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Daniel Herschlag

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TOP 3
Xuesong Shi; Daniel Herschlag; Pehr A B Harbury
Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations.
Eliza A Ruben; Jason P Schwans; Matthew Sonnett; Yingssu Tsai; Ana Gonzalez; Aditya Natarajan; Daniel Herschlag
Ground state destabilization from a positioned general base in the ketosteroid isomerase active site.
Adelene Y L Sim; Daniel Herschlag; Jan Lipfert; Sebastian Doniach
Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.

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All Publications

2013: Xuesong Shi; Daniel Herschlag; Pehr A B Harbury
Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(16):E1444-51.
2013: Eliza A Ruben; Jason P Schwans; Matthew Sonnett; Yingssu Tsai; Ana Gonzalez; Aditya Natarajan; Daniel Herschlag
Ground state destabilization from a positioned general base in the ketosteroid isomerase active site.
Biochemistry 2013;52(6):1074-81.
2012: Adelene Y L Sim; Daniel Herschlag; Jan Lipfert; Sebastian Doniach
Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.
Physical review. E, Statistical, nonlinear, and soft matter physics 2012;86(2 Pt 1):021901.
2012: Marcello Forconi; Kristin Rule Gleitsman; Clyde Metz; Eliza Ruben; Tara Benz-Moy; Daniel Herschlag
Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study.
RNA (New York, N.Y.) 2012;18(6):1222-9.
2012: John K Frederiksen; Daniel Herschlag; Nan-Sheng Li; Rhiju Das; Joseph A Piccirilli
Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.
RNA (New York, N.Y.) 2012;18(6):1123-41.
2012: Eric A Althoff; Lars Giger; Sanjay Hari; Daniel Herschlag; Donald Hilvert; Lin Jiang; Peter Kast; Jonathan K Lassila; Matthew Smith; Ling Wang; Zhizhi Wang; David Baker
Robust design and optimization of retroaldol enzymes.
Protein science : a publication of the Protein Society 2012;21(5):717-26.
2012: Peter C Anthony; Steven M Block; Vincent B Chu; Sebastian Doniach; Adelene Y L Sim; Daniel Herschlag
Electrostatics of nucleic acid folding under conformational constraint.
Journal of the American Chemical Society 2012;134(10):4607-14.
2012: Raghuvir N Sengupta; Daniel Herschlag; Joseph A Piccirilli
Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site.
ACS chemical biology 2012;7(2):294-9.
2012: Aaron T Fafarman; Timothy D Fenn; Daniel Herschlag; Jason P Schwans; Paul A Sigala; Steven G Boxer
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(6):E299-308.
2012: Xuesong Shi; Sergey V Solomatin; Daniel Herschlag
A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme.
Journal of the American Chemical Society 2012;134(4):1910-3.
2012: Max Greenfeld; Hideo Mabuchi; Dmitri S Pavlichin; Daniel Herschlag
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data.
PloS one 2012;7(2):e30024.
2011: Tara L Benz-Moy; Daniel Herschlag
Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles.
Biochemistry 2011;50(40):8733-55.
2011: Marcello Forconi; Joseph A Piccirilli; Rishi H Porecha; Jason P Schwans; Raghuvir N Sengupta; Daniel Herschlag
2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA.
Chemistry & biology 2011;18(8):949-54.
2011: Logan D Andrews; Hua Deng; Daniel Herschlag
Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization.
Journal of the American Chemical Society 2011;133(30):11621-31.
2011: Jonathan K Lassila; Jesse G Zalatan; Daniel Herschlag
Biological phosphoryl-transfer reactions: understanding mechanism and catalysis.
Annual review of biochemistry 2011;80():669-702.
2011: Max Greenfeld; Sergey V Solomatin; Daniel Herschlag
Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA.
The Journal of biological chemistry 2011;286(22):19872-9.
2011: Sergey V Solomatin; Max Greenfeld; Daniel Herschlag
Implications of molecular heterogeneity for the cooperativity of biological macromolecules.
