Rick Russell

Rick Russell

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Rick Russell

Publications by authors named "Rick Russell"

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Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq.

J Biol Chem 2019 Dec 11;294(51):19764-19784. Epub 2019 Nov 11.

Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712

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http://dx.doi.org/10.1074/jbc.RA119.011337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6926447PMC
December 2019

Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a.

Mol Cell 2018 09 2;71(5):816-824.e3. Epub 2018 Aug 2.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.06.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679935PMC
September 2018

Hidden Structural Modules in a Cooperative RNA Folding Transition.

Cell Rep 2018 03;22(12):3240-3250

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.02.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894117PMC
March 2018

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism.

J Biol Chem 2018 02 21;293(6):1924-1932. Epub 2017 Dec 21.

From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and

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http://dx.doi.org/10.1074/jbc.M117.815076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808756PMC
February 2018

Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs.

Biochem Soc Trans 2017 Dec 17;45(6):1313-1321. Epub 2017 Nov 17.

Department of Molecular Biosciences and the Institute for Cellular & Molecular Biology, University of Texas at Austin, Austin, TX 78712, U.S.A.

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http://dx.doi.org/10.1042/BST20170095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960804PMC
December 2017

The DEAD-Box Protein CYT-19 Uses Arginine Residues in Its C-Tail To Tether RNA Substrates.

Biochemistry 2017 07 7;56(28):3571-3578. Epub 2017 Jul 7.

Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States.

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http://pubs.acs.org/doi/10.1021/acs.biochem.7b00362
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http://dx.doi.org/10.1021/acs.biochem.7b00362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960805PMC
July 2017

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.

J Mol Biol 2016 10 22;428(20):3972-3985. Epub 2016 Jul 22.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048535PMC
http://dx.doi.org/10.1016/j.jmb.2016.07.013DOI Listing
October 2016

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Nat Commun 2016 06 13;7:ncomms11768. Epub 2016 Jun 13.

Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1038/ncomms11768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909931PMC
June 2016

Key points to consider when studying RNA remodeling by proteins.

Methods Mol Biol 2015 ;1259:1-16

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 105 E, 24th St. Stop A5300, Austin, TX, 78712, USA.

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http://dx.doi.org/10.1007/978-1-4939-2214-7_1DOI Listing
September 2015

Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations.

J Biol Chem 2015 Sep 24;290(37):22734-46. Epub 2015 Jul 24.

From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712

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http://dx.doi.org/10.1074/jbc.M115.663930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566245PMC
September 2015

Unwinding the mechanisms of a DEAD-box RNA helicase in cancer.

Authors:
Rick Russell

J Mol Biol 2015 May 30;427(9):1797-800. Epub 2015 Mar 30.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740914PMC
May 2015

Reflections on 20 years of RNA folding, dynamics, and structure.

Authors:
Rick Russell

RNA 2015 Apr;21(4):723-4

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA

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http://dx.doi.org/10.1261/rna.050781.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371351PMC
April 2015

RNA helicase proteins as chaperones and remodelers.

Annu Rev Biochem 2014 12;83:697-725. Epub 2014 Mar 12.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712; email: ,

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http://dx.doi.org/10.1146/annurev-biochem-060713-035546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143424PMC
January 2015

DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture.

PLoS Biol 2014 Oct 28;12(10):e1001981. Epub 2014 Oct 28.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211656PMC
October 2014

DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA.

Proc Natl Acad Sci U S A 2014 Jul 7;111(29):E2928-36. Epub 2014 Jul 7.

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; and

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http://dx.doi.org/10.1073/pnas.1404307111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115517PMC
July 2014

Chance, destiny, and the inner workings of ClpXP.

Cell 2014 Jul;158(3):479-80

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945115PMC
July 2014

Folding pathways of the Tetrahymena ribozyme.

J Mol Biol 2014 Jun 18;426(12):2300-12. Epub 2014 Apr 18.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177526PMC
June 2014

RNA catalytic activity as a probe of chaperone-mediated RNA folding.

