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BIOLOGICAL SCIENCES / BIOPHYSICS
Single-molecule tracking of mRNA exiting from RNA polymerase II

Joanna Andrecka^*,, Robert Lewis^*,, Florian Brückner^*,, Elisabeth Lehmann^*,, Patrick Cramer^*,, and Jens Michaelis^*,,

*Munich Center for Integrated Protein Science (CiPS^M) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 81377 Munich, Germany; Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 Munich, Germany; and Gene Center Munich and Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany

Edited by Steven M. Block, Stanford University, Stanford, CA, and approved November 5, 2007 (received for review April 25, 2007)

Single-pair fluorescence resonance energy transfer was used to track RNA exiting from RNA polymerase II (Pol II) in elongation complexes. Measuring the distance between the RNA 5' end and three known locations within the elongation complex allows us determine its position by means of triangulation. RNA leaves the polymerase active center cleft via the previously proposed exit tunnel and then disengages from the enzyme surface. When the RNA reaches lengths of 26 and 29 nt, its 5' end associates with Pol II at the base of the dock domain. Because the initiation factor TFIIB binds to the dock domain and exit tunnel, exiting RNA may prevent TFIIB reassociation during elongation. RNA further extends toward the linker connecting to the polymerase C-terminal repeat domain (CTD), which binds the 5'-capping enzyme and other RNA processing factors.

Pol II | transcription | FRET | triangulation | fluorescence

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0703815105/DC1.

To whom correspondence should be addressed. E-mail: michaelis{at}lmu.de

© 2008 by The National Academy of Sciences of the USA

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