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 Chemjournal_title
Computational biology and chemistryauthors
Bunta JK,Laaksonen A,Pinak M,Nemoto Tdoi
10.1016/j.compbiolchem.2005.12.001keywords:
subject
Has Abstractpub_date
2006-04-01 00:00:00pages
112-9issue
2eissn
1476-9271issn
1476-928Xpii
S1476-9271(05)00129-5journal_volume
30pub_type
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