Daniel Herschlag - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
ribozymes
Website:
http://cmgm.stanford.edu/biochem/herschlag/membersdanexpand.html

241 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31375637 DOI: 10.1073/pnas.1901530116  0.88
2019 Gebala M, Johnson SL, Narlikar GJ, Herschlag D. Ion counting demonstrates a high electrostatic field generated by the nucleosome. Elife. 8. PMID 31184587 DOI: 10.7554/eLife.44993  1
2019 Sengupta RN, Herschlag D. Enhancement of RNA•Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry. PMID 31117387 DOI: 10.1021/acs.biochem.9b00231  0.6
2019 Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Molecular Cell. PMID 31078383 DOI: 10.1016/j.molcel.2019.04.012  0.88
2019 Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind tests of RNA-protein binding affinity prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 30962376 DOI: 10.1073/pnas.1819047116  0.88
2019 Becker WR, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D. Demonstration of Protein Cooperativity Mediated by RNA Structure Using the Human Protein PUM2. Rna (New York, N.Y.). PMID 30914482 DOI: 10.1261/rna.068585.118  0.52
2018 Herschlag D, Bonilla S, Bisaria N. The Story of RNA Folding, as Told in Epochs. Cold Spring Harbor Perspectives in Biology. 10. PMID 30275276 DOI: 10.1101/cshperspect.a032433  0.52
2018 Pinney M, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov TI, Schwans JP, Martínez TJ, Herschlag D. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. Journal of the American Chemical Society. PMID 29990421 DOI: 10.1021/jacs.8b01596  0.72
2018 Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell. PMID 29961580 DOI: 10.1016/j.cell.2018.05.038  0.88
2018 Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X. Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Current Protocols in Nucleic Acid Chemistry. 73: e54. PMID 29927110 DOI: 10.1002/cpnc.54  0.88
2018 Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J. Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions. Science Advances. 4: eaar4418. PMID 29806025 DOI: 10.1126/sciadv.aar4418  0.88
2018 Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine p Kin the Active Site of Ketosteroid Isomerase. Biochemistry. PMID 29584413 DOI: 10.1021/acs.biochem.8b00246  0.72
2018 Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Reports. 22: 3240-3250. PMID 29562180 DOI: 10.1016/j.celrep.2018.02.101  0.88
2017 Bonilla S, Limouse C, Bisaria N, Gebala M, Mabuchi H, Herschlag D. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. Journal of the American Chemical Society. PMID 29185740 DOI: 10.1021/jacs.7b08870  0.52
2017 Gleitsman KR, Sengupta RN, Herschlag D. Slow Molecular Recognition by RNA. Rna (New York, N.Y.). PMID 28971853 DOI: 10.1261/rna.062026.117  0.6
2017 Bisaria N, Greenfeld M, Limouse C, Mabuchi H, Herschlag D. Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 28839094 DOI: 10.1073/pnas.1703507114  0.52
2017 Allred B, Gebala M, Herschlag D. Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH(+)•C Wobble Formation in Double-stranded DNA. Journal of the American Chemical Society. PMID 28489947 DOI: 10.1021/jacs.7b01830  0.44
2017 Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi H, Herschlag D. Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions. Rna (New York, N.Y.). PMID 28138061 DOI: 10.1261/rna.060053.116  0.44
2017 Bisaria N, Jarmoskaite I, Herschlag D. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Systems. 4: 21-29. PMID 28125791 DOI: 10.1016/j.cels.2016.12.010  0.52
2017 Shi X, Walker P, Harbury PB, Herschlag D. Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry. Nucleic Acids Research. PMID 28108663 DOI: 10.1093/nar/gkw1352  0.48
2017 Lamba V, Sanchez E, Fanning LR, Howe K, Gonzalez MA, Herschlag D, Forconi M. Kemp Eliminase Activity of Ketosteroid Isomerase. Biochemistry. PMID 28045505 DOI: 10.1021/acs.biochem.6b00762  0.68
2016 van Schie SN, Sengupta RN, Herschlag D. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes. Plos One. 11: e0160457. PMID 27501145 DOI: 10.1371/journal.pone.0160457  0.6
2016 Bisaria N, Greenfeld M, Limouse C, Pavlichin DS, Mabuchi H, Herschlag D. Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway. Proceedings of the National Academy of Sciences of the United States of America. PMID 27493222 DOI: 10.1073/pnas.1525082113  0.52
2016 Gebala M, Bonilla S, Bisaria N, Herschlag D. Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere? Journal of the American Chemical Society. PMID 27479701 DOI: 10.1021/jacs.6b04289  0.52
2016 Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. Journal of Molecular Biology. PMID 27452365 DOI: 10.1016/j.jmb.2016.07.013  0.52
2016 Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Correction to "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase". Journal of the American Chemical Society. PMID 27299372 DOI: 10.1021/jacs.6b04665  0.72
2016 Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nature Communications. 7: ncomms11768. PMID 27292179 DOI: 10.1038/ncomms11768  1
2016 Peck A, Sunden F, Andrews LD, Pande VS, Herschlag D. Tungstate as a transition state analog for catalysis by alkaline phosphatase. Journal of Molecular Biology. PMID 27189921 DOI: 10.1016/j.jmb.2016.05.007  1
2016 Shi X, Huang L, Lilley DM, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nature Chemical Biology. PMID 26727239 DOI: 10.1038/nchembio.1997  1
