Structures of Apurinic and Apyrimidinic Sites in Duplex DNAs

• Published in: The Journal of biological chemistry Vol. 273; no. 25; pp. 15565 - 15573
• Main Authors: Beger, R D, Bolton, P H
• Format: Journal Article
• Language: English
• Published: United States American Society for Biochemistry and Molecular Biology 19.06.1998
• Subjects: Apurinic Acid - chemistry; Computer Simulation; DNA - chemistry; Hydrogen Bonding; Magnetic Resonance Spectroscopy; Models, Chemical; Models, Molecular; Nucleic Acid Conformation; Polynucleotides - chemistry; Stereoisomerism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.273.25.15565

Natural and exogenous processes can give rise to abasic sites with either a purine or pyrimidine as the base on the opposing strand. The solution state structures of the apyrimidinic DNA duplex, with D 6 indicating an abasic site, referred to as AD, and the apurinic DNA duplex with a dC 17 , referred to as CD, have been determined. A particularly striking difference is that the abasic site in CD is predominantly a β hemiacetal, whereas in AD the α and β forms are equally present. Hydrogen bonding with water by the abasic site and the base on the opposite strand appears to play a large role in determining the structure near the damaged site. Comparison of these structures with that of a duplex DNA containing a thymine glycol at the same position as the abasic site and with that of a duplex DNA containing an abasic site in the middle of a curved DNA sequence offers some insight into the common and distinct structural features of damaged DNA sites.