Methods Mol Biol 2014 ;1086:225-37

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.1007/978-1-62703-667-2_13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5301988PMC
May 2014

Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET and single molecule TPM.

J Mol Biol 2014 Feb 25;426(4):793-815. Epub 2013 Nov 25.

Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2013.11.017DOI Listing
February 2014

Predicting RNA structure by multiple template homology modeling.

Pac Symp Biocomput 2010 :216-27

Bioengineering Department, Stanford University, Clark Center S231, 318 Campus Drive, Stanford, California 94305-5444, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872935PMC
http://dx.doi.org/10.1142/9789814295291_0024DOI Listing
November 2013

Visualization of local DNA unwinding by Mre11/Rad50/Nbs1 using single-molecule FRET.

Proc Natl Acad Sci U S A 2013 Nov 4;110(47):18868-73. Epub 2013 Nov 4.

Department of Chemistry and Biochemistry, Department of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, and Howard Hughes Medical Institute, University of Texas, Austin, TX 78712.

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http://dx.doi.org/10.1073/pnas.1309816110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839711PMC
November 2013

Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.

Proc Natl Acad Sci U S A 2013 Oct 16;110(40):E3800-9. Epub 2013 Sep 16.

Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Chemistry, University of Texas at Austin, Austin, TX 78712.

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http://dx.doi.org/10.1073/pnas.1315742110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791771PMC
October 2013

The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.

J Mol Biol 2013 Aug 20;425(15):2670-86. Epub 2013 May 20.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706569PMC
August 2013

A dual-mode single-molecule fluorescence assay for the detection of expanded CGG repeats in Fragile X syndrome.

Mol Biotechnol 2013 Jan;53(1):19-28

Department of Chemistry and Biochemistry and the Institute for Cellular and Molecular Biology, The University of Texas, 1 University Station A4800, Austin, TX 78712, USA.

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http://dx.doi.org/10.1007/s12033-012-9505-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398218PMC
January 2013

Toward a molecular understanding of RNA remodeling by DEAD-box proteins.

RNA Biol 2013 Jan 20;10(1):44-55. Epub 2012 Sep 20.

Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.4161/rna.22210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590237PMC
January 2013

Zeptomole detection of DNA nanoparticles by single-molecule fluorescence with magnetic field-directed localization.

Anal Biochem 2012 Dec 26;431(1):40-7. Epub 2012 Aug 26.

Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000326971200424
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http://dx.doi.org/10.1016/j.ab.2012.08.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478425PMC
December 2012

RNA catalysis as a probe for chaperone activity of DEAD-box helicases.

Methods Enzymol 2012 ;511:111-30

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1016/B978-0-12-396546-2.00005-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399669PMC
October 2012

DEAD-box proteins as RNA helicases and chaperones.

Wiley Interdiscip Rev RNA 2011 Jan-Feb;2(1):135-52

Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.1002/wrna.50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032546PMC
March 2012

The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins.

J Biol Chem 2011 Oct 30;286(43):37304-12. Epub 2011 Aug 30.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://www.jbc.org/content/early/2011/08/30/jbc.M111.287706.
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http://www.jbc.org/cgi/doi/10.1074/jbc.M111.287706
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http://dx.doi.org/10.1074/jbc.M111.287706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199477PMC
October 2011

ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo.

J Mol Biol 2011 Aug 7;411(3):661-79. Epub 2011 Jun 7.

Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.jmb.2011.05.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146569PMC
August 2011

Roles of DEAD-box proteins in RNA and RNP Folding.

RNA Biol 2010 Nov-Dec;7(6):667-76. Epub 2010 Nov 1.

Department of Chemistry and Biochemistry, University of Texas, Austin, TX, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073326PMC
http://dx.doi.org/10.4161/rna.7.6.13571DOI Listing
July 2011

Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail.

Proc Natl Acad Sci U S A 2011 Jul 11;108(30):12254-9. Epub 2011 Jul 11.

Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1073/pnas.1109566108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145681PMC
July 2011

Enhanced specificity against misfolding in a thermostable mutant of the Tetrahymena ribozyme.

