Becker, W.R., Jarmoskaite, I., Kappel, K., Vaidyanathan, P.P., Denny, S.K., Das, R., Greenleaf, W.J., Herschlag, D. (2019) bioRxiv Preprint. Quantitative High-throughput Tests of Ubiquitous RNA Secondary Structure Prediction Algorithms via RNA/protein Binding. (bioRxiv) (PDF File)

Yabukarski, F., Biel, J.T., Pinney, M.M., Doukov, T., Powers, A.S., Fraser, J.S., Herschlag, D. (2019) bioRxiv Preprint. Assessing Positioning in Enzymatic Catalysis via Ketosteroid Isomerase Conformational Ensembles. (bioRxiv) (PDF File)


274. Gebala, M., Herschlag, D. (2019) Biophys. J. 117, 1116-1124. Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting. PMID: 31466697. (Medline) (bioRxiv) (PDF File) (Supporting Info)

273. Choe, J.K., Pinney, M., Komaki, Y., Chuang, Y.-H., Herschlag, D., Simpson, A., Mitch, W. (2019) Free Radic. Biol. Med. 141, 475-482. Serum Electrolytes Can Promote Hydroxyl Radical-initiated Biomolecular Damage from Inflammation. PMID: 31349038. (Medline) (PDF File) (Supporting Info)

272. Yesselman, J.D., Eiler, D., Carlson, E.D., Gotrik, M., d’Aquino, A., Ooms, A.N., Kladwang, W., Carlson, P., Shi, X.S., Costantino, D.A., Herschlag, D., Lucks, A., Jewett, M.C., Kieft, J.S., Das, R. (2019) Nat. Nanotechnol. 14, 866-873. Computational Design of Three-dimensional RNA Structure and Function. PMID: 31427748. (Medline) (bioRxiv) (PDF File) (Supporting Info 1) (Supporting Info 2)

271. Yesselman, J.D., Denny, S.K., Bisaria, N., Herschlag, D., Greenleaf, W.J., Das, R. (2019) Proc. Natl. Acad. Sci. U.S.A. 116, 16847-16855. Sequence-dependent RNA Helix Conformational Preferences Predictably Impact Tertiary Structure Formation. PMID: 31375637. (Medline) (bioRxiv) (PDF File) (Supporting Info)

270. Gebala, M., Johnson, S.L., Narlikar, G.J., Herschlag, D. (2019) eLife 8, e44993. Ion Counting Demonstrates a High Electrostatic Field Generated by the Nucleosome. PMCID: PMC6584128. (Medline) (bioRxiv) (PDF File)

269. Sengupta, R.N., Piccirilli, J.A., Herschlag, D. (2019) Biochemistry 58, 2760-2768. Enhancement of RNA•Ligand Association Kinetics via an Electrostatic Anchor. PMCID: PMC6586055. (Medline) (PDF File) (Supporting Info)

268. Ganser, L.R., Kelly, M.L., Herschlag, D., Al-Hashimi, H.M. (2019) Nat. Rev. Mol. Cell Biol. 20, 474-489. The Roles of Structural Dynamics in the Cellular Functions of RNAs. PMID: 31182864. (Medline) (PDF File) (Supporting Info)

267. Becker, W.R., Jarmoskaite, I., Vaidyanathan, P.P., Greenleaf, W.J., Herschlag, D. (2019) RNA 25, 702-712. Demonstration of Protein Cooperativity Mediated by RNA Structure Using the Human Protein PUM2. PMID: 30914482. (Medline) (PDF File) (Supporting Info)

266. Kappel, K., Jarmoskaite, I., Vaidyanathan, P.P., Greenleaf, W.J., Herschlag, D., Das, R. (2019) Proc. Natl. Acad. Sci. U.S.A. 116, 8336-8341. Blind Tests of RNA-protein Binding Affinity Prediction. PMCID: PMC6486753. (Medline) (PDF File) (Supporting Info)

265. Jarmoskaite, I., Denny, S.K., Vaidyanathan, P.P., Becker, W.R., Andreasson, J.O.L., Layton, C.J., Kappel, K., Shivashankar, V., Sreenivasan, R., Das, R., Greenleaf, W.J., Herschlag, D. (2019) Molec. Cell 74, 966-981. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. PMCID: PMC6645366. (Medline) (bioRxiv) (PDF File) (Supporting Info)


264.  Herschlag, D., Bonilla, S., Bisaria, N. (2018) Cold Spring Harb. Perspect. Biol. 10, pii:a032433. The Story of RNA Folding, as Told in Epochs. PMID: 30275276. (Medline) (PDF File)
Also published in: Herschlag, D., Bonilla, S., Bisaria, N. (2019) RNA Worlds: New Tools for Deep Exploration Ed. Tom Cech, Ed. Joan Steitz. The Story of RNA Folding, as Told in Epochs.

