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Nucleic Acids Research Advance Access published online on October 28, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl594
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A real-time assay for monitoring nucleic acid cleavage by quadruplex formation

Besik I. Kankia

Department of Chemistry, University of Minnesota MN 55455, USA

Tel: +1 612 624 0510; Fax: +1 612 626 7541; Email: bkankia{at}umn.edu

Received July 11, 2006. Revised July 31, 2006. Accepted July 31, 2006.

Direct and straightforward methods to follow nucleic acid cleavage are needed. A spectrophotometric quadruplex formation assay (QFA) was developed, which allows real-time monitoring of site-specific cleavage of nucleic acids. QFA was applied to study both protein and nucleic acid restriction enzymes, and was demonstrated to accurately determine Michaelis–Menten parameters for the cleavage reaction catalyzed by EcoRI. QFA can be used to study the mechanisms of protein–nucleic acid recognition. QFA is also a useful tool for dissecting individual nicking rates of a double-stranded cleavage.


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