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  • 1
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    A not-so-cheap stunt (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Block, Steven M -- New York, N.Y. -- Science. 2002 Aug 2;297(5582):769-70; author reply 769-70.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12162317" target="_blank"〉PubMed〈/a〉
    Keywords: Bioterrorism/*trends ; Cell-Free System/virology ; DNA, Viral/*chemical synthesis/genetics ; HeLa Cells ; Humans ; Peer Review, Research/standards ; Poliovirus/genetics/*isolation & purification/*physiology ; Publishing/*standards ; Templates, Genetic ; Variola virus/genetics/physiology ; *Virus Replication
    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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    Direct observation of the binding state of the kinesin head to the microtubule (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-21
    Description: The dimeric motor protein kinesin-1 converts chemical energy from ATP hydrolysis into mechanical work used to transport cargo along microtubules. Cargo attached to the kinesin stalk moves processively in 8-nm increments as its twin motor domains (heads) carry out an asymmetric, 'hand-over-hand' walk. The extent of individual head interactions with the microtubule during stepping, however, remains controversial. A major experimental limitation has been the lack of a means to monitor the attachment of an individual head to the microtubule during movement, necessitating indirect approaches. Here we report the development of a single-molecule assay that can directly report head binding in a walking kinesin molecule, and show that only a single head is bound to the microtubule between steps at low ATP concentrations. A bead was linked to one of the two kinesin heads by means of a short DNA tether and used to apply rapidly alternating hindering and assisting loads with an optical trap. The time-dependent difference between forwards and backwards displacements of the bead alternated between two discrete values during stepping, corresponding to those intervals when the linked head adopted a bound or an unbound state. The linked head could only rebind the microtubule once ATP had become bound to its partner head.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859689/" 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/PMC2859689/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guydosh, Nicholas R -- Block, Steven M -- GM51453/GM/NIGMS NIH HHS/ -- R01 GM051453/GM/NIGMS NIH HHS/ -- R01 GM051453-15/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Sep 3;461(7260):125-8. doi: 10.1038/nature08259. Epub 2009 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693012" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism/pharmacology ; Animals ; DNA/chemistry/metabolism ; Drosophila melanogaster ; Kinesin/*chemistry/*metabolism ; Microspheres ; Microtubules/*metabolism ; Movement/drug effects ; Optical Tweezers ; Protein Binding/drug effects ; Time Factors
    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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    UK defence group's structure could limit its usefulness (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Block, Steven M -- England -- Nature. 2009 Dec 17;462(7275):847. doi: 10.1038/462847c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016574" target="_blank"〉PubMed〈/a〉
    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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  • 4
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    Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: Nucleic acid hairpins provide a powerful model system for understanding macromolecular folding, with free-energy landscapes that can be readily manipulated by changing the hairpin sequence. The full shapes of energy landscapes for the reversible folding of DNA hairpins under controlled loads exerted by an optical force clamp were obtained by deconvolution from high-resolution, single-molecule trajectories. The locations and heights of the energy barriers for hairpin folding could be tuned by adjusting the number and location of G:C base pairs, and the presence and position of folding intermediates were controlled by introducing single-nucleotide mismatches.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656380/" 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/PMC2656380/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woodside, Michael T -- Anthony, Peter C -- Behnke-Parks, William M -- Larizadeh, Kevan -- Herschlag, Daniel -- Block, Steven M -- P01-GM066275/GM/NIGMS NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- R01 GM057035-12/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):1001-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, Canada, T6G 2M9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095702" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pair Mismatch ; Base Pairing ; DNA/*chemistry ; Models, Chemical ; *Nucleic Acid Conformation ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Single-molecule, motion-based DNA sequencing using RNA polymerase (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-12
    Description: We present a method for sequencing DNA that relies on the motion of single RNA polymerase molecules. When a given nucleotide species limits the rate of transcription, polymerase molecules pause at positions corresponding to the rare base. An ultrastable optical trapping apparatus capable of base pair resolution was used to monitor transcription under limiting amounts of each of the four nucleotide species. From the aligned patterns of pauses recorded from as few as four molecules, we determined the DNA sequence. This proof of principle demonstrates that the motion of a processive nucleic acid enzyme may be used to extract sequence information directly from DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865524/" 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/PMC1865524/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenleaf, William J -- Block, Steven M -- GM057035/GM/NIGMS NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902131" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Base Pairing ; Cytidine Triphosphate/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/enzymology ; Guanosine Triphosphate/metabolism ; Motion ; Sequence Analysis, DNA/*methods ; Templates, Genetic ; Uridine Triphosphate/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Direct observation of cotranscriptional folding in an adenine riboswitch (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-23
