Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad

J Am Chem Soc. 2003 May 14;125(19):5654-62. doi: 10.1021/ja0344157.

Abstract

The solution structure of a cyclic oligonucleotide d<pCGCTCATT> has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson-Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson-Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na(+) cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson-Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA-DNA recognition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • DNA / chemistry*
  • G-Quadruplexes
  • Kinetics
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry
  • Solutions
  • Thermodynamics

Substances

  • Oligonucleotides
  • Solutions
  • DNA

Associated data

  • PDB/1N96