Triplex-directed self-assembly of an artificial sliding clamp on duplex DNA

Chem Biol. 1998 Feb;5(2):59-67. doi: 10.1016/s1074-5521(98)90140-5.

Abstract

Background: Circular triplex-forming oligonucleotides (CTFOs) have previously been shown to bind tightly to short single-stranded homopurine DNAs in a sequence-specific manner. In view of the importance of double-stranded DNA as a target in the development of gene-specific therapeutic and diagnostic agents, we have investigated the binding of CTFOs to double-helical DNA.

Results: DNA-binding experiments show that a CTFO can recognize its homopurine target when the target is embedded in a long duplex. Unlike their linear counterparts, CTFOs bind the double helix in two topologically distinct forms. The more stable of the two complexes is found to be a pseudorotaxane, having the same topology as the sliding clamp protein subunits associated with some DNA and RNA polymerases.

Conclusions: Circular triplex-forming oligonucleotides have been shown to bind the DNA double helix in a topological manner which is unprecedented among synthetic ligands. This novel binding motif allows a synthetic CTFO to be irreversibly locked onto a circular double-stranded DNA target without covalently modifying the target.

MeSH terms

  • Binding Sites
  • DNA / chemistry*
  • DNA, Circular / chemistry
  • Deoxyribonuclease HpaII / metabolism
  • Electrophoresis, Polyacrylamide Gel
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization
  • Oligodeoxyribonucleotides / chemistry

Substances

  • DNA, Circular
  • Oligodeoxyribonucleotides
  • triplex DNA
  • DNA
  • Deoxyribonuclease HpaII