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.

Základní údaje

Originální název

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

Autoři

DRSATA, Tomáš (203 Česká republika), Naďa ŠPAČKOVÁ (203 Česká republika), Petr JUREČKA (203 Česká republika), Marie ZGARBOVÁ (203 Česká republika), Jiří ŠPONER (203 Česká republika, garant, domácí) a Filip LANKAŠ (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.112

Kód RIV

RIV/00216224:14740/14:00076810

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000338769400055

Klíčová slova anglicky

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

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 10. 2014 10:39, Martina Prášilová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER a 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, roč. 42, č. 11, s. 7383-7394. ISSN 0305-1048. Dostupné z: 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 a 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, roč.~42, č.~11, s.~7383-7394. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku338.

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