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Nucleic Acids Research, 1989, Vol. 17, No. 1 171-183
© 1989

ENZYMOLOGY

An lmproved method for photofootprinting yeast genes in vivo using Taq polymerase

Jeffrey D. Axelrod and John Majors

Department of Biological Chemistry, Washington University School of Medicine St Louis, MO 63110, USA

Received October 7, 1988. Accepted November 28, 1988.

We have developed an improved method for photofootprinting in vivo which utilizes the thermostable DNA polymerase from T aquancus (Taq) in a primer extension assay. UV light is used to introduce photoproducts into the genomic DNA of intact yeast cells. The photoproducts are then detected and mapped at the nucleotide level by multiple rounds of annealing and extension using Taq polymerise, which is blocked by photoproducts in the template DNA. The method is more rapid, sensitive, and reproducible than the previously described chemical photofootprinting procedure developed In this laboratory(Nature 325. 173–177.). and detects photoproducts with a specificity which is similar, but not identical to that of the previously described procedure. Binding of GAL4 protein to its binding sites within the GAL1–10 upstream activating sequence is demonstrated using the primer extension photofootprinting method. The primer extension assay can also be used to map DNA strand breakage generated by other footprinting methods, and to determine DNA sequence directly from the yeast genome.


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