Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA

Nucleic Acids Res. 1995 Jan 25;23(2):217-22. doi: 10.1093/nar/23.2.217.

Abstract

The synthesis and DNA binding properties of bis-PNA (peptide nucleic acid) are reported. Two PNA segments each of seven nucleobases in length were connected in a continuous synthesis via a flexible linker composed of three 8-amino-3,6-dioxaoctanoic acid units. The sequence of the first strand was TCTCTTT (C- to N-terminal), while the second strand was TTTCTCT or TTTJTJT, where J is pseudoisocytosine. These bis-PNAs form triple-stranded complexes of somewhat higher thermal stability than monomeric PNA with complementary oligonucleotides and the thermal melting transition shows very little hysteresis. When the J base is placed in the strand parallel to the DNA complement ('Hoogsteen strand'), the DNA binding was pH independent. The bis-PNAs were also superior to monomeric PNAs for targeting double-stranded DNA by strand invasion.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Cytosine / analogs & derivatives*
  • Cytosine / chemistry
  • Cytosine / metabolism
  • DNA / metabolism*
  • Drug Stability
  • Hot Temperature
  • Hydrogen-Ion Concentration
  • Macromolecular Substances
  • Molecular Sequence Data
  • Molecular Structure
  • Potassium Permanganate
  • Structure-Activity Relationship

Substances

  • Macromolecular Substances
  • N-(2-(tert-butyloxycarbonyl)aminoethyl)-N-(N2-(benzyloxycarbonyl)isocytosin-5-ylacetyl)glycine
  • Potassium Permanganate
  • Cytosine
  • DNA