2015 Chen B, Lim S, Kannan A, Alford SC, Sunden F, Herschlag D, Dimov IK, Baer TM, Cochran JR. High-throughput analysis and protein engineering using microcapillary arrays. Nature Chemical Biology. PMID 26641932 DOI: 10.1038/nchembio.1978  1
2015 Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. Plos Biology. 13: e1002307. PMID 26587879 DOI: 10.1371/journal.pbio.1002307  1
2015 Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. Rna (New York, N.Y.). PMID 26567314 DOI: 10.1261/rna.053710.115  0.96
2015 Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. Journal of the American Chemical Society. PMID 26517731 DOI: 10.1021/jacs.5b08395  1
2015 Natarajan A, Yabukarski F, Lamba V, Schwans JP, Sunden F, Herschlag D. BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science (New York, N.Y.). 349: 936. PMID 26315426 DOI: 10.1126/science.aab1584  1
2015 Shi X, Bonilla S, Herschlag D, Harbury P. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. Methods in Enzymology. 558: 75-97. PMID 26068738 DOI: 10.1016/bs.mie.2015.02.001  1
2015 Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. Elife. 4. PMID 25902402 DOI: 10.7554/eLife.06181  1
2015 Sigala PA, Ruben EA, Liu CW, Piccoli PM, Hohenstein EG, Martínez TJ, Schultz AJ, Herschlag D. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability. Journal of the American Chemical Society. 137: 5730-40. PMID 25871450 DOI: 10.1021/ja512980h  1
2015 Bisaria N, Herschlag D. Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET. Biochemical Society Transactions. 43: 172-8. PMID 25849913 DOI: 10.1042/BST20140268  1
2015 Herschlag D. Learning from ribozymes. Rna (New York, N.Y.). 21: 527-8. PMID 25780124 DOI: 10.1261/rna.050914.115  1
2015 Herschlag D, Allred BE, Gowrishankar S. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Current Opinion in Structural Biology. 30: 125-33. PMID 25744941 DOI: 10.1016/j.sbi.2015.02.006  1
2015 Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL, Herschlag D. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. Bmc Bioinformatics. 16: 3. PMID 25591752 DOI: 10.1186/s12859-014-0429-4  1
2015 Shah N, Colbert KN, Enos MD, Herschlag D, Weis WI. Three αSNAP and 10 ATP molecules are used in SNARE complex disassembly by N-ethylmaleimide-sensitive factor (NSF). The Journal of Biological Chemistry. 290: 2175-88. PMID 25492864 DOI: 10.1074/jbc.M114.620849  1
2014 Andrews LD, Zalatan JG, Herschlag D. Probing the origins of catalytic discrimination between phosphate and sulfate monoester hydrolysis: comparative analysis of alkaline phosphatase and protein tyrosine phosphatases. Biochemistry. 53: 6811-9. PMID 25299936 DOI: 10.1021/bi500765p  1
2014 Gleitsman KR, Herschlag DH. A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction. Rna (New York, N.Y.). 20: 1732-46. PMID 25246656 DOI: 10.1261/rna.044362.114  1
2014 Natarajan A, Schwans JP, Herschlag D. Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. Journal of the American Chemical Society. 136: 7643-54. PMID 24787954 DOI: 10.1021/ja413174b  1
2014 Khosla C, Herschlag D, Cane DE, Walsh CT. Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry. 53: 2875-83. PMID 24779441 DOI: 10.1021/bi500290t  1
2014 Shi X, Bisaria N, Benz-Moy TL, Bonilla S, Pavlichin DS, Herschlag D. Roles of long-range tertiary interactions in limiting dynamics of the Tetrahymena group I ribozyme. Journal of the American Chemical Society. 136: 6643-8. PMID 24738560 DOI: 10.1021/ja413033d  1
2014 Shi X, Beauchamp KA, Harbury PB, Herschlag D. From a structural average to the conformational ensemble of a DNA bulge. Proceedings of the National Academy of Sciences of the United States of America. 111: E1473-80. PMID 24706812 DOI: 10.1073/pnas.1317032111  1
2014 Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/annurev-biochem-060409-092720  1
2014 Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry. 53: 2541-55. PMID 24597914 DOI: 10.1021/bi401671t  1
2014 Giamba?u GM, Luchko T, Herschlag D, York DM, Case DA. Ion counting from explicit-solvent simulations and 3D-RISM. Biophysical Journal. 106: 883-94. PMID 24559991 DOI: 10.1016/j.bpj.2014.01.021  1
2013 Wiersma-Koch H, Sunden F, Herschlag D. Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase. Biochemistry. 52: 9167-76. PMID 24261692 DOI: 10.1021/bi4010045  1
2013 Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. Biochemistry. 52: 7840-55. PMID 24151972 DOI: 10.1021/bi401083b  1
2013 Chen JK, Du Bois J, Glenn J, Herschlag D, Khosla C. The Stanford Institute for Chemical Biology. Acs Chemical Biology. 8: 1860-1. PMID 24053754 DOI: 10.1021/cb400641u  1
2013 Greenfeld M, Herschlag D. Fluorescently labeling synthetic RNAs. Methods in Enzymology. 530: 281-97. PMID 24034327 DOI: 10.1016/B978-0-12-420037-1.00015-4  1
2013 Porecha R, Herschlag D. RNA radiolabeling. Methods in Enzymology. 530: 255-79. PMID 24034326 DOI: 10.1016/B978-0-12-420037-1.00014-2  1
2013 Nguyen P, Shi X, Sigurdsson ST, Herschlag D, Qin PZ. A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem : a European Journal of Chemical Biology. 14: 1720-3. PMID 23900919 DOI: 10.1002/cbic.201300376  1
2013 Andrews LD, Fenn TD, Herschlag D. Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes. Plos Biology. 11: e1001599. PMID 23843744 DOI: 10.1371/journal.pbio.1001599  1
2013 Schwans JP, Sunden F, Lassila JK, Gonzalez A, Tsai Y, Herschlag D. Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: 11308-13. PMID 23798413 DOI: 10.1073/pnas.1206710110  1
2013 Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag D. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: E2552-61. PMID 23798390 DOI: 10.1073/pnas.1302191110  1
