Literature DB >> 33836446

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.

Bei Liu1, Honglue Shi2, Hashim M Al-Hashimi3.   

Abstract

Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to describe their propensities to cycle between different conformations when performing cellular functions. We review recent advances in solution-state nuclear magnetic resonance (NMR) methods and their integration with computational techniques that are improving the ability to probe the dynamic ensembles of DNA and RNA. These include computational approaches for predicting chemical shifts from structure and generating conformational libraries from sequence, measurements of exact nuclear Overhauser effects, development of new probes to study chemical exchange using relaxation dispersion, faster and more sensitive real-time NMR techniques, and new NMR approaches to tackle large nucleic acid assemblies. We discuss how these advances are leading to new mechanistic insights into gene expression and regulation.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Dynamic ensembles; Excited conformational states; Nucleic acids; Solution state NMR

Mesh:

Substances:

Year:  2021        PMID: 33836446      PMCID: PMC8714323          DOI: 10.1016/j.sbi.2021.02.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   7.786


  78 in total

1.  Structural basis for transcriptional start site control of HIV-1 RNA fate.

Authors:  Joshua D Brown; Siarhei Kharytonchyk; Issac Chaudry; Aishwarya S Iyer; Hannah Carter; Ghazal Becker; Yash Desai; Lindsay Glang; Seung H Choi; Karndeep Singh; Michael W Lopresti; Matthew Orellana; Tatiana Rodriguez; Ubiomo Oboh; Jana Hijji; Frances Grace Ghinger; Kailan Stewart; Dillion Francis; Bryce Edwards; Patrick Chen; David A Case; Alice Telesnitsky; Michael F Summers
Journal:  Science       Date:  2020-04-24       Impact factor: 47.728

Review 2.  The roles of DNA, RNA and histone methylation in ageing and cancer.

Authors:  Ewa M Michalak; Marian L Burr; Andrew J Bannister; Mark A Dawson
Journal:  Nat Rev Mol Cell Biol       Date:  2019-07-03       Impact factor: 94.444

3.  Fitting Corrections to an RNA Force Field Using Experimental Data.

Authors:  Andrea Cesari; Sandro Bottaro; Kresten Lindorff-Larsen; Pavel Banáš; Jiří Šponer; Giovanni Bussi
Journal:  J Chem Theory Comput       Date:  2019-05-23       Impact factor: 6.006

Review 4.  Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods.

Authors:  Anita Kotar; Hannah N Foley; Kirk M Baughman; Sarah C Keane
Journal:  Methods       Date:  2020-01-20       Impact factor: 3.608

5.  Parallel reaction pathways accelerate folding of a guanine quadruplex.

Authors:  Robert W Harkness; Christopher Hennecker; J Tassilo Grün; Anja Blümler; Alexander Heckel; Harald Schwalbe; Anthony K Mittermaier
Journal:  Nucleic Acids Res       Date:  2021-02-22       Impact factor: 16.971

6.  4'-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function.

Authors:  Qiang Li; Jialiang Chen; Marko Trajkovski; Yifei Zhou; Chaochao Fan; Kuan Lu; Pingping Tang; Xuncheng Su; Janez Plavec; Zhen Xi; Chuanzheng Zhou
Journal:  J Am Chem Soc       Date:  2020-02-26       Impact factor: 15.419

Review 7.  The role of dynamic conformational ensembles in biomolecular recognition.

Authors:  David D Boehr; Ruth Nussinov; Peter E Wright
Journal:  Nat Chem Biol       Date:  2009-11       Impact factor: 15.040

8.  Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme.

Authors:  Neil A White; Minako Sumita; Victor E Marquez; Charles G Hoogstraten
Journal:  RNA       Date:  2018-08-15       Impact factor: 4.942

Review 9.  Isotope labeling strategies for NMR studies of RNA.

Authors:  Kun Lu; Yasuyuki Miyazaki; Michael F Summers
Journal:  J Biomol NMR       Date:  2009-09-30       Impact factor: 2.835

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  13 in total

Review 1.  How does RNA fold dynamically?

Authors:  David Z Bushhouse; Edric K Choi; Laura M Hertz; Julius B Lucks
Journal:  J Mol Biol       Date:  2022-06-01       Impact factor: 6.151

2.  Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR.

Authors:  Hannes Feyrer; Cenk Onur Gurdap; Maja Marušič; Judith Schlagnitweit; Katja Petzold
Journal:  PLoS One       Date:  2022-07-08       Impact factor: 3.752

3.  Kinetics and thermodynamics of BI-BII interconversion altered by T:G mismatches in DNA.

Authors:  M N Westwood; C C Johnson; Nathan A Oyler; Gary A Meints
Journal:  Biophys J       Date:  2022-03-30       Impact factor: 3.699

4.  Measuring radiofrequency fields in NMR spectroscopy using offset-dependent nutation profiles.

Authors:  Ahallya Jaladeep; Claris Niya Varghese; Ashok Sekhar
Journal:  J Magn Reson       Date:  2021-07-06       Impact factor: 2.734

5.  Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.

Authors:  Christina Bergonzo; Alexander Grishaev; Sandro Bottaro
Journal:  RNA       Date:  2022-04-28       Impact factor: 5.636

6.  Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.

Authors:  Samuel W Olson; Anne-Marie W Turner; J Winston Arney; Irfana Saleem; Chase A Weidmann; David M Margolis; Kevin M Weeks; Anthony M Mustoe
Journal:  Mol Cell       Date:  2022-03-22       Impact factor: 19.328

Review 7.  Getting to the bottom of lncRNA mechanism: structure-function relationships.

Authors:  Karissa Sanbonmatsu
Journal:  Mamm Genome       Date:  2021-10-12       Impact factor: 3.224

8.  Rational design of hairpin RNA excited states reveals multi-step transitions.

Authors:  Ge Han; Yi Xue
Journal:  Nat Commun       Date:  2022-03-21       Impact factor: 14.919

9.  Synthesis of [7-15N]-GTPs for RNA structure and dynamics by NMR spectroscopy.

Authors:  Kehinde M Taiwo; Lukasz T Olenginski; Felix Nußbaumer; Hyeyeon Nam; Stefan Hilber; Christoph Kreutz; T Kwaku Dayie
Journal:  Monatsh Chem       Date:  2022-02-26       Impact factor: 1.451

10.  Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders.

Authors:  Amirhossein Taghavi; Ilyas Yildirim
Journal:  Front Mol Biosci       Date:  2022-04-11
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