Nature structural & molecular biology 2011;18(6):732-4.
2011: Marcello Forconi; Rishi H Porecha; Joseph A Piccirilli; Daniel Herschlag
Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme.
Journal of the American Chemical Society 2011;133(20):7791-800.
2011: Daniel P Riordan; Daniel Herschlag; Patrick O Brown
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.
Nucleic acids research 2011;39(4):1501-9.
2010: Philip Hanoian; Paul A Sigala; Daniel Herschlag; Sharon Hammes-Schiffer
Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling.
Biochemistry 2010;49(48):10339-48.
2010: Aaron T Fafarman; Paul A Sigala; Daniel Herschlag; Steven G Boxer
Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects.
Journal of the American Chemical Society 2010;132(37):12811-3.
2010: Yaqi Wan; Hyejean Suh; Rick Russell; Daniel Herschlag
Multiple unfolding events during native folding of the Tetrahymena group I ribozyme.
Journal of molecular biology 2010;400(5):1067-77.
2010: Jan Lipfert; Adelene Y L Sim; Daniel Herschlag; Sebastian Doniach
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding.
RNA (New York, N.Y.) 2010;16(4):708-19.
2010: Marcello Forconi; Raghuvir N Sengupta; Joseph A Piccirilli; Daniel Herschlag
A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site.
Biochemistry 2010;49(12):2753-62.
2010: Jonathan Kyle Lassila; David Baker; Daniel Herschlag
Origins of catalysis by computationally designed retroaldolase enzymes.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(11):4937-42.
2010: Mona Ali; Jan Lipfert; Soenke Seifert; Daniel Herschlag; Sebastian Doniach
The ligand-free state of the TPP riboswitch: a partially folded RNA structure.
Journal of molecular biology 2010;396(1):153-65.
2010: Sergey V Solomatin; Max Greenfeld; Steven Chu; Daniel Herschlag
Multiple native states reveal persistent ruggedness of an RNA folding landscape.
Nature 2010;463(7281):681-4.
2010: Daniel A. Kraut; Paul A Sigala; Timothy D Fenn; Daniel Herschlag
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(5):1960-5.
2010: Max Greenfeld; Daniel Herschlag
Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer.
Methods in enzymology 2010;472():205-20.
2009: Vincent B Chu; Jan Lipfert; Yu Bai; Vijay S Pande; Sebastian Doniach; Daniel Herschlag
Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
RNA (New York, N.Y.) 2009;15(12):2195-205.
2009: David G Hendrickson; Daniel J Hogan; Heather L McCullough; Jason W Myers; Daniel Herschlag; James E Ferrell; Patrick O Brown
Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.
PLoS biology 2009;7(11):e1000238.
2009: Jason P Schwans; Daniel A. Kraut; Daniel Herschlag
Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(34):14271-5.
2009: Jesse G Zalatan; Daniel Herschlag
The far reaches of enzymology.
Nature chemical biology 2009;5(8):516-20.
2009: Paul A Sigala; Jose M M Caaveiro; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Hydrogen bond coupling in the ketosteroid isomerase active site.
Biochemistry 2009;48(29):6932-9.
2009: Xuesong Shi; Emilia T Mollova; Goran Pljevaljcić; David P Millar; Daniel Herschlag
Probing the dynamics of the P1 helix within the Tetrahymena group I intron.
Journal of the American Chemical Society 2009;131(27):9571-8.
2009: Paul A Sigala; Mark Tsuchida; Daniel Herschlag
Hydrogen bond dynamics in the active site of photoactive yellow protein.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(23):9232-7.
2009: Daniel A. Kraut; Michael J Churchill; Phillip E Dawson; Daniel Herschlag
Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis.
ACS chemical biology 2009;4(4):269-73.
2009: Gian Paola G Grant; Nathan Boyd; Daniel Herschlag; Peter Z Qin
Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling.
Journal of the American Chemical Society 2009;131(9):3136-7.