2013 Shi X, Herschlag D, Harbury PA. 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. 110: E1444-51. PMID 23576725 DOI: 10.1073/pnas.1218830110  1
2013 Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry. 52: 2050-67. PMID 23488725 DOI: 10.1021/bi4000113  1
2013 Ruben EA, Schwans JP, Sonnett M, Natarajan A, Gonzalez A, Tsai Y, Herschlag D. Ground state destabilization from a positioned general base in the ketosteroid isomerase active site. Biochemistry. 52: 1074-81. PMID 23311398 DOI: 10.1021/bi301348x  1
2012 Sim AY, Lipfert J, Herschlag D, Doniach S. 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. 86: 021901. PMID 23005779 DOI: 10.1103/PhysRevE.86.021901  1
2012 Forconi M, Benz-Moy T, Gleitsman KR, Ruben E, Metz C, Herschlag D. Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study. Rna (New York, N.Y.). 18: 1222-9. PMID 22543863 DOI: 10.1261/rna.031567.111  1
2012 Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. Rna (New York, N.Y.). 18: 1123-41. PMID 22539523 DOI: 10.1261/rna.028738.111  1
2012 Althoff EA, Wang L, Jiang L, Giger L, Lassila JK, Wang Z, Smith M, Hari S, Kast P, Herschlag D, Hilvert D, Baker D. Robust design and optimization of retroaldol enzymes. Protein Science : a Publication of the Protein Society. 21: 717-26. PMID 22407837 DOI: 10.1002/pro.2059  1
2012 Anthony PC, Sim AY, Chu VB, Doniach S, Block SM, Herschlag D. Electrostatics of nucleic acid folding under conformational constraint. Journal of the American Chemical Society. 134: 4607-14. PMID 22369617 DOI: 10.1021/ja208466h  1
2012 Greenfeld M, Pavlichin DS, Mabuchi H, Herschlag D. Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data. Plos One. 7: e30024. PMID 22363412 DOI: 10.1371/journal.pone.0030024  1
2012 Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG. 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. 109: E299-308. PMID 22308339 DOI: 10.1073/pnas.1111566109  1
2012 Shi X, Solomatin SV, Herschlag D. A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme. Journal of the American Chemical Society. 134: 1910-3. PMID 22220837 DOI: 10.1021/ja2083575  1
2012 Bobyr E, Lassila JK, Wiersma-Koch HI, Fenn TD, Lee JJ, Nikolic-Hughes I, Hodgson KO, Rees DC, Hedman B, Herschlag D. High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. Journal of Molecular Biology. 415: 102-17. PMID 22056344 DOI: 10.1016/j.jmb.2011.10.040  1
2012 Sengupta RN, Herschlag D, Piccirilli JA. Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site. Acs Chemical Biology. 7: 294-9. PMID 22029738 DOI: 10.1021/cb200202q  1
2011 Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. Journal of the American Chemical Society. 133: 20052-5. PMID 22053826 DOI: 10.1021/ja208050t  1
2011 Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chemistry & Biology. 18: 949-54. PMID 21867910 DOI: 10.1016/j.chembiol.2011.07.014  1
2011 Benz-Moy TL, Herschlag D. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry. 50: 8733-55. PMID 21815635 DOI: 10.1021/bi2008245  1
2011 Andrews LD, Deng H, Herschlag D. 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. 133: 11621-31. PMID 21692505 DOI: 10.1021/ja203370b  1
2011 Solomatin SV, Greenfeld M, Herschlag D. Implications of molecular heterogeneity for the cooperativity of biological macromolecules. Nature Structural & Molecular Biology. 18: 732-4. PMID 21572445 DOI: 10.1038/nsmb.2052  1
2011 Forconi M, Porecha RH, Piccirilli JA, Herschlag D. 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. 133: 7791-800. PMID 21539364 DOI: 10.1021/ja111316y  1
2011 Lassila JK, Zalatan JG, Herschlag D. Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annual Review of Biochemistry. 80: 669-702. PMID 21513457 DOI: 10.1146/annurev-biochem-060409-092741  1
2011 Greenfeld M, Solomatin SV, Herschlag D. Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA. The Journal of Biological Chemistry. 286: 19872-9. PMID 21478155 DOI: 10.1074/jbc.M111.235465  1
2011 Riordan DP, Herschlag D, Brown PO. Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Research. 39: 1501-9. PMID 20959291 DOI: 10.1093/nar/gkq920  1
2010 Hanoian P, Sigala PA, Herschlag D, Hammes-Schiffer S. Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. Biochemistry. 49: 10339-48. PMID 21049962 DOI: 10.1021/bi101428e  1
2010 Fafarman AT, Sigala PA, Herschlag D, Boxer SG. Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. Journal of the American Chemical Society. 132: 12811-3. PMID 20806897 DOI: 10.1021/ja104573b  1
2010 Greenfeld M, Herschlag D. Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer. Methods in Enzymology. 472: 205-20. PMID 20580966 DOI: 10.1016/S0076-6879(10)72009-7  1
2010 Wan Y, Suh H, Russell R, Herschlag D. Multiple unfolding events during native folding of the Tetrahymena group I ribozyme. Journal of Molecular Biology. 400: 1067-77. PMID 20541557 DOI: 10.1016/j.jmb.2010.06.010  1
2010 Lassila JK, Baker D, Herschlag D. Origins of catalysis by computationally designed retroaldolase enzymes. Proceedings of the National Academy of Sciences of the United States of America. 107: 4937-42. PMID 20194782 DOI: 10.1073/pnas.0913638107  1
2010 Lipfert J, Sim AY, Herschlag D, Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. Rna (New York, N.Y.). 16: 708-19. PMID 20194520 DOI: 10.1261/rna.1985110  1
2010 Forconi M, Sengupta RN, Piccirilli JA, Herschlag D. A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site. Biochemistry. 49: 2753-62. PMID 20175542 DOI: 10.1021/bi902200n  1
2010 Solomatin SV, Greenfeld M, Chu S, Herschlag D. Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature. 463: 681-4. PMID 20130651 DOI: 10.1038/nature08717  1
