Literature DB >> 18835912

RNA folding: thermodynamic and molecular descriptions of the roles of ions.

David E Draper1.   

Abstract

The stability of a compact RNA tertiary structure is exquisitely sensitive to the concentrations and types of ions that are present. This review discusses the progress that has been made in developing a quantitative understanding of the thermodynamic parameters and molecular detail that underlie this sensitivity, including the nature of the ion atmosphere, the occurrence of specific ion binding sites, and the importance of the ensemble of partially unfolded states from which folding to the native structure occurs.

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Year:  2008        PMID: 18835912      PMCID: PMC2599833          DOI: 10.1529/biophysj.108.131813

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  47 in total

1.  A collapsed non-native RNA folding state.

Authors:  K L Buchmueller; A E Webb; D A Richardson; K M Weeks
Journal:  Nat Struct Biol       Date:  2000-05

2.  Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.

Authors:  K Chin; K A Sharp; B Honig; A M Pyle
Journal:  Nat Struct Biol       Date:  1999-11

3.  Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations.

Authors:  S L Heilman-Miller; D Thirumalai; S A Woodson
Journal:  J Mol Biol       Date:  2001-03-09       Impact factor: 5.469

4.  Is counterion delocalization responsible for collapse in RNA folding?

Authors:  V L Murthy; G D Rose
Journal:  Biochemistry       Date:  2000-11-28       Impact factor: 3.162

5.  The linkage between magnesium binding and RNA folding.

Authors:  Vinod K Misra; David E Draper
Journal:  J Mol Biol       Date:  2002-04-05       Impact factor: 5.469

6.  Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

Authors:  V K Misra; D E Draper
Journal:  J Mol Biol       Date:  2000-06-09       Impact factor: 5.469

7.  A compact RNA tertiary structure contains a buried backbone-K+ complex.

Authors:  Graeme L Conn; Apostolos G Gittis; Eaton E Lattman; Vinod K Misra; David E Draper
Journal:  J Mol Biol       Date:  2002-05-10       Impact factor: 5.469

8.  Ion-mediated nucleic acid helix-helix interactions.

Authors:  Zhi-Jie Tan; Shi-Jie Chen
Journal:  Biophys J       Date:  2006-04-28       Impact factor: 4.033

9.  A thermodynamic framework for Mg2+ binding to RNA.

Authors:  V K Misra; D E Draper
Journal:  Proc Natl Acad Sci U S A       Date:  2001-10-23       Impact factor: 11.205

10.  Stabilization of RNA tertiary structure by monovalent cations.

Authors:  R Shiman; D E Draper
Journal:  J Mol Biol       Date:  2000-09-08       Impact factor: 5.469

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  116 in total

1.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

2.  Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state.

Authors:  Shreyas S Athavale; J Jared Gossett; Chiaolong Hsiao; Jessica C Bowman; Eric O'Neill; Eli Hershkovitz; Thanawadee Preeprem; Nicholas V Hud; Roger M Wartell; Stephen C Harvey; Loren Dean Williams
Journal:  RNA       Date:  2012-02-14       Impact factor: 4.942

3.  Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.

Authors:  Huimin Chen; Steve P Meisburger; Suzette A Pabit; Julie L Sutton; Watt W Webb; Lois Pollack
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-27       Impact factor: 11.205

4.  Predicting ion binding properties for RNA tertiary structures.

Authors:  Zhi-Jie Tan; Shi-Jie Chen
Journal:  Biophys J       Date:  2010-09-08       Impact factor: 4.033

5.  Mapping L1 ligase ribozyme conformational switch.

Authors:  George M Giambaşu; Tai-Sung Lee; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

6.  How do metal ions direct ribozyme folding?

Authors:  Natalia A Denesyuk; D Thirumalai
Journal:  Nat Chem       Date:  2015-08-31       Impact factor: 24.427

7.  The Role of Correlation and Solvation in Ion Interactions with B-DNA.

Authors:  Maria L Sushko; Dennis G Thomas; Suzette A Pabit; Lois Pollack; Alexey V Onufriev; Nathan A Baker
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

8.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

9.  Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2016-10-27       Impact factor: 2.991

10.  Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg(II) and Ag(I) ions.

Authors:  Wei Ding; Mengze Xu; Hong Zhu; Haojun Liang
Journal:  Eur Phys J E Soft Matter       Date:  2013-09-19       Impact factor: 1.890

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