Conformational analysis of d(C3G3), a B-family duplex in solution

Biochemistry. 1989 Mar 21;28(6):2452-9. doi: 10.1021/bi00432a016.

Abstract

NMR and circular dichroism studies of the duplex formed by the self-complementary DNA hexanucleotide d(C3G3) indicate that it is a B-type structure but differs from standard B-form. An analysis of NMR coupling constants within the deoxyribose moieties yields a 70% or greater contribution from pseudorotation phase angles corresponding to the C3'-exo conformation, a conformation similar to the C2'-endo conformation associated with B-form DNA. Intranucleotide interproton distances are consistent with a B-form structure, but some internucleotide distances are intermediate between A- and B-form structures. Circular dichroism spectra have B-form characteristics but also include an unusual negative band at 282 nm. The solution spectroscopic results are in contrast with X-ray crystallographic studies which find A-form structures for similar sequences.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Circular Dichroism
  • DNA*
  • Magnetic Resonance Spectroscopy / methods
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides* / chemical synthesis
  • Solutions

Substances

  • Oligodeoxyribonucleotides
  • Solutions
  • DNA