Nucleic Acids Research Advance Access originally published online on September 29, 2006
Nucleic Acids Research 2006 34(19):5416-5425; doi:10.1093/nar/gkl668
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Nucleic Acids Research, 2006, Vol. 34, No. 19 5416-5425
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy
1 Department of Oral Biology, University of Leeds Leeds LS2 9LU, UK 2 Institute of Molecular Biophysics, School of Physics and Astronomy, University of Leeds Leeds LS2 9JT, UK 3 Department of Biochemistry and Molecular Biology, University of Parma 43100 Parma, Italy
*To whom correspondence should be addressed. Tel: +44 0113 3433817; Fax: +44 0113 3433900; Email: n.h.thomson{at}leeds.ac.uk
Received July 9, 2006. Revised July 14, 2006. Accepted August 30, 2006.
Atomic force microscopy (AFM) has been used to image, at single molecule resolution, transcription events by Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned 
pr promoters. For the first time experimentally, the outcome of collision events during convergent transcription by two identical RNAP has been studied. Measurement of the positions of the RNAP on the DNA, allows distinction of open promoter complexes (OPCs) and elongating complexes (EC) and collided complexes (CC). This discontinuous time-course enables subsequent analysis of collision events where both RNAP remain bound on the DNA. After collision, the elongating RNAP has caused the other (usually stalled) RNAP to back-track along the template. The final positions of the two RNAP indicate that these are collisions between an EC and a stalled EC (SEC) or OPC (previously referred to as sitting-ducks). Interestingly, the distances between the two RNAP show that they are not always at closest approach after ‘collision’ has caused their arrest.
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