2009: Magdalena A Jonikas; Randall J Radmer; Alain Laederach; Rhiju Das; Samuel Pearlman; Daniel Herschlag; Russ B Altman
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.
RNA (New York, N.Y.) 2009;15(2):189-99.
2009: Max Greenfeld; Daniel Herschlag
Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy.
Methods in enzymology 2009;469():375-89.
2009: Xuesong Shi; Daniel Herschlag
Fluorescence polarization anisotropy to measure RNA dynamics.
Methods in enzymology 2009;469():287-302.
2009: Sergey Solomatin; Daniel Herschlag
Methods of site-specific labeling of RNA with fluorescent dyes.
Methods in enzymology 2009;469():47-68.
2009: Marcello Forconi; Daniel Herschlag
Use of phosphorothioates to identify sites of metal-ion binding in RNA.
Methods in enzymology 2009;468():311-33.
2009: Marcello Forconi; Daniel Herschlag
Metal ion-based RNA cleavage as a structural probe.
Methods in enzymology 2009;468():91-106.
2009: Marcello Forconi; Raghuvir N Sengupta; Mao-Chin Liu; Alan C Sartorelli; Joseph A Piccirilli; Daniel Herschlag
Structure and function converge to identify a hydrogen bond in a group I ribozyme active site.
Angewandte Chemie (International ed. in English) 2009;48(39):7171-5.
2009: Jan Lipfert; Daniel Herschlag; Sebastian Doniach
Riboswitch conformations revealed by small-angle X-ray scattering.
Methods in molecular biology (Clifton, N.J.) 2009;540():141-59.
2008: Jesse G Zalatan; Timothy D Fenn; Daniel Herschlag
Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion.
Journal of molecular biology 2008;384(5):1174-89.
2008: Jonathan K Lassila; Daniel Herschlag
Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily.
Biochemistry 2008;47(48):12853-9.
2008: Daniel J Hogan; Daniel P Riordan; André P Gerber; Daniel Herschlag; Patrick O Brown
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.
PLoS biology 2008;6(10):e255.
2008: Paul A Sigala; Daniel A. Kraut; Jose M M Caaveiro; Brandon Pybus; Eliza A Ruben; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
Journal of the American Chemical Society 2008;130(41):13696-708.
2008: Yu Bai; Vincent B Chu; Jan Lipfert; Vijay S Pande; Daniel Herschlag; Sebastian Doniach
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble.
Journal of the American Chemical Society 2008;130(37):12334-41.
2008: Patrick O'Brien; Jonathan Kyle Lassila; Timothy D Fenn; Jesse G Zalatan; Daniel Herschlag
Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase.
Biochemistry 2008;47(29):7663-72.
2008: Marcello Forconi; Jihee Lee; Jungjoon K Lee; Joseph A Piccirilli; Daniel Herschlag
Functional identification of ligands for a catalytic metal ion in group I introns.
Biochemistry 2008;47(26):6883-94.
2008: Felix Mueller-Planitz; Daniel Herschlag
Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism.
The Journal of biological chemistry 2008;283(25):17463-76.
2008: Vincent B Chu; Daniel Herschlag
Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs.
Current opinion in structural biology 2008;18(3):305-14.
2008: Bernie D Sattin; Wei Zhao; Kevin J Travers; Steven Chu; Daniel Herschlag
Direct measurement of tertiary contact cooperativity in RNA folding.
Journal of the American Chemical Society 2008;130(19):6085-7.
2008: Rhiju Das; Madhuri Kudaravalli; Magdalena Jonikas; Alain Laederach; Robert Fong; Jason P Schwans; David Baker; Joseph A Piccirilli; Russ B Altman; Daniel Herschlag
Structural inference of native and partially folded RNA by high-throughput contact mapping.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(11):4144-9.
2008: Alain Laederach; Rhiju Das; Quentin Vicens; Samuel M Pearlman; Michael Brenowitz; Daniel Herschlag; Russ B Altman
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments.
