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Nucleic Acids Research, 1990, Vol. 18, No. 11 3363-3369
© 1990

MOLECULAR BIOLOGY

Supercoil-induced unusual DNA sturctures as transcriptional block

Rajesh Bagga, N. Ramesh and Samir K. Brahmachari*

Molecular Biophysics Unit, Indian Institute of Science Bangalore 560 012, India

*To whom correspondence should be addressed

Received December 14, 1989. Accepted April 30, 1990.

The transcriptional activity of pBR322 form V DNA template, a topologically unlinked, highly supercoiled molecule having unusual structures around or within coding regions was studied. Significant transcription was observed in vitro from this template despite high levels of supercoiling. An attenuated transcript, initiated accurately from the P4 promoter of rep gene, was observed which indicated pausing of E.coli RNA polymerase within the gene. This pausing could be removed by relieving the torsional stress implying that a supercoil induced structural alteration within the gene was acting as a transcriptional block. A stabilized unusual structure, most likely a cruciform, was found to be responsible for the elongation block. Absence of initiation from the tett gene was correlated with the unusual structure present within its promoter region in form V DNA. These in vitro studies show that structural alterations within natural DNA could act as transcriptional blocks both at the level of initiation and elongation.


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