Biochemistry 2011 Feb 11;50(5):864-74. Epub 2011 Jan 11.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States.

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http://dx.doi.org/10.1021/bi101467qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227551PMC
February 2011

Catalytic activity as a probe of native RNA folding.

Methods Enzymol 2009 17;468:195-218. Epub 2009 Nov 17.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texasat Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1016/S0076-6879(09)68010-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957300PMC
January 2011

Multiple unfolding events during native folding of the Tetrahymena group I ribozyme.

J Mol Biol 2010 Jul 10;400(5):1067-77. Epub 2010 Jun 10.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905490PMC
July 2010

Protein roles in group I intron RNA folding: the tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics.

J Mol Biol 2010 Jan 11;395(3):656-70. Epub 2009 Nov 11.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.jmb.2009.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813312PMC
January 2010

Mapping of the functional boundaries and secondary structure of the mouse mammary tumor virus Rem-responsive element.

J Biol Chem 2009 Sep 24;284(38):25642-52. Epub 2009 Jul 24.

Section of Molecular Genetics and Microbiology, The University of Texas, Austin, Texas 78712-0162, USA.

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http://dx.doi.org/10.1074/jbc.M109.012476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757966PMC
September 2009

DEAD-box proteins can completely separate an RNA duplex using a single ATP.

Proc Natl Acad Sci U S A 2008 Dec 16;105(51):20203-8. Epub 2008 Dec 16.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1073/pnas.0811075106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629298PMC
December 2008

DMS footprinting of structured RNAs and RNA-protein complexes.

Nat Protoc 2007 ;2(10):2608-23

Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1038/nprot.2007.380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701642PMC
January 2008

RNA misfolding and the action of chaperones.

Authors:
Rick Russell

Front Biosci 2008 Jan 1;13:1-20. Epub 2008 Jan 1.

Department of Chemistry and Biochemistry, The Institute For Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610265PMC
http://dx.doi.org/10.2741/2557DOI Listing
January 2008

Do DEAD-box proteins promote group II intron splicing without unwinding RNA?

Mol Cell 2007 Oct;28(1):159-66

Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.molcel.2007.07.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2062517PMC
October 2007

Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone.

Nature 2007 Oct;449(7165):1014-8

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1038/nature06235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581903PMC
October 2007

Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme.

Biochemistry 2007 May 10;46(17):4951-61. Epub 2007 Apr 10.

Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1021/bi0620149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582984PMC
May 2007

Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA.

Biochemistry 2007 Mar 21;46(11):3013-22. Epub 2007 Feb 21.

Department of Chemistry and Biochemistry, and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1021/bi0619472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2271177PMC
March 2007

Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone.

Proc Natl Acad Sci U S A 2006 Nov 30;103(45):16698-703. Epub 2006 Oct 30.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.

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http://www.pnas.org/content/103/45/16698.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.0603127103
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http://dx.doi.org/10.1073/pnas.0603127103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636518PMC
November 2006

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.

J Mol Biol 2006 Oct 15;363(2):531-44. Epub 2006 Aug 15.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360601038
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http://dx.doi.org/10.1016/j.jmb.2006.08.024DOI Listing
October 2006

The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.

J Mol Biol 2006 Jul 16;360(5):978-88. Epub 2006 Jun 16.

The Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360600683
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http://dx.doi.org/10.1016/j.jmb.2006.05.066DOI Listing
July 2006

Structural specificity conferred by a group I RNA peripheral element.

Proc Natl Acad Sci U S A 2005 Jul 11;102(29):10176-81. Epub 2005 Jul 11.

Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1073/pnas.0501498102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177367PMC
July 2005

Rapid compaction during RNA folding.

Proc Natl Acad Sci U S A 2002 Apr;99(7):4266-71

Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.072589599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123637PMC
April 2002

Exploring the folding landscape of a structured RNA.

Proc Natl Acad Sci U S A 2002 Jan 26;99(1):155-60. Epub 2001 Dec 26.

Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.221593598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117531PMC
January 2002