113d
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THE STRUCTURE OF GUANOSINE-THYMIDINE MISMATCHES IN B-DNA AT 2.5 ANGSTROMS RESOLUTION
OverviewOverview
The structure of the deoxyoligomer d(C-G-C-G-A-A-T-T-T-G-C-G) was, determined at 2.5-A resolution by single crystal x-ray diffraction, techniques. The final R factor is 18% with the location of 71 water, molecules. The oligomer crystallizes in a B-DNA-type conformation, with, two strands interacting to form a dodecamer duplex. The double helix, consists of four A X T and six G X C Watson-Crick base pairs and two G X T, mismatches. The G X T pairs adopt a "wobble" structure with the thymine, projecting into the major groove and the guanine into the minor groove., The mispairs are accommodated in the normal double helix by small, adjustments in the conformation of the sugar phosphate backbone. A, comparison with the isomorphous parent compound containing only, Watson-Crick base pairs shows that any changes in the structure induced by, the presence of G X T mispairs are highly localized. The global, conformation of the duplex is conserved. The G X T mismatch has already, been studied by x-ray techniques in A and Z helices where similar results, were found. The geometry of the mispair is essentially identical in all, structures so far examined, irrespective of the DNA conformation. The, hydration is also similar with solvent molecules bridging the functional, groups of the bases via hydrogen bonds. Hydration may be an important, factor in stabilizing G X T mismatches. A characteristic of Watson-Crick, paired A X T and G X C bases is the pseudo 2-fold symmetry axis in the, plane of the base pairs. The G X T wobble base pair is pronouncedly, asymmetric. This asymmetry, coupled with the disposition of functional, groups in the major and minor grooves, provides a number of features which, may contribute to the recognition of the mismatch by repair enzymes.
About this StructureAbout this Structure
113D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution., Hunter WN, Brown T, Kneale G, Anand NN, Rabinovich D, Kennard O, J Biol Chem. 1987 Jul 25;262(21):9962-70. PMID:3611072
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