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.
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.
Banks
K M
KM
Department of Chemistry, University of Washington, Seattle 98195.
Hare
D R
DR
Reid
B R
BR
D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides
D009838:Oligodeoxyribonucleotides; D004247:DNA; C041666:endodeoxyribonuclease BclI; D015252:Deoxyribonucleases, Type II Site-Specific