Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F10%3A00353245" target="_blank" >RIV/61388963:_____/10:00353245 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation

Original language description

We investigated the intercalation of an antitumor drug ellipticine into four adenine-thymine rich DNA duplexes with the focus on the configurational entropy, by means of molecular dynamics simulations. Two possible binding orientations of ellipticine inDNA were studied, and the orientation with the pyrrole nitrogen exposed into a major groove was identified as the more probable. The configurational entropy change of DNA is shown to contribute significantly to the binding free energy. The magnitude of this contribution depends on the exact DNA sequence. A detailed analysis revealed that the largest flexibility changes occurred in the sugar-phosphate backbone, resulting in an entropy gain in the most cases. The nucleobases were not involved in the changes of flexibility and entropy. BI/BII-like conformational transitions were observed after the intercalation of ellipticine, and the consequences of these transitions for the evaluation of entropy are discussed.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CC - Organic chemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2010

Confidentiality

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

Name of the periodical

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

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Volume of the periodical

114

Issue of the periodical within the volume

42

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

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UT code for WoS article

000283110500024

EID of the result in the Scopus database

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