TY - JOUR
T1 - Single-Molecule Analysis and Engineering of DNA Motors
AU - Mohapatra, Sonisilpa
AU - Lin, Chang Ting
AU - Feng, Xinyu A.
AU - Basu, Aakash
AU - Ha, Taekjip
N1 - Funding Information:
Sonisilpa Mohapatra received her Masters in Chemistry from National Institute of Science Education and Research (NISER), Bhubaneswar, India. She moved to the U.S. to pursue a Ph.D. in Chemistry at the University of Wisconsin—Madison under the supervision of Prof. James C. Weisshaar. Her thesis research was focused on investigating intracellular spatiotemporal organization of translation and ribosome binding dynamics of translation factors in E. coli using super-resolution fluorescence imaging. She is currently a postdoctoral research fellow with Prof. Taekjip Ha in the department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine.
Funding Information:
The authors acknowledge Dr. Carl Wu, Brian Y. Soong, Jasmin Zarb, Wesley Yon, and Vinu Harihar for helpful suggestions and critical reading of the manuscript. Research in the Ha laboratory is funded by the grants from the National Science Foundation (PHY 1430124, EFMA 1933303, and EF 1934864) and the National Institutes of Health (GM 112659, GM 122569). T.H. is an investigator of the Howard Hughes Medical Institute.
Publisher Copyright:
Copyright © 2019 American Chemical Society.
PY - 2019
Y1 - 2019
N2 - Molecular motors are diverse enzymes that transduce chemical energy into mechanical work and, in doing so, perform critical cellular functions such as DNA replication and transcription, DNA supercoiling, intracellular transport, and ATP synthesis. Single-molecule techniques have been extensively used to identify structural intermediates in the reaction cycles of molecular motors and to understand how substeps in energy consumption drive transitions between the intermediates. Here, we review a broad spectrum of single-molecule tools and techniques such as optical and magnetic tweezers, atomic force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), nanopore tweezers, and hybrid techniques that increase the number of observables. These methods enable the manipulation of individual biomolecules via the application of forces and torques and the observation of dynamic conformational changes in single motor complexes. We also review how these techniques have been applied to study various motors such as helicases, DNA and RNA polymerases, topoisomerases, nucleosome remodelers, and motors involved in the condensation, segregation, and digestion of DNA. In-depth analysis of mechanochemical coupling in molecular motors has made the development of artificially engineered motors possible. We review techniques such as mutagenesis, chemical modifications, and optogenetics that have been used to re-engineer existing molecular motors to have, for instance, altered speed, processivity, or functionality. We also discuss how single-molecule analysis of engineered motors allows us to challenge our fundamental understanding of how molecular motors transduce energy.
AB - Molecular motors are diverse enzymes that transduce chemical energy into mechanical work and, in doing so, perform critical cellular functions such as DNA replication and transcription, DNA supercoiling, intracellular transport, and ATP synthesis. Single-molecule techniques have been extensively used to identify structural intermediates in the reaction cycles of molecular motors and to understand how substeps in energy consumption drive transitions between the intermediates. Here, we review a broad spectrum of single-molecule tools and techniques such as optical and magnetic tweezers, atomic force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), nanopore tweezers, and hybrid techniques that increase the number of observables. These methods enable the manipulation of individual biomolecules via the application of forces and torques and the observation of dynamic conformational changes in single motor complexes. We also review how these techniques have been applied to study various motors such as helicases, DNA and RNA polymerases, topoisomerases, nucleosome remodelers, and motors involved in the condensation, segregation, and digestion of DNA. In-depth analysis of mechanochemical coupling in molecular motors has made the development of artificially engineered motors possible. We review techniques such as mutagenesis, chemical modifications, and optogenetics that have been used to re-engineer existing molecular motors to have, for instance, altered speed, processivity, or functionality. We also discuss how single-molecule analysis of engineered motors allows us to challenge our fundamental understanding of how molecular motors transduce energy.
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U2 - 10.1021/acs.chemrev.9b00361
DO - 10.1021/acs.chemrev.9b00361
M3 - Review article
C2 - 31661246
AN - SCOPUS:85074921070
SN - 0009-2665
JO - Chemical Reviews
JF - Chemical Reviews
ER -