Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA.

Journal of the American Chemical Society
Costin M GhergheKevin M Weeks

Abstract

The functions of most RNA molecules are critically dependent on the distinct local dynamics that characterize secondary structure and tertiary interactions and on structural changes that occur upon binding by proteins and small molecule ligands. Measurements of RNA dynamics at nucleotide resolution set the foundation for understanding the roles of individual residues in folding, catalysis, and ligand recognition. In favorable cases, local order in small RNAs can be quantitatively analyzed by NMR in terms of a generalized order parameter, S2. Alternatively, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry measures local nucleotide flexibility in RNAs of any size using structure-sensitive reagents that acylate the 2'-hydroxyl position. In this work, we compare per-residue RNA dynamics, analyzed by both S2 and SHAPE, for three RNAs: the HIV-1 TAR element, the U1A protein binding site, and the Tetrahymena telomerase stem loop 4. We find a very strong correlation between the two measurements: nucleotides with high SHAPE reactivities consistently have low S2 values. We conclude that SHAPE chemistry quantitatively reports local nucleotide dynamics and can be used with confidence to analyze dynamics in lar...Continue Reading

References

Oct 20, 1989·Cell·P A Sharp, R A Marciniak
May 10, 2000·Nature Structural Biology·K L BuchmuellerK M Weeks
Aug 10, 2000·Biochemistry·C G HoogstratenA Pardi
Feb 13, 2002·Current Opinion in Structural Biology·Traci M Tanaka Hall
Mar 21, 2002·Journal of Molecular Biology·Kwaku T DayieJames R Williamson
Sep 4, 2003·Journal of the American Chemical Society·Karen L BuchmuellerKevin M Weeks
Mar 9, 2004·Journal of Molecular Biology·Victoria D'SouzaMichael F Summers
Aug 12, 2004·Chemical Reviews·Arthur G Palmer
Mar 24, 2005·Journal of the American Chemical Society·Edward J MerinoKevin M Weeks
Mar 31, 2005·Journal of the American Chemical Society·Kevin A WilkinsonKevin M Weeks
Sep 27, 2005·Journal of Molecular Biology·Heike BladSamuel E Butcher
Oct 8, 2005·Journal of Biomolecular NMR·Elke Duchardt, Harald Schwalbe
Jun 17, 2006·The EMBO Journal·Yu ChenGabriele Varani
Jul 20, 2006·Journal of the American Chemical Society·Pramodh VallurupalliLewis E Kay
Jul 29, 2006·Journal of Molecular Biology·Gregory BokinskyXiaowei Zhuang
Dec 13, 2006·Biopolymers·Zahra Shajani, Gabriele Varani
Mar 21, 2007·Journal of the American Chemical Society·Stefanie A Mortimer, Kevin M Weeks
Apr 17, 2007·Journal of Molecular Biology·Tuhin Subhra Maity, Kevin M Weeks
Sep 4, 2007·Trends in Biochemical Sciences·Andrei Korostelev, Harry F Noller
Dec 1, 2007·Journal of the American Chemical Society·Alexandar L Hansen, Hashim M Al-Hashimi
Dec 13, 2007·Biology of the Cell·Jane N Kim, Ronald R Breaker
Feb 15, 2008·Nucleic Acids Research·Jan FernerHarald Schwalbe
Jun 13, 2008·Current Opinion in Structural Biology·Hashim M Al-Hashimi, Nils G Walter
Jun 19, 2008·Journal of the American Chemical Society·Costin M GhergheKevin M Weeks

❮ Previous
Next ❯

Citations

Aug 2, 2012·Quarterly Reviews of Biophysics·Robert T Batey
May 28, 2011·Accounts of Chemical Research·Kevin M Weeks, David M Mauger
Sep 8, 2011·Accounts of Chemical Research·Jörg RinnenthalHarald Schwalbe
Jan 16, 2013·Biochemistry·Christopher W LeonardKevin M Weeks
Jan 5, 2013·Biochemistry·Srinivas RamachandranNikolay V Dokholyan
Dec 14, 2011·ACS Chemical Biology·Kelly PhelpsPeter A Beal
Jul 6, 2010·Journal of the American Chemical Society·Kady-Ann SteenKevin M Weeks
Sep 3, 2011·Journal of the American Chemical Society·Marie F SoulièreRonald Micura
Dec 1, 2011·Journal of the American Chemical Society·Jacob K GrohmanKevin M Weeks
Apr 6, 2012·Journal of the American Chemical Society·Jennifer L McGinnisKevin M Weeks
Aug 3, 2012·Journal of the American Chemical Society·Kady-Ann SteenKevin M Weeks
Nov 21, 2012·Journal of the American Chemical Society·Daud I ColeMichael B Jarstfer
Mar 31, 2012·The Journal of Physical Chemistry. B·Ke ChenZaida Luthey-Schulten
Aug 8, 2009·Nature·Joseph M WattsKevin M Weeks
Nov 28, 2012·Nature Chemical Biology·Robert C SpitaleHoward Y Chang
Nov 1, 2011·Nature Methods·Jameson R BotheHashim M Al-Hashimi
Dec 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Katherine E DeiganKevin M Weeks
Sep 1, 2009·Proceedings of the National Academy of Sciences of the United States of America·Stefanie A Mortimer, Kevin M Weeks
Oct 27, 2010·Proceedings of the National Academy of Sciences of the United States of America·Cristina GhergheKevin M Weeks
Jun 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Julius B LucksAdam P Arkin
Jan 26, 2010·Nucleic Acids Research·Wei ChenLirong Zhang
Mar 1, 2012·Nucleic Acids Research·Irina V NovikovaKarissa Y Sanbonmatsu
Oct 16, 2012·Nucleic Acids Research·Cristina Romero-LópezAlfredo Berzal-Herranz
Dec 22, 2012·Nucleic Acids Research·Scott P HennellyKarissa Y Sanbonmatsu
Mar 9, 2013·Science·Jacob K GrohmanKevin M Weeks
May 22, 2009·RNA·Kevin A WilkinsonKevin M Weeks
May 14, 2014·Biochemistry·Jennifer L McGinnis, Kevin M Weeks
Aug 19, 2014·Wiley Interdisciplinary Reviews. RNA·Robert C SpitaleHoward Y Chang
Mar 15, 2013·Journal of Molecular Biology·Colby D StoddardRobert T Batey
Jul 29, 2018·Nature Reviews. Genetics·Eric J StrobelJulius B Lucks
Dec 30, 2014·Biopolymers·Kevin M Weeks
Nov 26, 2009·FEBS Letters·Rebecca W AlexanderZaida Luthey-Schulten
Apr 27, 2019·Wiley Interdisciplinary Reviews. RNA·Huaqun Zhang, Sarah C Keane
Mar 17, 2015·Proceedings of the National Academy of Sciences of the United States of America·David M MaugerKevin M Weeks
Jul 26, 2017·RNA·Edric K ChoiRachel M Mitton-Fry
May 5, 2018·Nature Protocols·Matthew J Smola, Kevin M Weeks

❮ 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.