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Nucleic Acids Research, 2001, Vol. 29, No. 16 3413-3423
© 2001 Oxford University Press

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

Silvia T. Hoehn1, Christopher J. Turner3 and JoAnne Stubbe1,2,*

1Department of Chemistry, 2Department of Biology and 3Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA

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 ß 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.

* To whom correspondence should be addressed at: Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Tel: +1 617 253 1814; Fax: +1 617 258 7247; Email: stubbe{at}mit.edu


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