A single-molecule technique to study sequence-dependent transcription pausing.
We present a technique that allows sequence-dependent analysis of transcription elongation using single-molecule optical trapping techniques. Observation of individual molecules of RNA polymerase (RNAP) allows determination of elongation kinetics that are difficult or impossible to accurately obtain from bulk studies, and provides high temporal resolution of the RNAP motion under a calibrated mechanical load. One limitation of previous single molecule studies was the difficulty in correlating the observed motion of RNAP with its actual position on the DNA template to better than approximately 100 bp. In this work, we improved the spatial precision of optical trapping studies of transcription to approximately 5 bp by using runoff transcription as an unambiguous marker of RNAP template position. This runoff method was sufficient to unequivocally locate and study a single known pause sequence (DeltatR2). By applying various loads to assist RNAP forward translocation, we specifically investigated elongation kinetics within this pause region and found that the dwell time at the pause sequence decreased with increasing assisting load. This observation is consistent with bulk biochemical studies that suggest RNAP reverse translocates, or "backtracks," at the DeltatR2 pause sequence.
Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, USA.
Alla
A
Shundrovsky
Thomas J
TJ
Santangelo
Jeffrey W
JW
Roberts
Michelle D
MD
Wang
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000032:analysis / Q000737:chemistry*; D004789:Enzyme Activation; D007700:Kinetics; D008846:Micromanipulation / Q000379:methods*; D008969:Molecular Sequence Data; D010812:Physical Stimulation / Q000379:methods*; D011485:Protein Binding; D014158:Transcription, Genetic
D004247:DNA; D012321:DNA-Directed RNA Polymerases