical Chemistry B. 2012 ; Vol. 116, No. 37. pp. 11447-11458.
@article{6139a3b9b5c8439db2e88926b3a2804f,
title = "Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins",
abstract = "In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.",
author = "Sameer Patwardhan and Stefano Tonzani and Lewis, {Frederick D.} and Siebbeles, {Laurens D A} and Schatz, {George C} and Grozema, {Ferdinand C.}",
year = "2012",
month = "9",
day = "20",
doi = "10.1021/jp307146u",
language = "English",
volume = "116",
pages = "11447--11458",
journal = "Journal of Physical Chemistry B",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "37",

}

TY - JOUR

T1 - Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins

AU - Patwardhan, Sameer

AU - Tonzani, Stefano

AU - Lewis, Frederick D.

AU - Siebbeles, Laurens D A

AU - Schatz, George C

AU - Grozema, Ferdinand C.

PY - 2012/9/20

Y1 - 2012/9/20

N2 - In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.

AB - In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.

UR - http://www.scopus.com/inward/record.url?scp=84866624939&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84866624939&partnerID=8YFLogxK

U2 - 10.1021/jp307146u

DO - 10.1021/jp307146u

M3 - Article

VL - 116

SP - 11447

EP - 11458

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

SN - 1520-6106

IS - 37

ER -