The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA

Dyakonova, Elena S.; Koval, Vladimir V.; Lomzov, Alexander A.; Ищенко, А. А.; Fedorova, Olga S.

doi:10.1016/j.bbagen.2015.03.001

Cited by 3 publications

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References 62 publications

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“…Expression and purification of wild type (WT) Apn1 and mutant form H83A Apn1 were carried out as previously described [6] , [7] , [8] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…Oligodeoxyribonucleotide (ODN) duplexes used as DNA-substrates were synthesized and purified according to [6] , [7] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…The DNA cleavage kinetics in vitro conditions was studied using electrophoresis in polyacrylamide gel (PAGE) as described previously [6] , [7] . The measurements were conducted at 25 °C in BER or NIR reaction buffer (BER buffer: 100 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)-KOH (pH 7.6), 100 mM KCl; NIR buffer: 20 mM HEPES-KOH (pH = 7.6), 50 mM KCl, 0.1 mg/mL BSA, 1 mM DTT, 5 mM MgCl 2 ).…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“… [17] . Structure refinement and molecular dynamic simulation were performed as in [7] using AMBER 14 molecular modeling suite [18] , [19] . The force field parameters for the 2-aminopurine-5′-phosphate residue were retrieved from ref.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

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Data on PAGE analysis and MD simulation for the interaction of endonuclease Apn1 from Saccharomyces cerevisiae with DNA substrates containing 5,6-dihydrouracyl and 2-aminopurine

et al. 2018

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This article presents new data on nucleotide incision repair (NIR) activity of apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae, which is known as a key player of the base excision DNA repair (BER) pathway, see “Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV” [1], “Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae” [2] and “Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases” [3]. The characterization of NIR activity of wild type Apn1 and mutant form Ape1 H83A were made by denaturing PAGE analysis, and MD simulations of Apn1 complexed with DNA containing 5,6-dihydro-2′-deoxyuridine (DHU) and 2-aminopurine (2-aPu) residues. This data article is associated to the manuscript titled “Apurinic/apyrimidinic endonuclease Apn1 from Saccharomyces cerevisiae is recruited to the nucleotide incision repair pathway: kinetic and structural features” [4].Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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“…Expression and purification of wild type (WT) Apn1 and mutant form H83A Apn1 were carried out as previously described [6] , [7] , [8] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…Oligodeoxyribonucleotide (ODN) duplexes used as DNA-substrates were synthesized and purified according to [6] , [7] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%