Nucleic Acids Research, 1990, Vol. 18, No. 2 267-275
© 1990
ENZYMOLOGY |
Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probe
Molecular Biophysics Unit, Indian Institute of Science Bangalore 560 01 2, India
* To whom correspondence should be addressed
Received October 10, 1989. Revised December 11, 1989. Accepted December 11, 1989.
The ability of DNA sequences to adopt unusual structures under the superhelical torsional stress has been studied. Sequences that are forced to adopt unusual conformation in topologically constrained pBR322 form V DNA (Lk=0) were mapped using restriction enzymes as probes. Restriction enzymes such as BamHI, Pstl, Aval and HindIII could not cleave their recognition sequences. The removal of topological constraint relieved this inhibition. The influence of neighbouring sequences on the ability of a given sequence to adopt unusual DNA structure, presumably left handed Z conformation, was studied through single hit analysis. Using multiple cut restriction enzymes such as Narl and Fspl, it could be shown that under identical topological strain, the extent of structural alteration is greatly influenced by the neighbouring sequences. In the light of the variety of sequences and locations that could be mapped to adopt non-6 conformation in pBR322 form V DNA, restriction enzymes appear as potential structural probes for natural DNA sequences.