2010 Kraut DA, Sigala PA, Fenn TD, Herschlag D. 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. 107: 1960-5. PMID 20080683 DOI: 10.1073/pnas.0911168107  1
2010 Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure. Journal of Molecular Biology. 396: 153-65. PMID 19925806 DOI: 10.1016/j.jmb.2009.11.030  1
2009 Greenfeld M, Herschlag D. Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy. Methods in Enzymology. 469: 375-89. PMID 20946799 DOI: 10.1016/S0076-6879(09)69018-2  1
2009 Shi X, Herschlag D. Fluorescence polarization anisotropy to measure RNA dynamics. Methods in Enzymology. 469: 287-302. PMID 20946795 DOI: 10.1016/S0076-6879(09)69014-5  1
2009 Solomatin S, Herschlag D. Methods of site-specific labeling of RNA with fluorescent dyes. Methods in Enzymology. 469: 47-68. PMID 20946784 DOI: 10.1016/S0076-6879(09)69003-0  1
2009 Forconi M, Herschlag D. Use of phosphorothioates to identify sites of metal-ion binding in RNA. Methods in Enzymology. 468: 311-33. PMID 20946776 DOI: 10.1016/S0076-6879(09)68015-0  1
2009 Forconi M, Herschlag D. Metal ion-based RNA cleavage as a structural probe. Methods in Enzymology. 468: 91-106. PMID 20946766 DOI: 10.1016/S0076-6879(09)68005-8  1
2009 Herschlag D. RNA. Preface. Methods in Enzymology. 469: xvii. PMID 19925922 DOI: 10.1016/S0076-6879(09)69028-5  1
2009 Herschlag D. Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A. Preface. Methods in Enzymology. 468: xv. PMID 19925921 DOI: 10.1016/S0076-6879(09)68020-4  1
2009 Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. Plos Biology. 7: e1000238. PMID 19901979 DOI: 10.1371/journal.pbio.1000238  1
2009 Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? Rna (New York, N.Y.). 15: 2195-205. PMID 19850914 DOI: 10.1261/rna.1747509  1
2009 Forconi M, Sengupta RN, Liu MC, Sartorelli AC, Piccirilli JA, Herschlag D. Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. Angewandte Chemie (International Ed. in English). 48: 7171-5. PMID 19708048 DOI: 10.1002/anie.200903006  1
2009 Schwans JP, Kraut DA, Herschlag D. 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. 106: 14271-5. PMID 19706511 DOI: 10.1073/pnas.0901032106  1
2009 Zalatan JG, Herschlag D. The far reaches of enzymology. Nature Chemical Biology. 5: 516-20. PMID 19620986 DOI: 10.1038/nchembio0809-516  1
2009 Shi X, Mollova ET, Pljevaljci? G, Millar DP, Herschlag D. Probing the dynamics of the P1 helix within the Tetrahymena group I intron. Journal of the American Chemical Society. 131: 9571-8. PMID 19537712 DOI: 10.1021/ja902797j  1
2009 Sigala PA, Tsuchida MA, Herschlag D. Hydrogen bond dynamics in the active site of photoactive yellow protein. Proceedings of the National Academy of Sciences of the United States of America. 106: 9232-7. PMID 19470452 DOI: 10.1073/pnas.0900168106  1
2009 Sigala PA, Caaveiro JM, Ringe D, Petsko GA, Herschlag D. Hydrogen bond coupling in the ketosteroid isomerase active site. Biochemistry. 48: 6932-9. PMID 19469568 DOI: 10.1021/bi900713j  1
2009 Lipfert J, Herschlag D, Doniach S. Riboswitch conformations revealed by small-angle X-ray scattering. Methods in Molecular Biology (Clifton, N.J.). 540: 141-59. PMID 19381558 DOI: 10.1007/978-1-59745-558-9_11  1
2009 Kraut DA, Churchill MJ, Dawson PE, Herschlag D. Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis. Acs Chemical Biology. 4: 269-73. PMID 19260691 DOI: 10.1021/cb900016q  1
2009 Grant GP, Boyd N, Herschlag D, Qin PZ. Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. Journal of the American Chemical Society. 131: 3136-7. PMID 19220053 DOI: 10.1021/ja808217s  1
2009 Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Rna (New York, N.Y.). 15: 189-99. PMID 19144906 DOI: 10.1261/rna.1270809  1
2009 Liu CW, Alekseyev VY, Allwardt JR, Bankovich AJ, Cade-Menun BJ, Davis RW, Du LS, Garcia KC, Herschlag D, Khosla C, Kraut DA, Li Q, Null B, Puglisi JD, Sigala PA, et al. The diversity of nuclear magnetic resonance spectroscopy Nato Science For Peace and Security Series B: Physics and Biophysics. 65-81.  1
2008 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. A repulsive field: advances in the electrostatics of the ion atmosphere. Current Opinion in Chemical Biology. 12: 619-25. PMID 19081286 DOI: 10.1016/j.cbpa.2008.10.010  1
2008 Lassila JK, Herschlag D. Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily. Biochemistry. 47: 12853-9. PMID 18975918 DOI: 10.1021/bi801488c  1
2008 Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. Plos Biology. 6: e255. PMID 18959479 DOI: 10.1371/journal.pbio.0060255  1
2008 Zalatan JG, Fenn TD, Herschlag D. Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion. Journal of Molecular Biology. 384: 1174-89. PMID 18851975 DOI: 10.1016/j.jmb.2008.09.059  1
2008 Sigala PA, Kraut DA, Caaveiro JM, Pybus B, Ruben EA, Ringe D, Petsko GA, Herschlag D. Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. Journal of the American Chemical Society. 130: 13696-708. PMID 18808119 DOI: 10.1021/ja803928m  1
2008 Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature Protocols. 3: 1395-401. PMID 18772866 DOI: 10.1038/nprot.2008.134  1
2008 Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society. 130: 12334-41. PMID 18722445 DOI: 10.1021/ja800854u  1
2008 O'Brien PJ, Lassila JK, Fenn TD, Zalatan JG, Herschlag D. Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. Biochemistry. 47: 7663-72. PMID 18627128 DOI: 10.1021/bi800545n  1
2008 Chu VB, Herschlag D. Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Current Opinion in Structural Biology. 18: 305-14. PMID 18555681 DOI: 10.1016/j.sbi.2008.05.002  1