    Description: Growing RNA chains fold cotranscriptionally as they are synthesized by RNA polymerase. Riboswitches, which regulate gene expression by adopting alternative RNA folds, are sensitive to cotranscriptional events. We developed an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it to monitor individual transcripts of the pbuE adenine riboswitch, visualizing distinct folding transitions. We report a particular folding signature for the riboswitch aptamer whose presence directs the gene-regulatory transcription outcome, and we measured the termination frequency as a function of adenine level and tension applied to the RNA. Our results demonstrate that the outcome is kinetically controlled. These experiments furnish a means to observe conformational switching in real time and enable the precise mapping of events during cotranscriptional folding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496414/" 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/PMC3496414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frieda, Kirsten L -- Block, Steven M -- R37 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087247" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*chemistry/metabolism ; Bacillus subtilis/genetics ; Base Sequence ; Kinetics ; Molecular Sequence Data ; *Optical Tweezers ; *RNA Folding ; Riboswitch/*genetics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Force and velocity measured for single molecules of RNA polymerase (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-10-30
    Description: RNA polymerase (RNAP) moves along DNA while carrying out transcription, acting as a molecular motor. Transcriptional velocities for single molecules of Escherichia coli RNAP were measured as progressively larger forces were applied by a feedback-controlled optical trap. The shapes of RNAP force-velocity curves are distinct from those of the motor enzymes myosin or kinesin, and indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling the data suggests that high loads may halt RNAP by promoting a structural change which moves all or part of the enzyme backwards through a comparatively large distance, corresponding to 5 to 10 base pairs. This contrasts with previous models that assumed force acts directly upon a single-base translocation step.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, M D -- Schnitzer, M J -- Yin, H -- Landick, R -- Gelles, J -- Block, S M -- New York, N.Y. -- Science. 1998 Oct 30;282(5390):902-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9794753" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/enzymology ; Mathematics ; *Models, Chemical ; Molecular Motor Proteins/*chemistry/metabolism ; RNA, Bacterial/biosynthesis ; RNA, Messenger/biosynthesis ; Templates, Genetic ; Thermodynamics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Sequence-dependent pausing of single lambda exonuclease molecules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGAT TCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539570/" 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/PMC1539570/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perkins, Thomas T -- Dalal, Ravindra V -- Mitsis, Paul G -- Block, Steven M -- GM 57035/GM/NIGMS NIH HHS/ -- HG 011821-01/HG/NHGRI NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1914-8. Epub 2003 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. tperkins@jila.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947034" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/enzymology ; Base Pairing ; *Base Sequence ; Binding Sites ; Consensus Sequence ; DNA/*chemistry/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Exodeoxyribonucleases/*metabolism ; Hydrogen Bonding ; Kinetics ; Models, Chemical ; Oligodeoxyribonucleotides/chemistry/metabolism ; Polymerase Chain Reaction ; Probability ; Stochastic Processes ; Time Factors ; Viral Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Kinesin moves by an asymmetric hand-over-hand mechanism (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-06
    Description: Kinesin is a double-headed motor protein that moves along microtubules in 8-nanometer steps. Two broad classes of model have been invoked to explain kinesin movement: hand-over-hand and inchworm. In hand-over-hand models, the heads exchange leading and trailing roles with every step, whereas no such exchange is postulated for inchworm models, where one head always leads. By measuring the stepwise motion of individual enzymes, we find that some kinesin molecules exhibit a marked alternation in the dwell times between sequential steps, causing these motors to "limp" along the microtubule. Limping implies that kinesin molecules strictly alternate between two different conformations as they step, indicative of an asymmetric, hand-over-hand mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523256/" 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/PMC1523256/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asbury, Charles L -- Fehr, Adrian N -- Block, Steven M -- R01 GM051453/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2130-4. Epub 2003 Dec 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657506" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Computer Simulation ; Decapodiformes/enzymology ; Dimerization ; Drosophila Proteins/chemistry/physiology ; Drosophila melanogaster/*enzymology ; Humans ; Kinesin/*chemistry/*physiology ; Kinetics ; Microspheres ; Microtubules/metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*physiology ; Movement ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Rotation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Real-time observation of the initiation of RNA polymerase II transcription (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-09-04
    Description: Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624315/" 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/PMC4624315/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fazal, Furqan M -- Meng, Cong A -- Murakami, Kenji -- Kornberg, Roger D -- Block, Steven M -- AI21144/AI/NIAID NIH HHS/ -- GM36659/GM/NIGMS NIH HHS/ -- GM57035/GM/NIGMS NIH HHS/ -- R01 AI021144/AI/NIAID NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM049985/GM/NIGMS NIH HHS/ -- R37 GM057035/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Sep 10;525(7568):274-7. doi: 10.1038/nature14882. Epub 2015 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, Stanford University, Stanford, California 94305, USA. ; Department of Chemistry, Stanford University, Stanford, California 94305, USA. ; Department of Structural Biology, Stanford University, Stanford, California 94305, USA. ; Department of Biology, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26331540" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing/genetics ; DNA/genetics/metabolism ; Optical Tweezers ; Promoter Regions, Genetic/genetics ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Messenger/biosynthesis/genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factor TFIIH/metabolism ; *Transcription Initiation, 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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