1G5D

NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER

Summary for 1G5D

• Entry DOI: 10.2210/pdb1g5d/pdb
• Related: 1A9I 1A9J 1G5E 1GIZ 1GJ0
• Descriptor: 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3', 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' (2 entities in total)
• Functional Keywords: damaged dna, apyrimidinic site, dna
• Total number of polymer chains: 2
• Total formula weight: 7835.10

Authors

Hoehn, S.T.,Turner, C.J.,Stubbe, J. (deposition date: 2000-10-31, release date: 2001-08-22, Last modification date: 2024-05-22)

Primary citation

Hoehn, S.T.,Turner, C.J.,Stubbe, J.
Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.
Nucleic Acids Res., 29:3413-3423, 2001

PubMed Abstract: The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.

PubMed: 11504879
DOI: 10.1093/nar/29.16.3413

Experimental method

SOLUTION NMR