Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase

Journal of Molecular Biology
C Liu, C T Martin

Abstract

The various kinetic and thermodynamic models for transcription elongation all require an understanding of the nature of the melted bubble which moves with the RNA polymerase active site. Is the general nature of the bubble system-dependent or are there common energetic requirements which constrain a bubble in any RNA polymerases? T7 RNA polymerase is one of the simplest RNA polymerases and is the system for which we have the highest-resolution structural information. However, there is no high-resolution information available for a stable elongation complex. In order to directly map melted regions of the DNA in a functionally paused elongation complex, we have introduced fluorescent probes site-specifically into the DNA. Like 2-aminopurine, which substitutes for adenine bases, the fluorescence intensity of the new probe, pyrrolo-dC, which substitutes for cytosine bases, is sensitive to its environment. Specifically, the fluorescence is quenched in duplex DNA relative to its fluorescence in single-stranded DNA, such that the probe provides direct information on local melting of the DNA. Placement of this new probe at specific positions in the non-template strand shows clearly that the elongation bubble extends about eight bases u...Continue Reading

References

Jun 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·R A Ikeda, C C Richardson
Aug 18, 1981·Biochemistry·H L Osterman, J E Coleman
Apr 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·P DavanlooF W Studier
Jun 6, 1995·Biochemical and Biophysical Research Communications·S S Sastry, P L Hoffman
Jan 10, 1997·Journal of Molecular Biology·R Guajardo, R Sousa
Jan 1, 1997·Annual Review of Biochemistry·S M UptainM J Chamberlin
Jan 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·M RongR K Durbin
Dec 22, 1999·Science·G M Cheetham, T A Steitz
Feb 2, 2000·Biophysical Journal·D G Xu, T M Nordlund
Oct 14, 2000·Journal of Molecular Biology·J Huang, R Sousa
Nov 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·D TemiakovW T McAllister

❮ Previous
Next ❯

Citations

May 19, 2010·Quarterly Reviews of Biophysics·L Marcus Wilhelmsson
Mar 9, 2010·Chemical Reviews·Renatus W SinkeldamYitzhak Tor
Jul 13, 2006·Journal of the American Chemical Society·Alex H F Lee, Eric T Kool
Jan 30, 2007·Journal of the American Chemical Society·Seergazhi G Srivatsan, Yitzhak Tor
Aug 27, 2011·Journal of the American Chemical Society·Dongwon ShinYitzhak Tor
Nov 8, 2002·Nature·Tahir H TahirovShigeyuki Yokoyama
Oct 23, 2009·The Journal of Biological Chemistry·Xiaoqing Liu, Craig T Martin
Jan 1, 2009·The Journal of Biological Chemistry·Guo-Qing TangSmita S Patel
Dec 11, 2007·Nucleosides, Nucleotides & Nucleic Acids·Robert H E Hudson, Arash Ghorbani Choghamarani
Jan 13, 2006·Nucleic Acids Research·Mary K Smalley, Scott K Silverman
Apr 6, 2006·Nucleic Acids Research·Angel A MartíNicholas J Turro
Aug 10, 2007·Nucleic Acids Research·Chongli YuanLynden A Archer
May 10, 2012·Nucleic Acids Research·Rasa SukackaiteVirginijus Siksnys
Sep 6, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Chandrika CanugoviAshok S Bhagwat
Dec 19, 2007·Photochemistry and Photobiology·Kongsheng Yang, Robert J Stanley
Nov 18, 2006·Science·Achillefs N KapanidisRichard H Ebright
Jun 8, 2007·Proceedings of the National Academy of Sciences of the United States of America·Yi ZhouCraig T Martin
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Neil P JohnsonPeter H von Hippel
Jan 27, 2011·Biochemical Society Transactions·Dina GrohmannFinn Werner
Dec 19, 2014·Journal of Biochemistry·Mayu FujikawaTakahiro Kozawa
Jun 20, 2006·Journal of Molecular Biology·Rajiv P BandwarSmita S Patel
Oct 18, 2007·Tetrahedron·James N WilsonEric T Kool
Jun 15, 2017·Journal of the American Chemical Society·Moa S WranneL Marcus Wilhelmsson
Dec 14, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Željka BanIvo Piantanida
Jun 3, 2016·Physical Chemistry Chemical Physics : PCCP·Quynh L NguyenSpiridoula Matsika
Sep 22, 2017·Methods and Applications in Fluorescence·Jong Jin RoByeang Hyean Kim
May 6, 2015·Chemical Communications : Chem Comm·Qinfeng XuChun-yang Zhang
Jun 16, 2007·Nature Protocols·Seergazhi G Srivatsan, Yitzhak Tor
Feb 7, 2019·Current Protocols in Nucleic Acid Chemistry·Sung Ju ChoRobert H E Hudson
Apr 4, 2008·Organic & Biomolecular Chemistry·Seergazhi G SrivatsanYitzhak Tor

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.