DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation.

Abstract:

:Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system with no surprising results, system with open valences of the atoms at the strand break ends as well as a system with filled valences were simulated. In both cases during the first few nanoseconds the broken ends of strand breaks are significantly exposed to the outside of the molecule. However, with increasing time, the system with single strand break with open valences is partially disrupted. On the contrary, the system with filled valences shows stable conformation with newly created hydrogen bond between the two strand break endings. Moreover, these endings are steadily situated in the inner part of the molecule, thus making the recognition and docking process of a repair enzyme more complicated in the case of filled valences.

journal_name

Comput Biol Chem

authors

Bunta JK,Laaksonen A,Pinak M,Nemoto T

doi

10.1016/j.compbiolchem.2005.12.001

keywords:

subject

Has Abstract

pub_date

2006-04-01 00:00:00

pages

112-9

issue

2

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(05)00129-5

journal_volume

30

pub_type

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