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Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine-thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6-44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism. We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed "click" reaction. Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.

Original publication

DOI

10.1021/ja804427q

Type

Journal article

Journal

J Am Chem Soc

Publication Date

05/11/2008

Volume

130

Pages

14651 - 14658

Keywords

Adenine, Base Pairing, Crystallization, DNA, Intercalating Agents, Kinetics, Luminescent Measurements, Nucleic Acid Conformation, Oligonucleotides, Organometallic Compounds, Ruthenium, Temperature, Thymine