Nature protocols 2008;3(9):1395-401.
2008: David G Hendrickson; Daniel J Hogan; Daniel Herschlag; James E Ferrell; Patrick O Brown
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.
PloS one 2008;3(5):e2126.
2007: Yu Bai; Max Greenfeld; Kevin J Travers; Vincent B Chu; Jan Lipfert; Sebastian Doniach; Daniel Herschlag
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.
Journal of the American Chemical Society 2007;129(48):14981-8.
2007: Vincent B Chu; Yu Bai; Jan Lipfert; Daniel Herschlag; Sebastian Doniach
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory.
Biophysical journal 2007;93(9):3202-9.
2007: Paul A Sigala; Aaron T Fafarman; Patrick E Bogard; Steven G Boxer; Daniel Herschlag
Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?
Journal of the American Chemical Society 2007;129(40):12104-5.
2007: Marcello Forconi; Joseph A Piccirilli; Daniel Herschlag
Modulation of individual steps in group I intron catalysis by a peripheral metal ion.
RNA (New York, N.Y.) 2007;13(10):1656-67.
2007: Jesse G Zalatan; Irina Catrina; Rebecca Mitchell; Piotr K Grzyska; Patrick O'Brien; Daniel Herschlag; Alvan C Hengge
Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis.
Journal of the American Chemical Society 2007;129(31):9789-98.
2007: Kevin J Travers; Nathan Boyd; Daniel Herschlag
Low specificity of metal ion binding in the metal ion core of a folded RNA.
RNA (New York, N.Y.) 2007;13(8):1205-13.
2007: Irina Catrina; Patrick O'Brien; Jamie Purcell; Ivana Nikolic-Hughes; Jesse G Zalatan; Alvan C Hengge; Daniel Herschlag
Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction.
Journal of the American Chemical Society 2007;129(17):5760-5.
2007: Tae-Hee Lee; Lisa J Lapidus; Wei Zhao; Kevin J Travers; Daniel Herschlag; Steven Chu
Measuring the folding transition time of single RNA molecules.
Biophysical journal 2007;92(9):3275-83.
2007: Katrin Karbstein; Jihee Lee; Daniel Herschlag
Probing the role of a secondary structure element at the 5'- and 3'-splice sites in group I intron self-splicing: the tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing.
Biochemistry 2007;46(16):4861-75.
2007: Jan Lipfert; Rhiju Das; Vincent B Chu; Madhuri Kudaravalli; Nathan Boyd; Daniel Herschlag; Sebastian Doniach
Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.
Journal of molecular biology 2007;365(5):1393-406.
2007: Felix Mueller-Planitz; Daniel Herschlag
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity.
Nucleic acids research 2007;35(11):3764-73.
2006: Michael T Woodside; Peter C Anthony; William M Behnke-Parks; Kevan Larizadeh; Daniel Herschlag; Steven M Block
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.
Science (New York, N.Y.) 2006;314(5801):1001-4.
2006: Rick Russell; Rhiju Das; Hyejean Suh; Kevin J Travers; Alain Laederach; Mark A Engelhardt; Daniel Herschlag
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.
Journal of molecular biology 2006;363(2):531-44.
2006: Felix Mueller-Planitz; Daniel Herschlag
Interdomain communication in DNA topoisomerase II. DNA binding and enzyme activation.
The Journal of biological chemistry 2006;281(33):23395-404.
2006: Jesse G Zalatan; Timothy D Fenn; Axel T Brunger; Daniel Herschlag
Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution.
Biochemistry 2006;45(32):9788-803.
2006: Michael T Woodside; William M Behnke-Parks; Kevan Larizadeh; Kevin Travers; Daniel Herschlag; Steven M Block
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(16):6190-5.
2006: Daniel A. Kraut; Paul A Sigala; Brandon Pybus; Corey W Liu; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.
PLoS biology 2006;4(4):e99.
