Literature DB >> 22036746

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.

Jameson R Bothe1, Evgenia N Nikolova, Catherine D Eichhorn, Jeetender Chugh, Alexandar L Hansen, Hashim M Al-Hashimi.   

Abstract

Many recently discovered noncoding RNAs do not fold into a single native conformation but sample many different conformations along their free-energy landscape to carry out their biological function. Here we review solution-state NMR techniques that measure the structural, kinetic and thermodynamic characteristics of RNA motions spanning picosecond to second timescales at atomic resolution, allowing unprecedented insights into the RNA dynamic structure landscape. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 22036746      PMCID: PMC3320163          DOI: 10.1038/nmeth.1735

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  93 in total

1.  The dynamic landscapes of RNA architecture.

Authors:  José Almeida Cruz; Eric Westhof
Journal:  Cell       Date:  2009-02-20       Impact factor: 41.582

2.  Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy.

Authors:  Alexandar L Hansen; Evgenia N Nikolova; Anette Casiano-Negroni; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2009-03-25       Impact factor: 15.419

3.  Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Authors:  Elizabeth A Dethoff; Alexandar L Hansen; Catherine Musselman; Eric D Watt; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

4.  RNA dynamics: it is about time.

Authors:  Hashim M Al-Hashimi; Nils G Walter
Journal:  Curr Opin Struct Biol       Date:  2008-06-09       Impact factor: 6.809

5.  Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states.

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Lewis E Kay
Journal:  J Biomol NMR       Date:  2008-06-24       Impact factor: 2.835

6.  Changes in dynamics of SRE-RNA on binding to the VTS1p-SAM domain studied by 13C NMR relaxation.

Authors:  Florian C Oberstrass; Frédéric H-T Allain; Sapna Ravindranathan
Journal:  J Am Chem Soc       Date:  2008-08-13       Impact factor: 15.419

7.  NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer.

Authors:  Michael P Latham; Grant R Zimmermann; Arthur Pardi
Journal:  J Am Chem Soc       Date:  2009-04-15       Impact factor: 15.419

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

Authors:  Costin M Gherghe; Zahra Shajani; Kevin A Wilkinson; Gabriele Varani; Kevin M Weeks
Journal:  J Am Chem Soc       Date:  2008-08-19       Impact factor: 15.419

Review 9.  RNA and disease.

Authors:  Thomas A Cooper; Lili Wan; Gideon Dreyfuss
Journal:  Cell       Date:  2009-02-20       Impact factor: 41.582

10.  How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape.

Authors:  Michael F Bardaro; Zahra Shajani; Krystyna Patora-Komisarska; John A Robinson; Gabriele Varani
Journal:  Nucleic Acids Res       Date:  2009-01-12       Impact factor: 16.971

View more
  64 in total

Review 1.  The RNA Base-Pairing Problem and Base-Pairing Solutions.

Authors:  Zhipeng Lu; Howard Y Chang
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-12-03       Impact factor: 10.005

2.  Mutational robustness and resilience of a replicative cis-element of RNA virus: Promiscuity, limitations, relevance.

Authors:  Maria A Prostova; Anatoly P Gmyl; Denis V Bakhmutov; Anna A Shishova; Elena V Khitrina; Marina S Kolesnikova; Marina V Serebryakova; Olga V Isaeva; Vadim I Agol
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

3.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

Authors:  Witold Andrałojć; Konstantin Berlin; David Fushman; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Luca Sgheri
Journal:  J Biomol NMR       Date:  2015-06-05       Impact factor: 2.835

4.  Chemo-enzymatic synthesis of selectively ¹³C/¹⁵N-labeled RNA for NMR structural and dynamics studies.

Authors:  Luigi J Alvarado; Andrew P Longhini; Regan M LeBlanc; Bin Chen; Christoph Kreutz; T Kwaku Dayie
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

5.  Riboswitch structure and dynamics by smFRET microscopy.

Authors:  Krishna C Suddala; Nils G Walter
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

Review 6.  Characterizing excited conformational states of RNA by NMR spectroscopy.

Authors:  Bo Zhao; Qi Zhang
Journal:  Curr Opin Struct Biol       Date:  2015-03-10       Impact factor: 6.809

7.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

8.  (13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI).

Authors:  Mitsuhiro Takeda; Yohei Miyanoiri; Tsutomu Terauchi; Masatsune Kainosho
Journal:  J Biomol NMR       Date:  2016-08-26       Impact factor: 2.835

Review 9.  Specificity and nonspecificity in RNA-protein interactions.

Authors:  Eckhard Jankowsky; Michael E Harris
Journal:  Nat Rev Mol Cell Biol       Date:  2015-08-19       Impact factor: 94.444

10.  Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.

Authors:  Aiming Ren; Yi Xue; Alla Peselis; Alexander Serganov; Hashim M Al-Hashimi; Dinshaw J Patel
Journal:  Cell Rep       Date:  2015-11-19       Impact factor: 9.423

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.