Mechanical Model of DNA Allostery

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F14%3A10287355" target="_blank" >RIV/00216208:11310/14:10287355 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/14:00437506 RIV/61388963:_____/14:00437506 RIV/00216224:14740/14:00077973 RIV/61989592:15310/14:33152185
Result on the web
<a href="http://dx.doi.org/10.1021/jz501826q" target="_blank" >http://dx.doi.org/10.1021/jz501826q</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jz501826q" target="_blank" >10.1021/jz501826q</a>

Result language
angličtina
Original language name
Mechanical Model of DNA Allostery
Original language description
The importance of allosteric effects in DNA is becoming increasingly appreciated, but the underlying mechanisms remain poorly understood. In this work, we propose a general modeling framework to study DNA allostery. We describe DNA in a coarse-grained manner by intra-base pair and base pair step coordinates, complemented by groove widths. Quadratic deformation energy is assumed, yielding linear relations between the constraints and their effect. Model parameters are inferred from standard unrestrained,explicit-solvent molecular dynamics simulations of naked DNA. We applied the approach to study minor groove binding of diamidines and pyrrole-imidazole polyamides. The predicted DNA bending is in quantitative agreement with experiment and suggests that diamidine binding to the alternating TA sequence brings the DNA closer to the A-tract conformation, with potentially important functional consequences. The approach can be readily applied to other allosteric effects in DNA and generalized
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BO - Biophysics
OECD FORD branch
—

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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