RNA Polymerase Can Track a DNA Groove during Promoter Search

Many proteins select special DNA sequences to form functional complexes. In one possible mechanism, protein molecules would scan DNA sequences by tracking a groove without complete dissociation. Upon dragging single molecules of DNA over a surface carrying fixed Escherichia coli RNA polymerase holoe...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2004-10, Vol.101 (41), p.14731-14735
Main Authors: Sakata-Sogawa, Kumiko, Shimamoto, Nobuo, Tomizawa, Jun-ichi
Format: Article
Language:English
Subjects:
Binding Sites
Biological Sciences
Control systems
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA, Viral - genetics
DNA, Viral - metabolism
DNA-Directed RNA Polymerases - chemistry
DNA-Directed RNA Polymerases - metabolism
Enzymes
Escherichia coli
Kinetics
Models, Molecular
Molecular Conformation
Molecules
Nucleotide sequences
Polymers
Promoter Regions, Genetic - genetics
Ribonucleic acid
RNA
Rotation
Sliding
Torque
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Summary:Many proteins select special DNA sequences to form functional complexes. In one possible mechanism, protein molecules would scan DNA sequences by tracking a groove without complete dissociation. Upon dragging single molecules of DNA over a surface carrying fixed Escherichia coli RNA polymerase holoenzyme, we detected rotation of individual DNA molecules, providing direct evidence that a DNA-binding protein can track a DNA groove. These results confirm our previous observations of longitudinal movement of RNA polymerase along fixed, extended DNA and, moreover, imply that groove tracking facilitates scanning of DNA sequences.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0406441101