2006: André P Gerber; Stefan Luschnig; Mark A Krasnow; Patrick O Brown; Daniel Herschlag
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(12):4487-92.
2006: Jesse G Zalatan; Daniel Herschlag
Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.
Journal of the American Chemical Society 2006;128(4):1293-303.
2005: James Hougland; Alexander V Kravchuk; Daniel Herschlag; Joseph A Piccirilli
Functional identification of catalytic metal ion binding sites within RNA.
PLoS biology 2005;3(9):e277.
2005: Travis H Johnson; Pilar Tijerina; Amanda B Chadee; Daniel Herschlag; Rick Russell
Structural specificity conferred by a group I RNA peripheral element.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(29):10176-81.
2005: Ivana Nikolic-Hughes; Patrick O'Brien; Daniel Herschlag
Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions.
Journal of the American Chemical Society 2005;127(26):9314-5.
2005: Rhiju Das; Kevin J Travers; Yu Bai; Daniel Herschlag
Determining the Mg2+ stoichiometry for folding an RNA metal ion core.
Journal of the American Chemical Society 2005;127(23):8272-3.
2005: Marcello Forconi; Daniel Herschlag
Promiscuous catalysis by the tetrahymena group I ribozyme.
Journal of the American Chemical Society 2005;127(17):6160-1.
2005: Rhiju Das; Alain Laederach; Samuel M Pearlman; Daniel Herschlag; Russ B Altman
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.
RNA (New York, N.Y.) 2005;11(3):344-54.
2005: Yu Bai; Rhiju Das; Ian S Millett; Daniel Herschlag; Sebastian Doniach
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(4):1035-40.
2005: Yoav Arava; F Edward Boas; Patrick O Brown; Daniel Herschlag
Dissecting eukaryotic translation and its control by ribosome density mapping.
Nucleic acids research 2005;33(8):2421-32.
2004: Kurt Andresen; Rhiju Das; Hye Yoon Park; H Smith; Lisa W Kwok; Jessica S Lamb; Earl J Kirkland; Daniel Herschlag; K D Finkelstein; Lois Pollack
Spatial distribution of competing ions around DNA in solution.
Physical review letters 2004;93(24):248103.
2004: Keiji Takamoto; Rhiju Das; Qin He; Sebastian Doniach; Michael Brenowitz; Daniel Herschlag; Mark R Chance
Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.
Journal of molecular biology 2004;343(5):1195-206.
2004: Katrin Karbstein; Joseph K.-H. Tang; Daniel Herschlag
A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect.
RNA (New York, N.Y.) 2004;10(11):1730-9.
2004: Ivana Nikolic-Hughes; Douglas C Rees; Daniel Herschlag
Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?
Journal of the American Chemical Society 2004;126(38):11814-9.
2004: André P Gerber; Daniel Herschlag; Patrick O Brown
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
PLoS biology 2004;2(3):E79.
2003: Matthew L Peck; Daniel Herschlag
Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A.
RNA (New York, N.Y.) 2003;9(10):1180-7.
2003: Kelly A Shepard; André P Gerber; Ashwini Jambhekar; Peter A Takizawa; Patrick O Brown; Daniel Herschlag; Joe L DeRisi; Ronald D Vale
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11429-34.
2003: Rhiju Das; Lisa W Kwok; Ian S Millett; Yu Bai; Thalia T Mills; Jaby Jacob; Gregory S Maskel; Soenke Seifert; Simon G J Mochrie; Pappannan Thiyagarajan; Sebastian Doniach; Lois Pollack; Daniel Herschlag
The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme.
Journal of molecular biology 2003;332(2):311-9.
2003: Laura E Bartley; Xiaowei Zhuang; Rhiju Das; Steven Chu; Daniel Herschlag
Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.
Journal of molecular biology 2003;328(5):1011-26.
2003: Rhiju Das; Thalia T Mills; Lisa W Kwok; G S Maskel; Ian S Millett; Sebastian Doniach; K D Finkelstein; Daniel Herschlag; Lois Pollack
Counterion distribution around DNA probed by solution X-ray scattering.
