Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation

The antitumor antibiotic bleomycin causes two major lesions in the deoxyrib ose backbone of DNA: formation of 4'-keto abasic sites and formation of str and breaks with 3'-phosphoglycolate and 5-phosphate ends. As a model for th e 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAG XACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 4 75 NOEs and 101 dihedral angles provided the restraints for molecular model ing. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjace nt protons of the deoxyribose of both the alpha and beta anomers, of the ab asic site were observed. The modeling suggests that for both anomers the ab asic site is extrahelical, without significant distortion of the backbone o pposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic si te in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.