Theoretical models of DNA flexibility

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F13%3A00428591" target="_blank" >RIV/61388963:_____/13:00428591 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1002/wcms.1144" target="_blank" >http://dx.doi.org/10.1002/wcms.1144</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/wcms.1144" target="_blank" >10.1002/wcms.1144</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Theoretical models of DNA flexibility

Popis výsledku v původním jazyce

DNA sequence-dependent three-dimensional structure and mechanical deformability play a large role in biological processes such as protein-DNA interactions, nucleosome positioning, promoter identification, and drug-DNA recognition. On the important scaleof 10-100 base pairs, models where DNA bases are represented by interacting rigid bodies have proved useful. We focus on a recently proposed rigid base model with nonlocal, harmonic interaction energy. We discuss the choice of internal coordinates and amethod to obtain model parameters from coordinate fluctuations. Parameter transformation upon change of reference strand, coordinate constraints, and models with reduced number of degrees of freedom are described. Relation to traditional local harmonic models is clarified. We outline recent attempts to include anharmonic effects. A rigid base model of a DNA oligomer containing A-tract is presented as an example. Perspectives of model development and application are discussed.

Název v anglickém jazyce

Theoretical models of DNA flexibility

Popis výsledku anglicky

DNA sequence-dependent three-dimensional structure and mechanical deformability play a large role in biological processes such as protein-DNA interactions, nucleosome positioning, promoter identification, and drug-DNA recognition. On the important scaleof 10-100 base pairs, models where DNA bases are represented by interacting rigid bodies have proved useful. We focus on a recently proposed rigid base model with nonlocal, harmonic interaction energy. We discuss the choice of internal coordinates and amethod to obtain model parameters from coordinate fluctuations. Parameter transformation upon change of reference strand, coordinate constraints, and models with reduced number of degrees of freedom are described. Relation to traditional local harmonic models is clarified. We outline recent attempts to include anharmonic effects. A rigid base model of a DNA oligomer containing A-tract is presented as an example. Perspectives of model development and application are discussed.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2013

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Wiley Interdisciplinary Reviews - Computational Molecular Science

ISSN

1759-0876

e-ISSN

—

Svazek periodika

3

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

9

Strana od-do

355-363

Kód UT WoS článku

000334577900003

EID výsledku v databázi Scopus

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