Physical review letters 2003;90(18):188103.
2003: Yoav Arava; Yulei Wang; John D Storey; Chih Long Liu; Patrick O Brown; Daniel Herschlag
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):3889-94.
2003: Katrin Karbstein; Daniel Herschlag
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(5):2300-5.
2003: Daniel A. Kraut; Kate S Carroll; Daniel Herschlag
Challenges in enzyme mechanism and energetics.
Annual review of biochemistry 2003;72():517-71.
2002: Hu Cheng; Ivana Nikolic-Hughes; Jianghua H Wang; Hua Deng; Patrick O'Brien; Li Wu; Zhong-Yin Zhang; Daniel Herschlag; Robert Callender
Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis.
Journal of the American Chemical Society 2002;124(38):11295-306.
2002: Katrin Karbstein; Kate S Carroll; Daniel Herschlag
Probing the Tetrahymena group I ribozyme reaction in both directions.
Biochemistry 2002;41(37):11171-83.
2002: Shu-ou Shan; Daniel Herschlag
Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis.
RNA (New York, N.Y.) 2002;8(7):861-72.
2002: Yulei Wang; Chih Long Liu; John D Storey; Robert Tibshirani; Daniel Herschlag; Patrick O Brown
Precision and functional specificity in mRNA decay.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5860-5.
2002: Eric J Sorin; Mark A Engelhardt; Daniel Herschlag; Vijay S Pande
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop.
Journal of molecular biology 2002;317(4):493-506.
2002: Rick Russell; Ian S Millett; Mark W Tate; Lisa W Kwok; Bradley Nakatani; Sol M Gruner; Simon G J Mochrie; Vijay Pande; Sebastian Doniach; Daniel Herschlag; Lois Pollack
Rapid compaction during RNA folding.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4266-71.
2002: Patrick O'Brien; Daniel Herschlag
Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.
Biochemistry 2002;41(9):3207-25.
2002: Rick Russell; Xiaowei Zhuang; Hazen P Babcock; Ian S Millett; Sebastian Doniach; Steven Chu; Daniel Herschlag
Exploring the folding landscape of a structured RNA.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(1):155-60.
2001: Paul Peluso; Shu-ou Shan; Steffen Nock; Daniel Herschlag; Peter Walter
Role of SRP RNA in the GTPase cycles of Ffh and FtsY.
Biochemistry 2001;40(50):15224-33.
2001: Rick Russell; Daniel Herschlag
Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway.
Journal of molecular biology 2001;308(5):839-51.
2001: Patrick O'Brien; Daniel Herschlag
Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase.
Biochemistry 2001;40(19):5691-9.
2001: S o Shan; A V Kravchuk; Joseph A Piccirilli; Daniel Herschlag
Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction.
Biochemistry 2001;40(17):5161-71.
2001: Jessica O'Rear; Shuying Wang; Andrew L Feig; Leonid Beigelman; Olke C Uhlenbeck; Daniel Herschlag
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.
RNA (New York, N.Y.) 2001;7(4):537-45.
2001: SJ Admiraal; P Meyer; B Schneider; Dominique Deville-Bonne; Joël Janin; Daniel Herschlag
Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis.
Biochemistry 2001;40(2):403-13.
2000: Xiaowei Zhuang; Laura E Bartley; Hazen P Babcock; Rick Russell; Taekjip Ha; Daniel Herschlag; Steven Chu
A single-molecule study of RNA catalysis and folding.
Science (New York, N.Y.) 2000;288(5473):2048-51.
2000: Paul Peluso; Daniel Herschlag; Steffen Nock; Douglas Freymann; A E Johnson; Peter Walter
Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor.
Science (New York, N.Y.) 2000;288(5471):1640-3.
2000: Shu-ou Shan; Daniel Herschlag
An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction.
RNA (New York, N.Y.) 2000;6(6):795-813.
