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Biophysical Journal
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A Magnetic Tweezers Study of a RNA-Dependant RNA Polymerase

Authors: Dulin, David; Vilfan, Igor; Depken, Martin; Hage, Susanne; Kamping, Wiecher; Poranen, Minna; Bamford, Dennis; +1 Authors

A Magnetic Tweezers Study of a RNA-Dependant RNA Polymerase

Abstract

RNA-dependent RNA Polymerases (RdRPs) are involved in the transcription and the replication of RNA genome of many viruses. The RdRP of the bacteriophage Φ6 (P2) is located inside the viral capsid where it transcribes double-stranded RNA to yield single-stranded RNA that infects the host cytosol.Here, we have studied the transcription activity of the P2 RdRP using magnetic tweezers. To do so, we tether a double-stranded RNA molecule between a glass surface and a magnetic bead. P2 then initiates at the free 3’ extremity of one of the strands constituting the duplex and in the process of transcription, dehybridizes it from the other. By observing the ensuing conversion of the tether from a double-stranded RNA to a single-stranded RNA under a constant applied force, we detect P2 transcription dynamics. In this manner, we directly measure the polymerization rate and the distribution of the dwell times. These measurements suggest that P2 has the ability to backtrack over several nucleotides along the template.Analysis of force dependence of the polymerization rate and pause density, as well as of the sequence-dependence of the polymerization rate indicates that the transcription activity of P2 RdRP is affected by the hybridization of the template and product strands. Though P2 is fully capable of unwinding and transcribing dsRNA in vitro unaided by other enzymes, we observe that the transcription velocity increases with increasing force, reaching a maximum at which the pause density is minimized. This behavior can be explained from the inability of the polymerase to backtrack at high forces where rehybridization is energetically unfavorable, diminishing the total time spent in pauses. The resulting relatively inefficient transcription process suggests that additional proteins may interact with the displaced strand inside the viral capsid to enhance overall transcription efficiency.

Keywords

Biophysics

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
hybrid