2008 Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 47: 6883-94. PMID 18517225 DOI: 10.1021/bi800519a  1
2008 Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. Plos One. 3: e2126. PMID 18461144 DOI: 10.1371/journal.pone.0002126  1
2008 Sattin BD, Zhao W, Travers K, Chu S, Herschlag D. Direct measurement of tertiary contact cooperativity in RNA folding. Journal of the American Chemical Society. 130: 6085-7. PMID 18429611 DOI: 10.1021/ja800919q  1
2008 Mueller-Planitz F, Herschlag D. Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism. The Journal of Biological Chemistry. 283: 17463-76. PMID 18403371 DOI: 10.1074/jbc.M710014200  1
2008 Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. 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. 105: 4144-9. PMID 18322008 DOI: 10.1073/pnas.0709032105  1
2007 Bai Y, Greenfeld M, Travers KJ, Chu VB, Lipfert J, Doniach S, Herschlag D. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. Journal of the American Chemical Society. 129: 14981-8. PMID 17990882 DOI: 10.1021/ja075020g  1
2007 Sigala PA, Fafarman AT, Bogard PE, Boxer SG, Herschlag D. 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. 129: 12104-5. PMID 17854190 DOI: 10.1021/ja075605a  1
2007 Forconi M, Piccirilli JA, Herschlag D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. Rna (New York, N.Y.). 13: 1656-67. PMID 17720880 DOI: 10.1261/rna.632007  1
2007 Zalatan JG, Catrina I, Mitchell R, Grzyska PK, O'brien PJ, Herschlag D, Hengge AC. Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. Journal of the American Chemical Society. 129: 9789-98. PMID 17630738 DOI: 10.1021/ja072196+  1
2007 Travers KJ, Boyd N, Herschlag D. Low specificity of metal ion binding in the metal ion core of a folded RNA. Rna (New York, N.Y.). 13: 1205-13. PMID 17616553 DOI: 10.1261/rna.566007  1
2007 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophysical Journal. 93: 3202-9. PMID 17604318 DOI: 10.1529/biophysj.106.099168  1
2007 Mueller-Planitz F, Herschlag D. DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Research. 35: 3764-73. PMID 17517767 DOI: 10.1093/nar/gkm335  1
2007 Catrina I, O'Brien PJ, Purcell J, Nikolic-Hughes I, Zalatan JG, Hengge AC, Herschlag D. Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. Journal of the American Chemical Society. 129: 5760-5. PMID 17411045 DOI: 10.1021/ja069111+  1
2007 Karbstein K, Lee J, Herschlag D. 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. 46: 4861-75. PMID 17385892 DOI: 10.1021/bi062169g  1
2007 Lee TH, Lapidus LJ, Zhao W, Travers KJ, Herschlag D, Chu S. Measuring the folding transition time of single RNA molecules. Biophysical Journal. 92: 3275-83. PMID 17307831 DOI: 10.1529/biophysj.106.094623  1
2007 Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/j.jmb.2006.10.022  1
2007 Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S. Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling Journal of Applied Crystallography. 40: s229-s234. DOI: 10.1107/S0021889807001707  1
2007 Fierke CA, Herschlag D. The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond. [Current Opinion in Chemical Biology 2006, 10:453-454] (DOI:10.1016/j.cbpa.2006.08.019) Current Opinion in Chemical Biology. 11: 111. DOI: 10.1016/j.cbpa.2006.11.001  1
2006 Woodside MT, Anthony PC, Behnke-Parks WM, Larizadeh K, Herschlag D, Block SM. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (New York, N.Y.). 314: 1001-4. PMID 17095702 DOI: 10.1126/science.1133601  1
2006 Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. Journal of Molecular Biology. 363: 531-44. PMID 16963081 DOI: 10.1016/j.jmb.2006.08.024  1
2006 Zalatan JG, Fenn TD, Brunger AT, Herschlag D. Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution. Biochemistry. 45: 9788-803. PMID 16893180 DOI: 10.1021/bi060847t  1
2006 Mueller-Planitz F, Herschlag D. Interdomain communication in DNA topoisomerase II. DNA binding and enzyme activation. The Journal of Biological Chemistry. 281: 23395-404. PMID 16782968 DOI: 10.1074/jbc.M604119200  1
2006 Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM. 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. 103: 6190-5. PMID 16606839 DOI: 10.1073/pnas.0511048103  1
2006 Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Plos Biology. 4: e99. PMID 16602823 DOI: 10.1371/journal.pbio.0040099  1
2006 Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D. 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. 103: 4487-92. PMID 16537387 DOI: 10.1073/pnas.0509260103  1
2006 Zalatan JG, Herschlag D. Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis. Journal of the American Chemical Society. 128: 1293-303. PMID 16433548 DOI: 10.1021/ja056528r  1
2006 Fierke CA, Herschlag D. The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond Mechanisms Current Opinion in Chemical Biology. 10: 453-454. DOI: 10.1016/j.cbpa.2006.08.019  1
2005 Hougland JL, Kravchuk AV, Herschlag D, Piccirilli JA. Functional identification of catalytic metal ion binding sites within RNA. Plos Biology. 3: e277. PMID 16092891 DOI: 10.1371/journal.pbio.0030277  1
2005 Johnson TH, Tijerina P, Chadee AB, Herschlag D, Russell R. Structural specificity conferred by a group I RNA peripheral element. Proceedings of the National Academy of Sciences of the United States of America. 102: 10176-81. PMID 16009943 DOI: 10.1073/pnas.0501498102  1
2005 Nikolic-Hughes I, O'brien PJ, Herschlag D. Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. Journal of the American Chemical Society. 127: 9314-5. PMID 15984827 DOI: 10.1021/ja051603j  1
