Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif

Nucleic Acids Res. 1994 Nov 11;22(22):4653-9. doi: 10.1093/nar/22.22.4653.

Abstract

Thermal denaturation profiles of an oligodeoxynucleotide that forms a hairpin structure with a cytidine-rich loop show an unexpected transition at 60 degrees C at pH 5.0 but not at pH 8.0. Analytical ultracentrifugation shows that this transition reflects dimer formation via the interaction of loops from two molecules to form a novel structure termed the h-dimer. The dependence of this structure on low pH implies the formation of cytosine-protonated cytosine base pairs. NMR spectroscopy, thermal denaturation and ultraviolet absorption spectral analysis suggest a similarity to the i-motif structure recently proposed for the interaction of deoxycytidine oligomers. The use of hairpin loops to form i-motif-like structures may prove useful in searches for cognate proteins and possibly in the production of antibodies.

MeSH terms

  • Base Sequence
  • Centrifugation, Density Gradient
  • Circular Dichroism
  • DNA / chemistry*
  • Hydrogen-Ion Concentration
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • Poly C / chemistry*
  • Polydeoxyribonucleotides / chemistry
  • Spectrophotometry, Ultraviolet
  • Temperature

Substances

  • Polydeoxyribonucleotides
  • Poly C
  • DNA