263. Pinney, M.M., Natarajan, A., Yabukarski, F., Sanchez, D.M., Liu, F., Liang, R., Doukov, T., Schwans, J.P., Martinez, T.J., Herschlag, D. (2018) J. Am. Chem. Soc. 140, 9827-9843. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. PMID: 29990421. (Medline) (PDF File) (Supporting Info)

262. Merriman, D.K., Yuan, J., Shi, J., Majumdar, A., Herschlag, D., Al-Hashimi, H.M. (2018) RNA 24, 1363-1376. Increasing the Length of Poly-pyrimidine Bulges Broadens RNA Conformational Ensembles with Minimal Impact on Stacking Energetics. PMCID: PMC6140463. (Medline) (PDF File) (Supporting Info)

261. Denny, S.K., Bisaria, N., Yesselman, J.D., Das, R., Herschlag, D., Greenleaf, W.J. (2018) Cell 174, 377-390.e20.  High-throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. PMCID: PMC6053692. (Medline) (PDF File) (Supporting Info)
        See also: Boerneke, M.A., Weeks, K.M. (2019) Biochemistry 57, 6129-6131. Viewpoint. High-throughput Explorations of RNA Structural Modularity. (PDF File)

260. Herschlag, D., Pinney, M. (2018) Biochemistry 57, 3338-3352. Hydrogen Bonds: Simple After All? PMID: 29678112. (Medline) (PDF File) (Supporting Info)

259. Zettl, T., Mathew, R.S., Shi, X.S., Doniach, S., Herschlag, D., Harbury, P.A.B., Lipfert, J. (2018)  Sci. Adv. 4, earr4418.  Gold Nanocrystal Labels Provide a Sequence-to-3D Structure Map in SAXS Reconstructions. PMCID: PMC5969820. (Medline) (PDF File) (Supporting Info)

258. Gracia, B., Al-Hashimi, H.M., Bisaria, N., Das, R., Herschlag, D., Russell, R. (2018) Cell Rep. 22, 3240-3250. Hidden Structural Modules in a Cooperative RNA Folding Transition. PMCID: PMC5894117. (Medline) (PDF File) (Supporting Info)

257. Zettl, T., Das, R., Harbury, P.B., Herschlag, D., Lipfert, J., Mathew, R.S., Shi, X.S. (2018) Curr. Protoc. Nucleic Acid Chem. 73, e54. Recording and Analyzing Nucleic Acid Distance Distributions with X-ray Scattering Interferometry (XSI). PMCID: PMC6082382. (Medline) (PDF File)

256. Herschlag, D., Sengupta, R.N. (2018) Catalysis in Chemistry and Biology: Proceedings of the 24th International Solvay Conference on Chemistry Ed. Kurt Wüthrich, Ed. R.H. Grubbs. 361-367. Lessons from Catalysis by RNA Enzymes. (PDF File)


255. Bonilla, S., Limouse, C., Bisaria, N., Gebala, M., Mabuchi, H., Herschlag, D. (2017) J. Am. Chem. Soc. 139, 18576-18589. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. PMCID: PMC5748328. (Medline) (PDF File) (Supporting Information) (Supporting Data)
        See also: Stone, M.D. (2018) Faculty of 1000 Article Recommendation (Link)

254. Sunden, F., AlSadhan, I., Lyubimov, A., Doukov, T., Swan, J., Herschlag, D. (2017) J. Biol. Chem. 292, 20960-20974. Differential Catalytic Promiscuity of the Alkaline Phosphatase Superfamily Bimetallo Core Reveals Mechanistic Features Underlying Enzyme Evolution. PMCID: PMC5743071. (Medline) (PDF File) (Supporting Info)

253. Bisaria, N., Greenfeld, M., Limouse, C., Mabuchi, H.M., Herschlag, D. (2017) Proc. Natl. Acad. Sci. U.S.A. 114, E7688-E7696. Quantitative Tests of a Reconstitution Model for RNA Folding Thermodynamics and Kinetics. PMCID: PMC5604005. (Medline) (PDF File) (Supporting Info

