Document Detail

Influence of alpha-deoxyadenosine on the stability and structure of DNA. Thermodynamic and molecular mechanics studies.
MedLine Citation:
PMID:  7766604     Owner:  NLM     Status:  MEDLINE    
The alpha anomer of deoxyadenosine (alpha) and an abasic site (tetrahydrofuran, F), which are DNA lesions produced by free radicals, were site-specifically incorporated in 9-mer duplexes d(TGAGXGTAC).d-(GTACNCTCA), where X = alpha or F and N = A, G, C, or T. Their influence on thermodynamic stability and structure of DNA was assessed by UV-melting measurements and molecular mechanics calculations. UV-melting studies revealed that a duplex containing an alpha T pair was as stable as the parental duplex containing an AT pair at the same site. Furthermore, the stability of duplexes containing alpha varied depending on the base opposite this lesion, with the Tm decreasing in the following order: alpha T > alpha C approximately alpha A > alpha G. On the contrary, an abasic site introduced in the same site showed a significantly greater destabilizing effect than alpha, but variation of Tm with the bases opposite F was less evident. To delineate the molecular mechanism of thermodynamic effects of an alpha lesion, molecular mechanics calculations were performed for the same duplexes as used for UV-melting measurements. The results suggest that the structural perturbation introduced into DNA by an alpha N pair is alpha G > alpha A > alpha C > alpha T, showing a parallel correlation with the destabilizing effects of alpha N pairs. On the basis of these results, it is discussed how the perturbations introduced by these DNA lesions may influence the selection of nucleotides opposite the lesions by DNA polymerases and the interaction with DNA repair enzymes such as Escherichia coli endonuclease IV and exonuclease III.
H Ide; H Shimizu; Y Kimura; S Sakamoto; K Makino; M Glackin; S S Wallace; H Nakamuta; M Sasaki; N Sugimoto
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Biochemistry     Volume:  34     ISSN:  0006-2960     ISO Abbreviation:  Biochemistry     Publication Date:  1995 May 
Date Detail:
Created Date:  1995-07-03     Completed Date:  1995-07-03     Revised Date:  2007-11-14    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  6947-55     Citation Subset:  IM    
Department of Polymer Science and Engineering, Kyoto Institute of Technology, Japan.
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MeSH Terms
Base Sequence
DNA / chemistry*
Deoxyadenosines / chemistry*
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
Spectrophotometry, Ultraviolet
Grant Support
Reg. No./Substance:
0/Deoxyadenosines; 9007-49-2/DNA

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