Nucleic Acids Research Advance Access published online on August 22, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn531
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Methods Online |
An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase–DNA complexes to surfaces
Advanced Research & Development, LI-COR Biosciences, Lincoln, NE, USA
*To whom correspondence should be addressed. Tel: +1 402 467 0714; Fax: +1 402 4670825; Email: john.williams{at}licor.com
Received June 27, 2008. Revised July 30, 2008. Accepted August 1, 2008.
Single molecule analysis of individual enzymes can require oriented immobilization of the subject molecules on a detection surface. As part of a technology development project for single molecule DNA sequencing, we faced the multiple challenges of immobilizing both a DNA polymerase and its DNA template together in an active, stable complex capable of highly processive DNA synthesis on a nonstick surface. Here, we report the genetic modification of the archaeal DNA polymerase 9°N in which two biotinylated peptide ‘legs’ are inserted at positions flanking the DNA-binding cleft. Streptavidin binding on either side of the cleft both traps the DNA template in the polymerase and orients the complex on a biotinylated surface. We present evidence that purified polymerase–DNA–streptavidin complexes are active both in solution and immobilized on a surface. Processivity is improved from <20 nt in the unmodified polymerase to several thousand nucleotides in the engineered complexes. High-molecular weight DNA synthesized by immobilized complexes is observed moving above the surface even as it remains tethered to the polymerase. Pre-formed polymerase–DNA–streptavidin complexes can be stored frozen and subsequently thawed without dissociation or loss of activity, making them convenient for use in single molecule analysis.