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Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.

K M Banks·D R Hare·B R Reid
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Abstract

A three-dimensional solution structure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)]2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)]2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences.

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Base SequenceComputer GraphicsDNADeoxyribonucleases, Type II Site-SpecificMagnetic Resonance SpectroscopyModels, MolecularMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotidesJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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K M Banks, D R Hare, B R Reid. 1989-08-22. Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.. https://doi.org/10.1021/bi00443a033

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