Mechanical properties of symmetric and asymmetric DNA A-tracts:
implications for looping and nucleosome positioning

J 2014

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER et. al.

Basic information

Original name

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Authors

DRSATA, Tomáš (203 Czech Republic), Naďa ŠPAČKOVÁ (203 Czech Republic), Petr JUREČKA (203 Czech Republic), Marie ZGARBOVÁ (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Filip LANKAŠ (203 Czech Republic)

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2014, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.112

RIV identification code

RIV/00216224:14740/14:00076810

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gku338

UT WoS

000338769400055

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; SEQUENCE-DIRECTED CURVATURE; ADENINE-THYMINE TRACT; BASE-PAIR LEVEL; INDIRECT READOUT; NUCLEIC-ACIDS; B-DNA; CONFORMATIONAL-ANALYSIS; DISFAVORING SEQUENCES; ELASTIC PROPERTIES

Abstract

V originále

A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A(n)T(n) and asymmetric A(2n) tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER and Filip LANKAŠ. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Research. Oxford: Oxford University Press, 2014, vol. 42, No 11, p. 7383-7394. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku338.

@article{1202574,
   author = {Drsata, Tomáš and Špačková, Naďa and Jurečka, Petr and Zgarbová, Marie and Šponer, Jiří and Lankaš, Filip},
   article_location = {Oxford},
   article_number = {11},
   doi = {http://dx.doi.org/10.1093/nar/gku338},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; SEQUENCE-DIRECTED CURVATURE; ADENINE-THYMINE TRACT; BASE-PAIR LEVEL; INDIRECT READOUT; NUCLEIC-ACIDS; B-DNA; CONFORMATIONAL-ANALYSIS; DISFAVORING SEQUENCES; ELASTIC PROPERTIES},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning},
   url = {http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338},
   volume = {42},
   year = {2014}
}

TY  - JOUR
ID  - 1202574
AU  - Drsata, Tomáš - Špačková, Naďa - Jurečka, Petr - Zgarbová, Marie - Šponer, Jiří - Lankaš, Filip
PY  - 2014
TI  - Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning
JF  - Nucleic Acids Research
VL  - 42
IS  - 11
SP  - 7383-7394
EP  - 7383-7394
PB  - Oxford University Press
SN  - 03051048
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - SEQUENCE-DIRECTED CURVATURE
KW  - ADENINE-THYMINE TRACT
KW  - BASE-PAIR LEVEL
KW  - INDIRECT READOUT
KW  - NUCLEIC-ACIDS
KW  - B-DNA
KW  - CONFORMATIONAL-ANALYSIS
KW  - DISFAVORING SEQUENCES
KW  - ELASTIC PROPERTIES
UR  - http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338
L2  - http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338
N2  - A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A(n)T(n) and asymmetric A(2n) tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.
ER  -

DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER and Filip LANKAŠ. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2014, vol.~42, No~11, p.~7383-7394. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku338.

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