252. Lamba, V., Yabukarski, F., Herschlag, D. (2017) J. Am. Chem. Soc. 139, 11089-11095. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Keotsteroid Isomerase Active Site Mutant. PMID: 28719738. (Medline) (PDF File) (Supporting Info)

251. Gleitsman, K.R., Sengupta, R.N., Herschlag, D. (2017) RNA 23, 1745-1753. Slow Molecular Recognition by RNA. PMCID: PMC5688996. (Medline) (PDF File) (Supporting Info 1) (Supporting Info 2) (Supporting Info 3) (Supporting Info 4) (Supporting Info 5)

250. Allred, B.D., Gebala, M., Herschlag, D. (2017)  J. Am. Chem. Soc. 139, 7540-7548. Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+•C Wobble Formation in Double-stranded DNA. PMCID: PMC5466006. (Medline) (PDF File) (Supporting Info)

249. Vaidyanathan, P.P., AlSadhan, I., Merriman, D.K., Al-Hashimi, H.M., Herschlag, D. (2017) RNA 23, 611-618. Pseudoridine and N-6 Methyladenosine Modifications Weaken PUF Protein/RNA Interactions. PMCID: PMC5393172. (Medline) (PDF File) (Supporting Info)

248. Lamba, V., Sanchez, E., Fanning, L.R., Howe, K., Gonzalez, M.A., Herschlag, D., Forconi, M. (2017) Biochemistry 56, 582-591. Kemp Eliminase Activity of Ketosteroid Isomerase. PMCID: PMC5446047. (Medline) (PDF File) (Supporting Info

247. Shi, X.S., Walker, P., Harbury, P., Herschlag, D. (2017) Nucleic Acids Res. 45, e64. Determination of the Conformational Ensemble of the TAR RNA by X-ray Scattering Interferometry. PMCID: PMC5416899. (Medline) (PDF File) (Supporting Info)

246. Bisaria, N., Jarmoskaite, I., Herschlag, D. (2017) Cell Syst. 4, 21-29. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. PMCID: PMC5308874. (Medline) (PDF File)


245. Sunden, F., AlSadhan, I., Lyubimov, A., Ressl, S., Wiersma-Koch, H., Borland, J., Brown, C., Johnson, T., Singh, Z., Herschlag, D. (2016) J. Am. Chem. Soc. 138, 14273-14287. Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases Across the Alkaline Phosphatase Superfamily. PMCID: PMC5096464. (Medline) (PDF File) (Supporting Info)

244. Gebala, M., Bonilla, S., Bisaria, N., Herschlag, D. (2016) J. Am. Chem. Soc.  138, 10925-10934. Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? PMCID: PMC5010015. (Medline) (PDF File) (Supporting Info)

243. van Schie, S.N.S., Sengupta, R.N., Herschlag, D. (2016) PLOS ONE 11, e0160457. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two RNA Enzymes. PMCID: PMC4976970. (Medline) (PDF File

242. Lamba, V., Yabukarski, F., Pinney, M., Herschlag, D. (2016) J. Am. Chem. Soc. 138, 9902-9909. Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase. PMID: 27410422. (Medline) (PDF File) (Supporting Info)

241. Gracia, B., Xue, Y., Bisaria, N., Herschlag, D., Al-Hashimi, H.M., Russell, R. (2016) J. Mol. Biol. 428, 3972-3985. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. PMCID: PMC5048535. (Medline) (PDF File) (Supporting Info)

240. Bisaria, N., Greenfeld, M., Limouse, C., Pavlichin, D., Mabuchi, H., Herschlag, D. (2016) Proc. Natl. Acad. Sci. U.S.A. 113, e4956-4965. Kinetic and Thermodynamic Framework for P4-P6 RNA Reveals Tertiary Motif Modularity and Modulation of the Folding Preferred Pathway. PMCID: PMC5003260. (Medline) (PDF File) (Supporting Info) (Data)

239. Peck, A., Sunden, F., Andrews, L.D., Pande, V.S., Herschlag, D. (2016) J. Mol. Biol. 428, 2758-2768. Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase. PMCID: PMC6169531. (Medline) (PDF File) (Supporting Info)
        See also: Allen, K. (2016) Faculty of 1000 Article Recommendation (Link)

