Early events in RNA folding

Annual Review of Physical Chemistry
D ThirumalaiD Klimov

Abstract

We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.

References

Aug 7, 1990·Biochemistry·K A Dill
Jan 1, 1966·Cold Spring Harbor Symposia on Quantitative Biology·J R FrescoT Lindahl
Aug 12, 1994·Science·P P Zarrinkar, J R Williamson
Jan 1, 1997·Nature Structural Biology·K A Dill, H S Chan
Nov 21, 1997·Journal of Molecular Biology·J PanS A Woodson
Apr 16, 1998·Science·D K TreiberJ R Williamson
Jul 25, 1998·Journal of Molecular Biology·J Pan, S A Woodson
Aug 26, 1998·Journal of Molecular Biology·M S RookJ R Williamson
Sep 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·D Thirumalai
Sep 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·M Wu, I Tinoco
Feb 20, 1999·Journal of Molecular Biology·T PanT Sosnick
Jun 11, 1999·Current Opinion in Structural Biology·D K Treiber, J R Williamson
Jun 17, 2000·Science·X ZhuangS Chu
Jun 23, 2000·RNA·D Thirumalai, S A Woodson
Sep 22, 2000·Biochemistry·M L DerasS A Woodson
Oct 4, 2000·Biochemistry·S K SilvermanT R Cech
Dec 5, 2000·Nature Structural Biology·R B Russell, D S Eggleston

❮ Previous
Next ❯

Citations

Feb 9, 2002·Proteins·Eaton E Lattman, David E Draper
Apr 7, 2005·Current Opinion in Chemical Biology·Sarah A Woodson
Nov 8, 2002·Journal of Molecular Biology·Amy Diegelman-Parente, Philip C Bevilacqua
Jul 20, 2002·Current Opinion in Structural Biology·Renée SchroederChristina Waldsich
Feb 13, 2003·Current Opinion in Structural Biology·Xiaowei Zhuang, Matthias Rief
May 7, 2002·RNA·Amanda SolemMark G Caprara
May 27, 2004·Journal of the American Chemical Society·Jennifer C TakachAndrew L Feig
Feb 14, 2007·Journal of the American Chemical Society·Eda KoculiSarah A Woodson
Jan 9, 2008·Journal of the American Chemical Society·Seema Chauhan, Sarah A Woodson
Jul 6, 2010·Journal of the American Chemical Society·Joon Ho RohSarah A Woodson
Sep 17, 2010·Journal of the American Chemical Society·Jacob B SwadlingH Christopher Greenwell
Nov 3, 2010·Journal of the American Chemical Society·Nathan J BairdTobin R Sosnick
Mar 8, 2011·Journal of the American Chemical Society·Jun FengCharles L Brooks
Oct 1, 2011·Journal of the American Chemical Society·Ranjani NarayananAnjum Ansari
Nov 16, 2011·Journal of the American Chemical Society·Shi BiyunD Thirumalai
Jul 7, 2012·Journal of the American Chemical Society·Xiaojun Xu, Shi-Jie Chen
Jul 19, 2013·Journal of the American Chemical Society·Jeseong YoonChangbong Hyeon
Jun 4, 2010·The Journal of Physical Chemistry. B·Serdal Kirmizialtin, Ron Elber
Jul 12, 2002·Nature·Jennifer A Doudna, Thomas R Cech
Sep 29, 2011·Nature Communications·Changbong Hyeon, D Thirumalai
Jun 5, 2012·The Journal of Biological Chemistry·Cordula BöhmH Ulrich Göringer
Oct 3, 2002·The EMBO Journal·Christina WaldsichRenée Schroeder
Oct 18, 2007·Nucleic Acids Research·Zhuoyun ZhuangJoan-Emma Shea
May 30, 2012·Nucleic Acids Research·Eda KoculiSarah A Woodson
May 28, 2010·Cold Spring Harbor Perspectives in Biology·Eric WesthofFabrice Jossinet
Sep 5, 2002·Genes & Development·Christina WaldsichRenée Schroeder
Oct 15, 2013·Journal of Synchrotron Radiation·Rita GraceffaThomas C Irving
Mar 20, 2010·Annual Review of Biochemistry·Joachim Frank, Ruben L Gonzalez
Mar 3, 2010·Annual Review of Biophysics·Sarah A Woodson
Jun 25, 2008·Annual Review of Biophysics·Shi-Jie Chen
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
May 28, 2010·RNA·Ivo L HofackerPeter F Stadler
Mar 4, 2014·PloS One·Jörg C SchlattererMichael Brenowitz
Oct 5, 2013·The Journal of Chemical Physics·Martin Gruebele, D Thirumalai
Apr 20, 2005·The Journal of Chemical Physics·Zoia Kopeikin, Shi-Jie Chen
Jan 21, 2014·The Journal of Chemical Physics·Jiawen ChenWenbing Zhang
Feb 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Wenbing Zhang, Shi-Jie Chen

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA folding
protein folding
NMR
footprinting
electrophoresis
fluorescent
FRET
X-ray

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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Rick RussellD Herschlag
Proceedings of the National Academy of Sciences of the United States of America
S J Chen, K A Dill
Proceedings of the National Academy of Sciences of the United States of America
Andrea SorannoBenjamin Schuler
© 2021 Meta ULC. All rights reserved