The algorithm of estimation of the Km values for primers in DNA synthesis catalyzed by human DNA polymerase α
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TLDR
DNA synthesis with various deoxyribo homo‐ and heterooligoprimers in the presence of complementary templates was investigated and the objective laws of the changes of the KM and V max values were revealed.About:
This article is published in FEBS Letters.The article was published on 1996-12-09 and is currently open access. It has received 7 citations till now. The article focuses on the topics: Primer (molecular biology) & DNA polymerase II.read more
Citations
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Journal ArticleDOI
Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition.
TL;DR: The structure of UNG proteins from several species has been solved, revealing a specific uracil-binding pocket located in a DNA-binding groove, and Thermodynamic studies suggest that UNG binds with appreciable affinity to any DNA, mainly due to the interactions with the charged backbone.
Journal ArticleDOI
Recognition of damaged DNA by Escherichia coli Fpg protein: insights from structural and kinetic data
Dmitry O. Zharkov,Alexander A. Ishchenko,Kenneth T. Douglas,Georgy A. Nevinsky,Georgy A. Nevinsky +4 more
TL;DR: The structural data for Fpg is analyzed in the light of the kinetic and thermodynamic data obtained by the method of stepwise increase in ligand complexity to estimate relative contributions of individual nucleotide units of lesion-containing DNA to its total affinity for this enzyme.
Journal ArticleDOI
Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta
Beloglazova Ng,Oleg O. Kirpota,Konstantin V. Starostin,Alexander A. Ishchenko,Vitaly I. Yamkovoy,Dmitry O. Zharkov,Kenneth T. Douglas,Georgy A. Nevinsky +7 more
TL;DR: It is concluded that the enzyme's specificity for abasic sites in DNA is mostly due to a great increase in the reaction rate with specific DNA, with formation of the Michaelis complex contributing to the substrate preference only marginally.
Journal ArticleDOI
The Role of Weak Specific and Nonspecific Interactions in Enzymatic Recognition and Conversion of Long DNAs
TL;DR: It has been shown that high affinity of all studied enzymes for long DNAs is provided by the formation of many weak contacts of the enzyme with all nucleotide units covered by the protein globule, which indicates that all enzyme-dependent changes in DNA are effected through weak specific (rather than strong) interactions.
Journal ArticleDOI
Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase
Oleg O. Kirpota,Anton V. Endutkin,Michail P. Ponomarenko,P. M. Ponomarenko,Dmitry O. Zharkov,Georgy A. Nevinsky +5 more
TL;DR: A stepwise increase in ligand complexity approach is used to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA and predict the KM and kcat values for different sequences containing oxoG.
References
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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
TL;DR: Two ternary complexes of rat DNA polymerase beta, a DNA template-primer, and dideoxycytidine triphosphate have been determined at 2.9 A and 3.6 A resolution, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces.
Journal ArticleDOI
Insights into dna polymerization mechanisms from structure and function analysis of hiv-1 reverse transcriptase
Premal H. Patel,Alfredo Jacobo-Molina,Jianping Ding,Chris Tantillo,Arthur D. Clark,Reetta Raag,Raymond G. Nanni,Stephen H. Hughes,Edward Arnold +8 more
TL;DR: The genetic data and biochemical mechanism of DNA polymerization with the structure of HIV-1 RT complexed with a dsDNA template-primer is integrated and it is suggested that nucleotide incorporation is accompanied by a protein conformational change that positions the dNTP for nucleophilic attack.
Journal ArticleDOI
DNA polymerase I: from crystal structure to function via genetics
TL;DR: This work uses combination of X-ray crystallography and molecular genetics to investigate the mechanisms of both reactions and the way that these two distant active sites can work together to enhance the fidelity of DNA synthesis.
Journal ArticleDOI
NMR studies of conformations and interactions of substrates and ribonucleotide templates bound to the large fragment of DNA polymerase I.
TL;DR: In the presence of such oligoribonucleotide templates, nuclear Overhauser effects were used to determine interproton distances within and conformations of substrates bound to the large fragment of Pol I, as well as conformations and interactions of the enzyme-bound templates.
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