1qe7 | pdb_00001qe7
SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA
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| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Overview
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(1)H 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.
About this Structure
1QE7 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics., Ghosh M, Kumar NV, Varshney U, Chary KV, Nucleic Acids Res. 1999 Oct 1;27(19):3938-44. PMID:10481034
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