title: Triplex-directed self-assembly of an artificial sliding clamp on duplex DNA.
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.
authors.affiliation: Department of Chemistry, University of Rochester, NY 14627, USA.
authors.forename: K
authors.initials: K
authors.lastname: Ryan
authors.forename: E T
authors.initials: ET
authors.lastname: Kool
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry; D019003:Deoxyribonuclease HpaII / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry
chemical_list: D004270:DNA, Circular; D009838:Oligodeoxyribonucleotides; C051802:triplex DNA; D004247:DNA; D019003:Deoxyribonuclease HpaII