2005 Das R, Travers KJ, Bai Y, Herschlag D. Determining the Mg2+ stoichiometry for folding an RNA metal ion core. Journal of the American Chemical Society. 127: 8272-3. PMID 15941246 DOI: 10.1021/ja051422h  1
2005 Arava Y, Boas FE, Brown PO, Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Research. 33: 2421-32. PMID 15860778 DOI: 10.1093/nar/gki331  1
2005 Forconi M, Herschlag D. Promiscuous catalysis by the tetrahymena group I ribozyme. Journal of the American Chemical Society. 127: 6160-1. PMID 15853307 DOI: 10.1021/ja050180i  1
2005 Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna (New York, N.Y.). 11: 344-54. PMID 15701734 DOI: 10.1261/rna.7214405  1
2005 Bai Y, Das R, Millett IS, Herschlag D, Doniach S. 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. 102: 1035-40. PMID 15647360 DOI: 10.1073/pnas.0404448102  1
2004 Andresen K, Das R, Park HY, Smith H, Kwok LW, Lamb JS, Kirkland EJ, Herschlag D, Finkelstein KD, Pollack L. Spatial distribution of competing ions around DNA in solution. Physical Review Letters. 93: 248103. PMID 15697865 DOI: 10.1103/PhysRevLett.93.248103  1
2004 Karbstein K, Tang KH, Herschlag D. A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect. Rna (New York, N.Y.). 10: 1730-9. PMID 15496521 DOI: 10.1261/rna.7118104  1
2004 Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. Journal of Molecular Biology. 343: 1195-206. PMID 15491606 DOI: 10.1016/j.jmb.2004.08.080  1
2004 Nikolic-Hughes I, Rees DC, Herschlag D. Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer? Journal of the American Chemical Society. 126: 11814-9. PMID 15382915 DOI: 10.1021/ja0480421  1
2004 Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. Plos Biology. 2: E79. PMID 15024427 DOI: 10.1371/journal.pbio.0020079  1
2003 Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. 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. 100: 11429-34. PMID 13679573 DOI: 10.1073/pnas.2033246100  1
2003 Peck ML, Herschlag D. 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.). 9: 1180-7. PMID 13130132 DOI: 10.1261/rna.2103703  1
2003 Das R, Kwok LW, Millett IS, Bai Y, Mills TT, Jacob J, Maskel GS, Seifert S, Mochrie SG, Thiyagarajan P, Doniach S, Pollack L, Herschlag D. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. Journal of Molecular Biology. 332: 311-9. PMID 12948483 DOI: 10.1016/S0022-2836(03)00854-4  1
2003 Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, Doniach S, Finkelstein KD, Herschlag D, Pollack L. Counterion distribution around DNA probed by solution X-ray scattering. Physical Review Letters. 90: 188103. PMID 12786045  1
2003 Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. Journal of Molecular Biology. 328: 1011-26. PMID 12729738 DOI: 10.1016/S0022-2836(03)00272-9  1
2003 Kraut DA, Carroll KS, Herschlag D. Challenges in enzyme mechanism and energetics. Annual Review of Biochemistry. 72: 517-71. PMID 12704087 DOI: 10.1146/annurev.biochem.72.121801.161617  1
2003 Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 100: 3889-94. PMID 12660367 DOI: 10.1073/pnas.0635171100  1
2003 Karbstein K, Herschlag D. 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. 100: 2300-5. PMID 12591943 DOI: 10.1073/pnas.252749799  1
2002 O'Brien PJ, Herschlag D. Alkaline Phosphatase Revisited:  Hydrolysis of Alkyl Phosphates (†). Biochemistry. 41: 3207-3225. PMID 28212002 DOI: 10.1021/bi012166y  1
2002 Cheng H, Nikolic-Hughes I, Wang JH, Deng H, O'Brien PJ, Wu L, Zhang ZY, Herschlag D, Callender R. Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis. Journal of the American Chemical Society. 124: 11295-306. PMID 12236744 DOI: 10.1021/ja026481z  1
2002 Karbstein K, Carroll KS, Herschlag D. Probing the Tetrahymena group I ribozyme reaction in both directions. Biochemistry. 41: 11171-83. PMID 12220182 DOI: 10.1021/bi0202631  1
2002 Shan SO, Herschlag D. Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis. Rna (New York, N.Y.). 8: 861-72. PMID 12166641 DOI: 10.1017/S1355838202020216  1
2002 Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences of the United States of America. 99: 5860-5. PMID 11972065 DOI: 10.1073/pnas.092538799  1
2002 Sorin EJ, Engelhardt MA, Herschlag D, Pande VS. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. Journal of Molecular Biology. 317: 493-506. PMID 11955005 DOI: 10.1006/jmbi.2002.5447  1
2002 Russell R, Millett IS, Tate MW, Kwok LW, Nakatani B, Gruner SM, Mochrie SG, Pande V, Doniach S, Herschlag D, Pollack L. Rapid compaction during RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 4266-71. PMID 11929997 DOI: 10.1073/pnas.072589599  1
2002 O'Brien PJ, Herschlag D. Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. Biochemistry. 41: 3207-25. PMID 11863460 DOI: 10.1021/bi012166y  1
2002 Russell R, Zhuang X, Babcock HP, Millett IS, Doniach S, Chu S, Herschlag D. Exploring the folding landscape of a structured RNA. Proceedings of the National Academy of Sciences of the United States of America. 99: 155-60. PMID 11756689 DOI: 10.1073/pnas.221593598  1
2001 Peluso P, Shan SO, Nock S, Herschlag D, Walter P. Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 40: 15224-33. PMID 11735405 DOI: 10.1021/bi011639y  1
2001 Russell R, Herschlag D. Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. Journal of Molecular Biology. 308: 839-51. PMID 11352576 DOI: 10.1006/jmbi.2001.4751  1
2001 O'Rear JL, Wang S, Feig AL, Beigelman L, Uhlenbeck OC, Herschlag D. Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. Rna (New York, N.Y.). 7: 537-45. PMID 11345432 DOI: 10.1017/S1355838201002461  1
