A two-stranded template-based approach to G.(C-A) triad formation: designing novel structural elements into an existing DNA framework

J Mol Biol. 2000 Aug 4;301(1):129-46. doi: 10.1006/jmbi.2000.3932.

Abstract

We have designed a DNA sequence, d(G-G-G-T-T-C-A-G-G), which dimerizes to form a 2-fold symmetric G-quadruplex in which G(syn). G(anti).G(syn).G(anti) tetrads are sandwiched between all trans G. (C-A) triads. The NMR-based solution structural analysis was greatly aided by monitoring hydrogen bond alignments across N-H...N and N-H...O==C hydrogen bonds within the triad and tetrad, in a uniformly ((13)C,(15)N)-labeled sample of the d(G-G-G-T-T-C-A-G-G) sequence. The solution structure establishes that the guanine base-pairs with the cytosine through Watson-Crick G.C pair formation and with adenine through sheared G.A mismatch formation within the G.(C-A) triad. A model of triad DNA was constructed that contains the experimentally determined G.(C-A) triad alignment as the repeating stacked unit.

Publication types

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

MeSH terms

  • Base Pair Mismatch / genetics
  • Base Pairing / genetics
  • Base Sequence
  • DNA / chemistry*
  • DNA / genetics*
  • DNA / metabolism
  • G-Quadruplexes
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation*
  • Phosphorus / chemistry
  • Phosphorus / metabolism
  • Protons
  • Structure-Activity Relationship
  • Templates, Genetic

Substances

  • Protons
  • Phosphorus
  • DNA

Associated data

  • PDB/1FS3