2000: GJ Narlikar; Laura E Bartley; Daniel Herschlag
Use of duplex rigidity for stability and specificity in RNA tertiary structure.
Biochemistry 2000;39(20):6183-9.
2000: Rick Russell; Ian S Millett; Sebastian Doniach; Daniel Herschlag
Small angle X-ray scattering reveals a compact intermediate in RNA folding.
Nature structural biology 2000;7(5):367-70.
2000: M A Engelhardt; E A Doherty; D S Knitt; Jennifer A Doudna; Daniel Herschlag
The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis.
Biochemistry 2000;39(10):2639-51.
2000: A Yoshida; S o Shan; Daniel Herschlag; Joseph A Piccirilli
The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction.
Chemistry & biology 2000;7(2):85-96.
1999: Jon R Lorsch; Daniel Herschlag
Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro.
The EMBO journal 1999;18(23):6705-17.
1999: Shuying Wang; Katrin Karbstein; A Peracchi; Leonid Beigelman; Daniel Herschlag
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.
Biochemistry 1999;38(43):14363-78.
1999: GJ Narlikar; Laura E Bartley; M Khosla; Daniel Herschlag
Characterization of a local folding event of the Tetrahymena group I ribozyme: effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps.
Biochemistry 1999;38(43):14192-204.
1999: S o Shan; A Yoshida; S Sun; Joseph A Piccirilli; Daniel Herschlag
Three metal ions at the active site of the Tetrahymena group I ribozyme.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(22):12299-304.
1999: Rick Russell; Daniel Herschlag
New pathways in folding of the Tetrahymena group I RNA enzyme.
Journal of molecular biology 1999;291(5):1155-67.
1999: M L Peck; Daniel Herschlag
Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity of translation initiation factor elF4A.
RNA (New York, N.Y.) 1999;5(9):1210-21.
1999: Shu-ou Shan; GJ Narlikar; Daniel Herschlag
Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme.
Biochemistry 1999;38(34):10976-88.
1999: Shu-ou Shan; Daniel Herschlag
Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2'-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme.
Biochemistry 1999;38(34):10958-75.
1999: SJ Admiraal; B Schneider; P Meyer; Joël Janin; Michel Véron; Dominique Deville-Bonne; Daniel Herschlag
Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
Biochemistry 1999;38(15):4701-11.
1999: Patrick O'Brien; Daniel Herschlag
Catalytic promiscuity and the evolution of new enzymatic activities.
Chemistry & biology 1999;6(4):R91-R105.
1999: Rick Russell; Daniel Herschlag
Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme.
RNA (New York, N.Y.) 1999;5(2):158-66.
1999: Shu-ou Shan; Daniel Herschlag
Hydrogen bonding in enzymatic catalysis: analysis of energetic contributions.
Methods in enzymology 1999;308():246-76.
1998: A Peracchi; Jasenka Matulic-Adamic; Shuying Wang; Leonid Beigelman; Daniel Herschlag
Structure-function relationships in the hammerhead ribozyme probed by base rescue.
RNA (New York, N.Y.) 1998;4(11):1332-46.
1998: A Peracchi; Alexander Karpeisky; L Maloney; Leonid Beigelman; Daniel Herschlag
A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations.
Biochemistry 1998;37(42):14765-75.
1998: GJ Narlikar; Daniel Herschlag
Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction.
Biochemistry 1998;37(28):9902-11.
1998: Jon R Lorsch; Daniel Herschlag
The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes.
Biochemistry 1998;37(8):2194-206.
1998: Jon R Lorsch; Daniel Herschlag
The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide.
Biochemistry 1998;37(8):2180-93.
1997: A Peracchi; Leonid Beigelman; E C Scott; Olke C Uhlenbeck; Daniel Herschlag
Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation.
The Journal of biological chemistry 1997;272(43):26822-6.
1997: K J Hertel; A Peracchi; Olke C Uhlenbeck; Daniel Herschlag
Use of intrinsic binding energy for catalysis by an RNA enzyme.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(16):8497-502.
1997: GJ Narlikar; M Khosla; N Usman; Daniel Herschlag
Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme.
Biochemistry 1997;36(9):2465-77.
1997: GJ Narlikar; Daniel Herschlag
Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes.
Annual review of biochemistry 1997;66():19-59.
1996: Shu-ou Shan; Daniel Herschlag
The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(25):14474-9.
1996: A Peracchi; Leonid Beigelman; N Usman; Daniel Herschlag
Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(21):11522-7.
1996: K A Maegley; S J Admiraal; Daniel Herschlag
Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(16):8160-6.
1996: GJ Narlikar; Daniel Herschlag
Isolation of a local tertiary folding transition in the context of a globally folded RNA.
Nature structural biology 1996;3(8):701-10.
1996: K J Hertel; Daniel Herschlag; Olke C Uhlenbeck
Specificity of hammerhead ribozyme cleavage.
The EMBO journal 1996;15(14):3751-7.
1996: R Mei; Daniel Herschlag
Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron: insights into catalysis and the second step of self-splicing.
Biochemistry 1996;35(18):5796-809.
1996: Shu-ou Shan; S Loh; Daniel Herschlag
The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis.
Science (New York, N.Y.) 1996;272(5258):97-101.
1996: D S Knitt; Daniel Herschlag
pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa.
Biochemistry 1996;35(5):1560-70.
1995: S J Admiraal; Daniel Herschlag
Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis.
Chemistry & biology 1995;2(11):729-39.
1995: F Hollfelder; Daniel Herschlag
The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase.
Biochemistry 1995;34(38):12255-64.
1995: Daniel Herschlag
RNA chaperones and the RNA folding problem.
The Journal of biological chemistry 1995;270(36):20871-4.
1995: GJ Narlikar; V Gopalakrishnan; T S McConnell; N Usman; Daniel Herschlag
Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(9):3668-72.
1994: D S Knitt; GJ Narlikar; Daniel Herschlag
Dissection of the role of the conserved G.U pair in group I RNA self-splicing.
Biochemistry 1994;33(46):13864-79.
1994: Daniel Herschlag; M Khosla; Z Tsuchihashi; Richard L Karpel
An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis.
The EMBO journal 1994;13(12):2913-24.
1994: Daniel Herschlag; M Khosla
Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step.
Biochemistry 1994;33(17):5291-7.
1994: K J Hertel; Daniel Herschlag; Olke C Uhlenbeck
A kinetic and thermodynamic framework for the hammerhead ribozyme reaction.
Biochemistry 1994;33(11):3374-85.
1993: Z Tsuchihashi; M Khosla; Daniel Herschlag
Protein enhancement of hammerhead ribozyme catalysis.
Science (New York, N.Y.) 1993;262(5130):99-102.
1993: T S McConnell; Thomas R Cech; Daniel Herschlag
Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(18):8362-6.
1993: Daniel Herschlag; F Eckstein; Thomas R Cech
The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction.
Biochemistry 1993;32(32):8312-21.
1993: Daniel Herschlag; F Eckstein; Thomas R Cech
Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA.
Biochemistry 1993;32(32):8299-311.
1992: P Legault; Daniel Herschlag; D W Celander; Thomas R Cech
Mutations at the guanosine-binding site of the Tetrahymena ribozyme also affect site-specific hydrolysis.
Nucleic acids research 1992;20(24):6613-9.
1992: Thomas R Cech; Daniel Herschlag; Joseph A Piccirilli; Anna Marie Pyle
RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization.
The Journal of biological chemistry 1992;267(25):17479-82.
1991: Daniel Herschlag; Joseph A Piccirilli; Thomas R Cech
Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom.
Biochemistry 1991;30(20):4844-54.
1990: Daniel Herschlag; Thomas R Cech
DNA cleavage catalysed by the ribozyme from Tetrahymena.
Nature 1990;344(6265):405-9.