All Publications

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function

Dan Herschlag, Benjamin E Allred, Seshadri Gowrishankar

Curr Opin Struct Biol. 2015 Mar 2;30:125-133. doi: 10.1016/j.sbi.2015.02.006

DOI:

10.1016/j.sbi.2015.02.006

Quantifying Nucleic Acid Ensembles with X-ray Interferometry

Xuesong Shi, Steve Bonilla, Daniel Herschlag and Pehr Harbury

Methods in Enzymology

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

Anthony Mustoe, Charles L Brooks 3rd, Hashim Al Hashimi

Nucleic Acids Res. 2014 Sep 12. pii: gku807

DOI:

10.1093/nar/gku807

Observation of correlated X-ray scattering at atomic resolution

Derek Mendez, Thomas J. Lane, Jongmin Sung, Jonas Sellberg, Clément Levard, Herschel Watkins, Aina E. Cohen, Michael Soltis, Shirley Sutton, James Spudich, Vijay Pande, Daniel Ratner, Sebastian Doniach

Philos Trans R Soc Lond B Biol Sci. 2014 Jul 17;369(1647):20130315

DOI:

10.1098/rstb.2013.0315

An RNA tertiary switch by modifying how helices are tethered

Laura Ganser, Anthony Mustoe, Hashim Al Hashimi

Genome Biology 15:425

DOI:

10.1186/s13059-014-0425-z

Structural dynamics of a single-stranded RNA-helix junction using NMR

Catherine D. Eichhorn, Hashim Al Hashimi

RNA. 2014 Jun;20(6):782-91

DOI:

10.1261/rna.043711.113

Hierarchy of RNA Functional Dynamics

Anthony Mustoe, Charles L Brooks 3rd, Hashim Al Hashimi

Ann Rev Biochem Vol. 83: 441-466 2014

DOI:

10.1146/annurev-biochem-060713-035524

Measuring similarity between dynamic ensembles of biomolecules

Shan Yang, Loic Salmon, Hashim Al Hashimi

Nat Methods. 2014 May;11(5):552-4.

DOI:

10.1038/nmeth.2921

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

Kyle A. Beauchamp, Vijay S. Pande, Rhiju Das

Biophys J. 2014 Mar 18;106(6):1381-90

DOI:

10.1016/j.bpj.2014.02.009

Understanding nucleic acid-ion interactions

Jan Lipfert, Sebastian Doniach, Rhiju Das, Dan Herschlag

Annu Rev Biochem. 2014;83:813-41

DOI:

10.1146/annurev-biochem-060409-092720

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

Anthony Mustoe, Hashim Al Hashimi, Charles L Brooks 3rd

J Phys Chem B. 2014 Mar 13

DOI:

10.1021/jp411478x

A Single-Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme

Phuong Nguyen, Xuesong Shi, Snorri Th. Sigurdsson, Dan Herschlag, Peter Z. Qin

Chembiochem. 2013 Sep 23;14(14):1720-3

DOI:

10.1002/cbic.201300376

All Publications

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

DOI:

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

DOI:

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function

DOI:

Multiscale methods for computational RNA enzymology

DOI:

Quantifying Nucleic Acid Ensembles with X-ray Interferometry

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

DOI:

Observation of correlated X-ray scattering at atomic resolution

DOI:

An RNA tertiary switch by modifying how helices are tethered

DOI:

Structural dynamics of a single-stranded RNA-helix junction using NMR

DOI:

Hierarchy of RNA Functional Dynamics

DOI:

Measuring similarity between dynamic ensembles of biomolecules

DOI:

From a Structural Average to the Conformational Ensemble of a DNA Bulge

DOI:

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

DOI:

Understanding nucleic acid-ion interactions

DOI:

Ion counting from explicit solvent simulations and 3D-RISM

DOI:

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

DOI:

A Single-Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme

DOI:

Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations

DOI:

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All Publications

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

DOI:

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

DOI:

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function

DOI:

Multiscale methods for computational RNA enzymology

DOI:

Quantifying Nucleic Acid Ensembles with X-ray Interferometry

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

DOI:

Observation of correlated X-ray scattering at atomic resolution

DOI:

An RNA tertiary switch by modifying how helices are tethered

DOI:

Structural dynamics of a single-stranded RNA-helix junction using NMR

DOI:

Hierarchy of RNA Functional Dynamics

DOI:

Measuring similarity between dynamic ensembles of biomolecules

DOI:

From a Structural Average to the Conformational Ensemble of a DNA Bulge

DOI:

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

DOI:

Understanding nucleic acid-ion interactions

DOI:

Ion counting from explicit solvent simulations and 3D-RISM

DOI:

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

DOI:

A Single-Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme

DOI:

Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations

DOI: