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  • 1
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    Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-18
    Description: Using single-molecule DNA nanomanipulation, we show that abortive initiation involves DNA "scrunching"--in which RNA polymerase (RNAP) remains stationary and unwinds and pulls downstream DNA into itself--and that scrunching requires RNA synthesis and depends on RNA length. We show further that promoter escape involves scrunching, and that scrunching occurs in most or all instances of promoter escape. Our results support the existence of an obligatory stressed intermediate, with approximately one turn of additional DNA unwinding, in escape and are consistent with the proposal that stress in this intermediate provides the driving force to break RNAP-promoter and RNAP-initiation-factor interactions in escape.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754787/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754787/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Revyakin, Andrey -- Liu, Chenyu -- Ebright, Richard H -- Strick, Terence R -- GM41376/GM/NIGMS NIH HHS/ -- R01 GM041376/GM/NIGMS NIH HHS/ -- R01 GM041376-15/GM/NIGMS NIH HHS/ -- R01 GM041376-16/GM/NIGMS NIH HHS/ -- R01 GM041376-17/GM/NIGMS NIH HHS/ -- R01 GM041376-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1139-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110577" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biomechanical Phenomena ; DNA/chemistry/*metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; RNA/biosynthesis ; Transcription Initiation Site/physiology ; Transcription, Genetic/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Initiation of transcription-coupled repair characterized at single-molecule resolution (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-11
    Description: Transcription-coupled DNA repair uses components of the transcription machinery to identify DNA lesions and initiate their repair. These repair pathways are complex, so their mechanistic features remain poorly understood. Bacterial transcription-coupled repair is initiated when RNA polymerase stalled at a DNA lesion is removed by Mfd, an ATP-dependent DNA translocase. Here we use single-molecule DNA nanomanipulation to observe the dynamic interactions of Escherichia coli Mfd with RNA polymerase elongation complexes stalled by a cyclopyrimidine dimer or by nucleotide starvation. We show that Mfd acts by catalysing two irreversible, ATP-dependent transitions with different structural, kinetic and mechanistic features. Mfd remains bound to the DNA in a long-lived complex that could act as a marker for sites of DNA damage, directing assembly of subsequent DNA repair factors. These results provide a framework for considering the kinetics of transcription-coupled repair in vivo, and open the way to reconstruction of complete DNA repair pathways at single-molecule resolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475728/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475728/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howan, Kevin -- Smith, Abigail J -- Westblade, Lars F -- Joly, Nicolas -- Grange, Wilfried -- Zorman, Sylvain -- Darst, Seth A -- Savery, Nigel J -- Strick, Terence R -- BB/I001859/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I003142/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM073829/GM/NIGMS NIH HHS/ -- R01 GM073829/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Oct 18;490(7420):431-4. doi: 10.1038/nature11430. Epub 2012 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cite F-75205 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22960746" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Bacterial Proteins/*metabolism ; Biocatalysis ; DNA Damage ; *DNA Repair ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/enzymology/genetics/metabolism ; Hydrolysis ; Kinetics ; Promoter Regions, Genetic/genetics ; Pyrimidine Dimers/chemistry/metabolism ; Transcription Elongation, Genetic ; Transcription Factors/*metabolism ; Transcription Initiation, Genetic ; Transcription Termination, Genetic ; *Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The elasticity of a single supercoiled DNA molecule (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-29
    Description: Single linear DNA molecules were bound at multiple sites at one extremity to a treated glass cover slip and at the other to a magnetic bead. The DNA was therefore torsionally constrained. A magnetic field was used to rotate the beads and thus to coil and pull the DNA. The stretching force was determined by analysis of the Brownian fluctuations of the bead. Here the elastic behavior of individual lambda DNA molecules over- and underwound by up to 500 turns was studied. A sharp transition was discovered from a low to a high extension state at a force of approximately 0.45 piconewtons for underwound molecules and at a force of approximately 3 piconewtons for overwound ones. These transitions, probably reflecting the formation of alternative structures in stretched coiled DNA molecules, might be relevant for DNA transcription and replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strick, T R -- Allemand, J F -- Bensimon, D -- Bensimon, A -- Croquette, V -- New York, N.Y. -- Science. 1996 Mar 29;271(5257):1835-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Physique Statistique de l'ENS, associe aux universites Paris VI et VII, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8596951" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/genetics ; DNA, Superhelical/*chemistry ; DNA, Viral/chemistry ; Elasticity ; Magnetics ; *Nucleic Acid Conformation ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
    Electronic Resource
    Electronic Resource
    STRESS-INDUCED STRUCTURAL TRANSITIONS IN DNA AND PROTEINS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 523-543 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The ability to manipulate, stretch and twist biomolecules opens the way to an understanding of their structural transitions. We review some of the recently discovered stress-induced structural transitions in DNA as well as the application of single molecule manipulation techniques to DNA unzipping and to the study of protein folding/unfolding transitions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.523
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  • 5
    Electronic Resource
    Electronic Resource
    Physical Approaches to the Study of DNA (1998)
    Springer
    Journal of statistical physics 93 (1998), S. 647-672 
    Details
    ISSN: 1572-9613
    Keywords: DNA micromanipulation ; DNA supercoiling ; DNA structural transitions ; Brownian motion analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract New micromanipulation techniques now enable physicists and biologists to study the behavior of single biomolecules such as DNA. In particular, it is possible to measure the elastic response of individual DNA molecules to changes in the double helix's supercoiling. The force versus extension diagram for torsionally relaxed DNA is continuous and allows one to evaluate the persistence length of the polymer. When the molecule is supercoiled, however, stretching leads to the buildup of torsional stress in the double helix's axis. When the twist energy thus generated increases beyond a critical value, the molecule is locally destabilized and changes conformation. This structural transition occurs at stretching forces which can be exerted in vivo by molecular motors and at degrees of supercoiling found in the cell, and may have implications for DNA structure and function within the nucleus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/B:JOSS.0000033247.51868.be
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  • 6
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    Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation (2004)
    National Academy of Sciences
    Details
    Publication Date: 2004-03-22
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Homologous pairing in stretched supercoiled DNA (1998)
    National Academy of Sciences
    Details
    Publication Date: 1998-09-01
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Topological characterization of the DnaA-oriC complex using single-molecule nanomanipuation (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-23
    Description: In most bacteria, the timing and synchrony of initiation of chromosomal replication are determined by the binding of the AAA + protein DnaA to a set of high- and low-affinity sites found within the origin of chromosomal replication ( oriC ). Despite the large amount of information on the role and regulation of DnaA, the actual structure of the DnaA– oriC complex and the mechanism by which it primes the origin for the initiation of replication remain unclear. In this study, we have performed magnetic tweezers experiments to investigate the structural properties of the DnaA– oriC complex. We show that the DnaA-ATP– oriC complex adopts a right-handed helical conformation involving a variable amount of DNA and protein whose features fit qualitatively as well as quantitatively with an existing model based on the crystal structure of a truncated DnaA tetramer obtained in the absence of DNA. We also investigate the topological effect of oriC ’s DNA unwinding element.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Backtracking and pausing in E. coli RNAP [Biochemistry] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-10-26
    Description: Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g.,...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Stress-Induced Structural Transitions in DNA and Proteins (2000)
    Annual Reviews
    Details
    Publication Date: 2000-06-01
    Print ISSN: 1056-8700
    Electronic ISSN: 1545-4266
    Topics: Biology , Physics
    Published by Annual Reviews
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