Triplex-directed self-assembly of an artificial sliding clamp on duplex DNA.
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.
Ryan
K
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Department of Chemistry, University of Rochester, NY 14627, USA.
Kool
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ET
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
D004270:DNA, Circular; D009838:Oligodeoxyribonucleotides; C051802:triplex DNA; D004247:DNA; D019003:Deoxyribonuclease HpaII