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Title: Full molecular trajectories of RNA polymerase at single base-pair resolution

Abstract

In recent years, highly stable optical tweezers systems have enabled the characterization of the dynamics of molecular motors at very high resolution. However, the motion of many motors with angstrom-scale dynamics cannot be consistently resolved due to poor signal-to-noise ratio. Using an acousto-optic deflector to generate a “time-shared” dual-optical trap, we decreased low-frequency noise by more than one order of magnitude compared with conventional dual-trap optical tweezers. Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space Hidden Markov Model algorithm to recover their individual steps. We then used this algorithm on real transcription data obtained in the same instrument to fully uncover the molecular trajectories of Escherichia coli RNA polymerase. We applied this procedure to reveal the effect of pyrophosphate on the distribution of dwell times between consecutive polymerase steps.

Authors:
; ; ; ; ; ORCiD logo; ; ORCiD logo
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1417527
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 115 Journal Issue: 6; Journal ID: ISSN 0027-8424
Publisher:
Proceedings of the National Academy of Sciences
Country of Publication:
United States
Language:
English

Citation Formats

Righini, Maurizio, Lee, Antony, Cañari-Chumpitaz, Cristhian, Lionberger, Troy, Gabizon, Ronen, Coello, Yves, Tinoco, Jr., Ignacio, and Bustamante, Carlos. Full molecular trajectories of RNA polymerase at single base-pair resolution. United States: N. p., 2018. Web. doi:10.1073/pnas.1719906115.
Righini, Maurizio, Lee, Antony, Cañari-Chumpitaz, Cristhian, Lionberger, Troy, Gabizon, Ronen, Coello, Yves, Tinoco, Jr., Ignacio, & Bustamante, Carlos. Full molecular trajectories of RNA polymerase at single base-pair resolution. United States. doi:10.1073/pnas.1719906115.
Righini, Maurizio, Lee, Antony, Cañari-Chumpitaz, Cristhian, Lionberger, Troy, Gabizon, Ronen, Coello, Yves, Tinoco, Jr., Ignacio, and Bustamante, Carlos. Fri . "Full molecular trajectories of RNA polymerase at single base-pair resolution". United States. doi:10.1073/pnas.1719906115.
@article{osti_1417527,
title = {Full molecular trajectories of RNA polymerase at single base-pair resolution},
author = {Righini, Maurizio and Lee, Antony and Cañari-Chumpitaz, Cristhian and Lionberger, Troy and Gabizon, Ronen and Coello, Yves and Tinoco, Jr., Ignacio and Bustamante, Carlos},
abstractNote = {In recent years, highly stable optical tweezers systems have enabled the characterization of the dynamics of molecular motors at very high resolution. However, the motion of many motors with angstrom-scale dynamics cannot be consistently resolved due to poor signal-to-noise ratio. Using an acousto-optic deflector to generate a “time-shared” dual-optical trap, we decreased low-frequency noise by more than one order of magnitude compared with conventional dual-trap optical tweezers. Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space Hidden Markov Model algorithm to recover their individual steps. We then used this algorithm on real transcription data obtained in the same instrument to fully uncover the molecular trajectories of Escherichia coli RNA polymerase. We applied this procedure to reveal the effect of pyrophosphate on the distribution of dwell times between consecutive polymerase steps.},
doi = {10.1073/pnas.1719906115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 6,
volume = 115,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1073/pnas.1719906115

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Cited by: 3 works
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