A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts

Nat Commun. 2014 Dec 15:5:5831. doi: 10.1038/ncomms6831.

Abstract

DNA can form diverse higher-order structures, whose details are greatly dependent on nucleotide sequence. G-rich sequences containing four or more repeats of three guanines are expected to form G-quadruplexes. Here we show that DNA sequences with GGGAGCG repeats found in the regulatory region of the PLEKHG3 gene are capable of forming tetrahelical DNA structures that are distinct from G-quadruplexes. The d(GGGAGCGAGGGAGCG) sequence, VK1, forms a dimer. Two VK1 sequences connected by an adenine residue, VK2, fold into a monomer, which shares identical structural characteristics with the VK1 fold. Their four-stranded architectures are stabilized by four G-C, four G-A and six G-G base pairs. No G-quartets or Hoogsteen-type hydrogen-bonded guanine residues are present and the overall topology is conserved in the presence of Li(+), Na(+), K(+) and NH4(+) ions. Unique structural features include two edgewise loops on each side of the structure stabilized by three G-G base pairs in N1-carbonyl symmetric geometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Carbon Isotopes
  • Cations, Monovalent
  • DNA / chemistry*
  • Dimerization
  • G-Quadruplexes*
  • Guanine Nucleotide Exchange Factors / chemistry*
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nitrogen Isotopes
  • Oligonucleotides / chemistry*
  • Poly G / chemistry*
  • Tandem Repeat Sequences*

Substances

  • Carbon Isotopes
  • Cations, Monovalent
  • Guanine Nucleotide Exchange Factors
  • Nitrogen Isotopes
  • Oligonucleotides
  • Poly G
  • DNA

Associated data

  • PDB/2MJJ