2001 O'Brien PJ, Herschlag D. Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase. Biochemistry. 40: 5691-9. PMID 11341834 DOI: 10.1021/bi0028892  1
2001 Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 40: 5161-71. PMID 11318638  1
2001 Admiraal SJ, Meyer P, Schneider B, Deville-Bonne D, Janin J, Herschlag D. Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis. Biochemistry. 40: 403-13. PMID 11148034 DOI: 10.1021/bi002472w  1
2001 Ha T, Zhuang X, Babcock H, Kim H, Orr JW, Williamson JR, Bartley L, Russell R, Herschlag D, Chu S. The study of single biomolecules with fluorescence methods Springer Series in Chemical Physics. 67: 326-337.  1
2000 Shan SO, Herschlag D. An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction. Rna (New York, N.Y.). 6: 795-813. PMID 10864040 DOI: 10.1017/S1355838200000649  1
2000 Zhuang X, Bartley LE, Babcock HP, Russell R, Ha T, Herschlag D, Chu S. A single-molecule study of RNA catalysis and folding. Science (New York, N.Y.). 288: 2048-51. PMID 10856219 DOI: 10.1126/science.288.5473.2048  1
2000 Peluso P, Herschlag D, Nock S, Freymann DM, Johnson AE, Walter P. Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor. Science (New York, N.Y.). 288: 1640-3. PMID 10834842 DOI: 10.1126/science.288.5471.1640  1
2000 Narlikar GJ, Bartley LE, Herschlag D. Use of duplex rigidity for stability and specificity in RNA tertiary structure. Biochemistry. 39: 6183-9. PMID 10821693 DOI: 10.1021/bi992858a  1
2000 Russell R, Millett IS, Doniach S, Herschlag D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Structural Biology. 7: 367-70. PMID 10802731 DOI: 10.1038/75132  1
2000 Engelhardt MA, Doherty EA, Knitt DS, Doudna JA, Herschlag D. The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry. 39: 2639-51. PMID 10704214  0.92
2000 Yoshida A, Shan So, Herschlag D, Piccirilli JA. The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. Chemistry & Biology. 7: 85-96. PMID 10662698 DOI: 10.1016/S1074-5521(00)00074-0  1
2000 Admiraal SJ, Herschlag D. The substrate-assisted general base catalysis model for phosphate monoester hydrolysis: Evaluation using reactivity comparisons Journal of the American Chemical Society. 122: X. DOI: 10.1021/ja993942g  1
2000 Zhuang X, Bartley L, Babcock H, Russell R, Ha T, Herschlag D, Chu S. Observing folding and catalysis of a single RNA enzyme molecule Pacific Rim Conference On Lasers and Electro-Optics, Cleo - Technical Digest. 588-589.  1
1999 Lorsch JR, Herschlag D. Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro. The Embo Journal. 18: 6705-17. PMID 10581244 DOI: 10.1093/emboj/18.23.6705  1
1999 Wang S, Karbstein K, Peracchi A, Beigelman L, Herschlag D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry. 38: 14363-78. PMID 10572011 DOI: 10.1021/bi9913202  1
1999 Narlikar GJ, Bartley LE, Khosla M, Herschlag D. 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. 38: 14192-204. PMID 10571993 DOI: 10.1021/bi9914309  1
1999 Gerton JL, Herschlag D, Brown PO. Stereospecificity of reactions catalyzed by HIV-1 integrase Journal of Biological Chemistry. 274: 33480-33487. PMID 10559232 DOI: 10.1074/jbc.274.47.33480  1
1999 Shan So, Yoshida A, Sun S, Piccirilli JA, Herschlag D. 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. 96: 12299-304. PMID 10535916 DOI: 10.1073/pnas.96.22.12299  1
1999 Russell R, Herschlag D. New pathways in folding of the Tetrahymena group I RNA enzyme Journal of Molecular Biology. 291: 1155-1167. PMID 10518951 DOI: 10.1006/jmbi.1999.3026  1
1999 Zhang YL, Hollfelder F, Gordon SJ, Chen L, Keng YF, Wu L, Herschlag D, Zhang ZY. Impaired transition state complementarity in the hydrolysis of O- arylphosphorothioates by protein-tyrosine phosphatases Biochemistry. 38: 12111-12123. PMID 10508416 DOI: 10.1021/bi990836i  1
1999 Shan SO, Herschlag D. Hydrogen bonding in enzymatic catalysis: analysis of energetic contributions. Methods in Enzymology. 308: 246-76. PMID 10507008 DOI: 10.1016/S0076-6879(99)08013-1  1
1999 Peck ML, Herschlag D. Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity of translation initiation factor elF4A. Rna (New York, N.Y.). 5: 1210-21. PMID 10496222 DOI: 10.1017/S1355838299990817  1
1999 Shan SO, Narlikar GJ, Herschlag D. Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme. Biochemistry. 38: 10976-88. PMID 10460152 DOI: 10.1021/bi9903897  1
1999 Shan SO, Herschlag D. 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. 38: 10958-75. PMID 10460151 DOI: 10.1021/bi990388e  1
1999 Admiraal SJ, Schneider B, Meyer P, Janin J, Véron M, Deville-Bonne D, Herschlag D. Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase Biochemistry. 38: 4701-4711. PMID 10200157 DOI: 10.1021/bi9827565  1
1999 O'Brien PJ, Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chemistry & Biology. 6: R91-R105. PMID 10099128 DOI: 10.1016/S1074-5521(99)80033-7  1
1999 Doherty EA, Herschlag D, Doudna JA. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry. 38: 2982-90. PMID 10074350 DOI: 10.1021/bi982113p  0.92
1999 Russell R, Herschlag D. Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme Rna. 5: 158-166. PMID 10024168 DOI: 10.1017/S1355838299981839  1
1999 Korber P, Zander T, Herschlag D, Bardwell JCA. A new heat shock protein that binds nucleic acids Journal of Biological Chemistry. 274: 249-256. PMID 9867837 DOI: 10.1074/jbc.274.1.249  1
1999 O'Brien PJ, Herschlag D. Does the active site arginine change the nature of the transition state for alkaline phosphatase-catalyzed phosphoryl transfer? [[11] Journal of the American Chemical Society. 121: 11022-11023. DOI: 10.1021/ja9932582  1
