PMID: 7544889Aug 11, 1995Paper

Targeting pyrimidine single strands by triplex formation: structural optimization of binding

Nucleic Acids Research
T VoE T Kool

Abstract

Recent reports describe a new strategy for the binding of single-stranded pyrimidine sequences by triple helix formation. In this approach, a double-length purine-rich oligonucleotide binds a target strand, folding back to form an antiparallel pur.pur.pyr triple helix. We now describe a series of studies in which sequence and structural variations are made in such purine-rich ligands, in an effort to optimize binding properties. Comparison is made between the use of two separate strands and the use of single two-domain ligands; the latter are found to bind more tightly and to aggregate less in media containing Na+ or K+. Placement of mismatched bases in the target shows that sequence selectivity of binding is as high as that for Watson-Crick duplex formation. Variation of the lengths and sequences of loops bridging the binding domains demonstrates that dinucleotide loops composed of pyrimidines give the highest stability. Oligoethylene glycol-derived loop replacements are shown to give good binding affinity as well. The binding of an RNA target is shown to occur with the same affinity as the binding of DNA. In general, it is found that circular variants bind more tightly than do either separate strands or singly-linked ligands ...Continue Reading

References

Feb 25, 1988·Nucleic Acids Research·A M Beasty, M J Behe

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Citations

Dec 25, 2007·Oligonucleotides·Zhaoyang YeRam I Mahato
Apr 1, 1997·Nucleic Acids Research·A S KrasilnikovS M Mirkin
Jul 11, 2003·Nucleic Acids Research·Sergei IvanovMarina B Gottikh
Jun 6, 2000·Biological Chemistry·K WeiszH Welfle
Dec 29, 2006·Chemistry & Biodiversity·Marta G GrimauRamon Eritja
May 10, 2005·Chembiochem : a European Journal of Chemical Biology·Anna NadalMaria Pla
Jan 24, 2015·Molecular Pharmaceutics·Laura RodríguezVéronique Noé
Aug 18, 1998·Accounts of Chemical Research·Eric T Kool
Oct 16, 1999·Journal of Molecular Biology·M MillsJ L Mergny
May 12, 2000·Biochimica Et Biophysica Acta·D PraseuthC Hélène
Dec 18, 2003·Journal of the American Chemical Society·Anna AviñóModesto Orozco

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