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

Author

Listed:
  • Vojč Kocman

    (Slovenian NMR Centre, National Institute of Chemistry)

  • Janez Plavec

    (Slovenian NMR Centre, National Institute of Chemistry
    EN-FIST Centre of Excellence
    Faculty of Chemistry and Chemical Technology, University of Ljubljana)

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.

Suggested Citation

  • Vojč Kocman & Janez Plavec, 2014. "A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts," Nature Communications, Nature, vol. 5(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6831
    DOI: 10.1038/ncomms6831
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