1999 Admiraal SJ, Herschlag D. Catalysis of phosphoryl transfer from ATP by amine nucleophiles Journal of the American Chemical Society. 121: 5837-5845. DOI: 10.1021/ja990903w  1
1998 Peracchi A, Matulic-Adamic J, Wang S, Beigelman L, Herschlag D. Structure-function relationships in the hammerhead ribozyme probed by base rescue Rna. 4: 1332-1346. PMID 9814755 DOI: 10.1017/S1355838298980979  1
1998 Herschlag D. RNA structure: Ribozyme crevices and catalysis Nature. 395: 548-549. PMID 9783578 DOI: 10.1038/26864  1
1998 Peracchi A, Karpeisky A, Maloney L, Beigelman L, Herschlag D. A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations Biochemistry. 37: 14765-14775. PMID 9778351 DOI: 10.1021/bi980867y  1
1998 Narlikar GJ, Herschlag D. Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction Biochemistry. 37: 9902-9911. PMID 9665695 DOI: 10.1021/bi980495t  1
1998 Lorsch JR, Herschlag D. The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry. 37: 2194-206. PMID 9485365 DOI: 10.1021/bi9724319  1
1998 Lorsch JR, Herschlag D. The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry. 37: 2180-93. PMID 9485364 DOI: 10.1021/bi972430g  1
1998 O'Brien PJ, Herschlag D. Sulfatase activity of E. coli alkaline phosphatase demonstrates a functional link to arylsulfatases, an evolutionarily related enzyme family [10] Journal of the American Chemical Society. 120: 12369-12370. DOI: 10.1021/ja983390m  1
1997 Peracchi A, Beigelman L, Scott EC, Uhlenbeck OC, Herschlag D. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. The Journal of Biological Chemistry. 272: 26822-6. PMID 9341112 DOI: 10.1074/jbc.272.43.26822  1
1997 Narlikar GJ, Herschlag D. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes Annual Review of Biochemistry. 66: 19-59. PMID 9242901 DOI: 10.1146/annurev.biochem.66.1.19  1
1997 Hertel KJ, Peracchi A, Uhlenbeck OC, Herschlag D. Use of intrinsic binding energy for catalysis by an RNA enzyme. Proceedings of the National Academy of Sciences of the United States of America. 94: 8497-502. PMID 9238005 DOI: 10.1073/pnas.94.16.8497  1
1997 McConnell TS, Herschlag D, Cech TR. Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction. Biochemistry. 36: 8293-303. PMID 9204875 DOI: 10.1021/bi9700678  1
1997 Narlikar GJ, Khosla M, Usman N, Herschlag D. Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: Intrinsic binding energy in an RNA enzyme Biochemistry. 36: 2465-2477. PMID 9054551 DOI: 10.1021/bi9610820  1
1997 Herschlag D, Narlikar QJ, Peracchi A, Shan S. Biological catalysis: Lessons from the comparison of RNA and protein enzymes Faseb Journal. 11: A852.  1
1996 Shan SO, Herschlag D. 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. 93: 14474-9. PMID 8962076 DOI: 10.1073/pnas.93.25.14474  1
1996 Shan SO, Loh S, Herschlag D. The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis. Science (New York, N.Y.). 272: 97-101. PMID 8600542  1
1993 Labow BI, Herschlag D, Jencks WP. Catalysis of the hydrolysis of phosphorylated pyridines by alkaline phosphatase has little or no dependence on the pKa of the leaving group. Biochemistry. 32: 8737-41. PMID 8395879  1
1993 McConnell TS, Cech TR, Herschlag D. Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding. Proceedings of the National Academy of Sciences of the United States of America. 90: 8362-6. PMID 8378306  1
1993 Herschlag D, Eckstein F, Cech TR. The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction. Biochemistry. 32: 8312-21. PMID 7688573  1
1993 Herschlag D, Eckstein F, Cech TR. 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. 32: 8299-311. PMID 7688572  1
1992 Legault P, Herschlag D, Celander DW, Cech TR. Mutations at the guanosine-binding site of the Tetrahymena ribozyme also affect site-specific hydrolysis. Nucleic Acids Research. 20: 6613-9. PMID 1480482 DOI: 10.1093/nar/20.24.6613  1
1992 Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. The Journal of Biological Chemistry. 267: 17479-82. PMID 1381347  1
1991 Herschlag D, Piccirilli JA, Cech TR. Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. Biochemistry. 30: 4844-54. PMID 2036355  1
1991 Young B, Herschlag D, Cech TR. Mutations in a nonconserved sequence of the Tetrahymena ribozyme increase activity and specificity. Cell. 67: 1007-19. PMID 1959129  1
1990 Herschlag D, Jencks WP. Catalysis of the hydrolysis of phosphorylated pyridines by Mg(OH)+: a possible model for enzymatic phosphoryl transfer. Biochemistry. 29: 5172-9. PMID 2378873  1
1990 Herschlag D, Cech TR. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry. 29: 10172-80. PMID 2271646  1
1990 Herschlag D, Cech TR. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 29: 10159-71. PMID 2271645  1
1990 Herschlag D, Cech TR. DNA cleavage catalysed by the ribozyme from Tetrahymena. Nature. 344: 405-9. PMID 1690858 DOI: 10.1038/344405a0  1
1986 Jencks WP, Haber MT, Herschlag D, Nazaretian KL. Decreasing reactivity with increasing nucleophile basicity. The effect of solvation on .beta.nuc for phosphoryl transfer to amines. Journal of the American Chemical Society. 108: 479-83. PMID 22175464 DOI: 10.1021/ja00263a019  0.44
1986 Jencks WP, Haber MT, Herschlag D, Nazaretian KL. Additions and Corrections: Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on (nuc) for Phosphoryl Transfer to Amines. Journal of the American Chemical Society. 108: 6100. PMID 22175415 DOI: 10.1021/ja00279a603  0.44
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