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


Journal Article

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 10 4, 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 (pMP 32) 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.

Duke Authors

Cited Authors

  • Allison, DP; Thundat, TG; Modrich, P; Isfort, RJ; Doktycz, MJ; Kerper, PS; Warmack, RJ

Published Date

  • December 1, 1995

Published In

Volume / Issue

  • 2386 /

Start / End Page

  • 24 - 29

International Standard Serial Number (ISSN)

  • 0277-786X

Citation Source

  • Scopus