PMID: 8610123Apr 2, 1996Paper

Sequence specificity of triplex DNA formation: Analysis by a combinatorial approach, restriction endonuclease protection selection and amplification

Proceedings of the National Academy of Sciences of the United States of America
P Hardenbol, M W Van Dyke

Abstract

We have devised a combinatorial method, restriction endonuclease protection selection and amplification (REPSA), to identify consensus ligand binding sequences in DNA. In this technique, cleavage by a type IIS restriction endonuclease (an enzyme that cleaves DNA at a site distal from its recognition sequence) is prevented by a bound ligand while unbound DNA is cleaved. Since the selection step of REPSA is performed in solution under mild conditions, this approach is amenable to the investigation of ligand-DNA complexes that are either insufficiently stable or not readily separable by other methods. Here we report the use of REPSA to identify the consensus duplex DNA sequence recognized by a G/T-rich oligodeoxyribonucleotide under conditions favoring purine-motif triple-helix formation. Analysis of 47 sequences indicated that recognition between 13 bases on the oligonucleotide 3' end and the duplex DNA was sufficient for triplex formation and indicated the possible existence of a new base triplet, G.AT. This information should help identify appropriate target sequences for purine-motif triplex formation and demonstrates the power of REPSA for investigating ligand-DNA interactions.

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Citations

Jan 1, 1996·Biochimie·J J ToulméE Brossalina
Jul 17, 1998·Current Opinion in Structural Biology·J B Chaires
Sep 13, 2001·Bioorganic & Medicinal Chemistry·J ShenM W Van Dyke
Jan 21, 2000·Natural Product Reports·G Lowe
Aug 1, 1997·Antisense & Nucleic Acid Drug Development·C BoiziauJ J Toulmé
Aug 15, 1997·Nucleic Acids Research·P HardenbolM W Van Dyke
Mar 21, 1998·Nucleic Acids Research·B Ward, T Juehne
Jun 22, 1999·Nucleic Acids Research·A DebinF Svinarchuk
Nov 1, 2000·Nucleic Acids Research·M MussoM W Van Dyke
Dec 20, 2011·Nucleic Acids Research·Antonia S CardewKeith R Fox
Nov 9, 2007·Current Opinion in Biotechnology·Rahul Palchaudhuri, Paul J Hergenrother
Mar 30, 2016·Science China. Life Sciences·Yongyao XieLetian Chen
May 3, 2007·Methods : a Companion to Methods in Enzymology·Michael W Van DykeGulshan Sunavala-Dossabhoy
Jul 21, 1998·Antisense & Nucleic Acid Drug Development·A J ChengM W Van Dyke
Oct 30, 2020·International Journal of Molecular Sciences·Kristi Moncja, Michael W Van Dyke
Jun 1, 2010·Bioconjugate Chemistry·Akash K Jain, Santanu Bhattacharya

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