The Solution Structure of DNA Duplex-Decamer Containing the (6-4) Photoproduct of Thymidylyl(3'5')Thymidine by NMR and Relaxation Matrix Refinement

• DOI: 10.1111/j.1432-1033.1995.0849m.x
• Publication Date: 2005-03-04T11:48:10Z
• Authors: Jong-Ki Kim; Byong-Seok Choi
• Keywords: Duplex (building); Thymidine; Matrix (chemical analysis)

The DNA duplex-decamer containing a site-specific (6-4) photoadduct of thymidylyl(3'-->5')thymidine was generated by direct photolytic ultraviolet C irradiation of d(CGCATTACGC). The three-dimensional structure of the duplex (6-4) decamer, d(CGCAT[6-4]TACGC).d(GCGTAATGCG), has been determined by two-dimensional NMR spectroscopy and a relaxation matrix refinement method. NMR data and structural calculations established that the formation of the (6-4) adduct in the B-DNA duplex retains Watson-Crick-type hydrogen bonding throughout the duplex except at the 3'-side of the (6-4) lesion where the T-->C transition mutation is predominantly targeted [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl Acad. Sci. USA 88, 9685-9689], but leads to a 44 degrees bending in the overall DNA helix. Perpendicular base orientation of the (6-4) lesion provides a structural basis where potential hydrogen bonding at the 3' sides of the (6-4) adduct with substituted nucleotide is improbable during replication under stringent conditions.