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Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics

Ghosh, Mahua and Kumar, NV and Kumar, Vinay N and Varshney, Umesh (1999) Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics. In: Nucleic Acids Research, 27 (19). pp. 3938-3944.

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Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The H-1 resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T-12 and U-15 nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T-14 stacks upon both T-12 and U-15 while T-13 partially stacks upon T-14. Very weak stacking interaction is observed between T-13 and T-12. All the individual nucleotide bases adopt 'anti' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T-13 and T-14. The stereochemistry of U-15 mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.

Item Type: Journal Article
Publication: Nucleic Acids Research
Publisher: Oxford University Press
Additional Information: Copyright of this article belongs to Oxford University Press.
Department/Centre: Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited: 30 Jun 2011 07:52
Last Modified: 30 Jun 2011 07:52
URI: http://eprints.iisc.ac.in/id/eprint/38794

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