Structure, Stiffness and Substates of the Dickerson-Drew
Dodecamer

J 2013

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER et. al.

Basic information

Original name

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

Authors

DRŠATA, Tomáš (203 Czech Republic), Alberto PEREZ (840 United States of America), Modesto OROZCO (724 Spain), Alexandre V MOROZOV (840 United States of America), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Filip LANKAŠ (203 Czech Republic)

Edition

Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2013, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.310

RIV identification code

RIV/00216224:14740/13:00067939

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ct300671y

UT WoS

000313378700071

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION

Abstract

V originále

The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER and Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, vol. 9, No 1, p. 707-721. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct300671y.

@article{1092256,
   author = {Dršata, Tomáš and Perez, Alberto and Orozco, Modesto and Morozov, Alexandre V and Šponer, Jiří and Lankaš, Filip},
   article_location = {WASHINGTON},
   article_number = {1},
   doi = {http://dx.doi.org/10.1021/ct300671y},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer},
   url = {http://pubs.acs.org/toc/jctcce/9/1},
   volume = {9},
   year = {2013}
}

TY  - JOUR
ID  - 1092256
AU  - Dršata, Tomáš - Perez, Alberto - Orozco, Modesto - Morozov, Alexandre V - Šponer, Jiří - Lankaš, Filip
PY  - 2013
TI  - Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
JF  - Journal of Chemical Theory and Computation
VL  - 9
IS  - 1
SP  - 707-721
EP  - 707-721
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - UNIQUE TETRANUCLEOTIDE SEQUENCES
KW  - NUCLEIC-ACID STRUCTURES
KW  - B-DNA DODECAMER
KW  - BASE-PAIR LEVEL
KW  - X-RAY
KW  - COUPLING-CONSTANTS
KW  - MONOVALENT CATIONS
KW  - CRYSTAL-STRUCTURES
KW  - ATOMIC-RESOLUTION
UR  - http://pubs.acs.org/toc/jctcce/9/1
L2  - http://pubs.acs.org/toc/jctcce/9/1
N2  - The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
ER  -

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER and Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, vol.~9, No~1, p.~707-721. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct300671y.

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