An Abasic Site in DNA. Solution Conformation Determined by Proton NMR and Molecular Mechanics Calculations

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1987 Oct 12

PMID 3671070

Citations 27

Authors

P Cuniasse

L C Sowers

R Eritja

B Kaplan

M F Goodman

J A Cognet

M Lebret

W GUSCHLBAUER

G V Fazakerley

Affiliations

Soon will be listed here.

Abstract

We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and H2O. We have measured the initial slope of buildup of NOEs in NOESY spectra at very short mixing times (25 to 50 ms), and from these were able to establish interproton distances for the central part of the duplex. We propose a different strategy for proton-proton distance determinations which takes into account the observed variations in correlation times for particular proton-proton vectors. A set of 31 measured interproton distances was incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. Two structures were obtained which retain all aspects of a classical B DNA in which the unpaired adenine and the abasic deoxyribose lie inside the helix. We observe that the non-hydrogen bonded adenine is held well in the helix, the Tm of this base being the same as that of the A.T base pairs in the same duplex.

Citing Articles

Structure of a Stable Interstrand DNA Cross-Link Involving a β--Glycosyl Linkage Between an -dA Amino Group and an Abasic Site.

Kellum Jr A, Qiu D, Voehler M, Martin W, Gates K, Stone M Biochemistry. 2020; 60(1):41-52.

PMID: 33382597 PMC: 7952047. DOI: 10.1021/acs.biochem.0c00596.

New insights into abasic site repair and tolerance.

Thompson P, Cortez D DNA Repair (Amst). 2020; 90:102866.

PMID: 32417669 PMC: 7299775. DOI: 10.1016/j.dnarep.2020.102866.

Solvent exposure associated with single abasic sites alters the base sequence dependence of oxidation of guanine in DNA in GG sequence contexts.

Lee Y, Liu Z, Dedon P, Geacintov N, Shafirovich V Chembiochem. 2011; 12(11):1731-9.

PMID: 21656632 PMC: 3517150. DOI: 10.1002/cbic.201100140.

DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase.

Nair D, Johnson R, Prakash L, Prakash S, Aggarwal A J Mol Biol. 2010; 406(1):18-28.

PMID: 21167175 PMC: 3127253. DOI: 10.1016/j.jmb.2010.12.016.

NMR solution structures of clustered abasic site lesions in DNA: structural differences between 3'-staggered (-3) and 5'-staggered (+3) bistranded lesions.

Hazel R, de Los Santos C Biochemistry. 2010; 49(41):8978-87.

PMID: 20825249 PMC: 3017401. DOI: 10.1021/bi101021e.

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