Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)

David P. Allison; Thomas G. Thundat; P. Modrich; R. J. Isfort; Mitchel J. Doktycz; P. S. Kerper; R. J. Warmack

doi:10.1117/12.206037

3 April 1995 Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)

David P. Allison, Thomas G. Thundat, P. Modrich, R. J. Isfort, Mitchel J. Doktycz, P. S. Kerper, R. J. Warmack

Proceedings Volume 2386, Ultrasensitive Instrumentation for DNA Sequencing and Biochemical Diagnostics; (1995) https://doi.org/10.1117/12.206037
Event: Photonics West '95, 1995, San Jose, CA, United States

Abstract

Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10⁴, we demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS⁺) or two (pMP³²) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in our preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

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David P. Allison, Thomas G. Thundat, P. Modrich, R. J. Isfort, Mitchel J. Doktycz, P. S. Kerper, and R. J. Warmack "Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)", Proc. SPIE 2386, Ultrasensitive Instrumentation for DNA Sequencing and Biochemical Diagnostics, (3 April 1995); https://doi.org/10.1117/12.206037

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