238. Xue, Y., Gracia, B., Herschlag, D., Russell, R., Al-Hashimi, H.M. (2016) Nat. Commun. 7, ncomms11768. Visualizing the Formation of an RNA Folding Intermediate through a Fast Highly Modular Secondary Structure Switch. PMCID: PMC4909931. (Medline) (PDF File) (Supporting Info)

237. Shi, X.S., Huang, L., Lilley, D.M.J., Harbury, P.A.B., Herschlag, D. (2016) Nat. Chem. Biol. 12, 146-152. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes. PMCID: PMC4755865. (Medline) (PDF File) (Supporting Info)
        See also: Wang, Y-X. (2016) Nat. Chem. Biol. 12, 126-127. News and Views. RNA Conformation: Lightening Up Invisible States (PDF File
        See also: SLAC Science Highlight (2016) The Solution Structural Ensembles of RNA and RNA Protein Complexes (PDF File)


236. Chen, B., Lim, S., Kannan, A., Alford, S., Sunden, F., Herschlag, D., Dimov, I., Baer, T., Cochran, J. (2015) Nat. Chem. Biol. 12, 76-81. High-throughput Analysis and Protein Engineering Using Microcapillary Arrays. PMCID: PMC6215714. (Medline) (PDF File) (Supporting Info)
        See also: Bornscheuer, U. (2016) Nat. Chem. Biol. News and Views. Protein Engineering: Beating the Odds. (PDF File
        See also: Arora, P. and Wuo, M. (2016) Faculty of 1000 Article Recommendation (Link)

235. Sengupta, R.N., van Schie, S.N.S., Giambasu, G., Dai, Q., Yesselman, J.D., York, D., Piccirilli, J.A., Herschlag, D. (2015) RNA 22, 32-48. An Active Site Rearrangement within the Tetrahymena Group I Ribozyme Releases Non-Productive Interactions and Allows Formation of Catalytic Interactions. PMCID: PMC4691833. (Medline) (PDF File) (Supporting Info)

234. Gebala, M., Giambasu, G., Lipfert, J., Bisaria, N., Bonilla, S., Li, G., York, D., Herschlag, D. (2015) J. Am. Chem. Soc. 137, 14705-14715. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. PMCID: PMC4739826.  (Medline) (PDF File) (Supporting Info)

233. Hogan, G., Brown, P., Herschlag, D. (2015) PLoS Biol. 13, e1002307. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and their mRNA Targets. PMICD: PMC4654594. (Medline) (PDF File) (Supporting Info)

232. Natarajan, A., Yabukarski, F., Lamba, V., Schwans, J., Sunden, F., Herschlag, D. (2015) Science (Technical Comment) 349, 936. Extreme Electric Fields Power Catalysis in the Active Site of Ketosteroid Isomerase. PMID: 26315426   (Medline) (PDF File)

231. Shi, X.S., Bonilla, S., Herschlag, D., Harbury, P. (2015) Methods in Enzymology: Structures of Large RNA Molecules and Their Complexes 558, 75-97. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. PMID: 26068738 (Medline) (PDF File) (Supporting Info)

230. Sunden, F., Peck, A., Salzman, J., Ressl, S., Herschlag, D. (2015) eLife 4, e06181. Extensive Site-directed Mutagenesis Reveals Interconnected Functional Units in the Alkaline Phosphatase Active Site. PMCID: PMC4438272 (Medline) (PDF File) (Supporting Info)

229. Sigala, P., Ruben, E., Liu, C., Piccoli, P., Hohenstein, E., Martinez, T., Schultz, A., Herschlag, D. (2015) J. Am. Chem. Soc. 137, 5730-5740. Determination of Hydrogen Bond Structure in Water Versus Aprotic Environments to Test the Relationship Between Length and Stability. PMID: 25871450 (Medline) (PDF File) (Supporting Info)

228. Herschlag, D. (2015) RNA 21, 527-528. Learning from Ribozymes. PMCID: PMC4371266. (Medline) (PDF File)

227. Bisaria, N., Herschlag, D. (2015) Biochem. Soc. Trans. 43, 172-178. Probing the Kinetic and Thermodynamic Consequences of the Tetraloop/Tetraloop Receptor Monovalent Ion-Binding Site in P4-P6 RNA by smFRET. PMCID: PMC4739851. (Medline) (PDF File) (Supporting Info)

226. Herschlag, D., Allred, B.E., Gowrishankar, S. (2015) Curr. Opin. Struct. Biol. 30, 125-133. From Static to Dynamic: The Need for Structural Ensembles and a Predictive Model of RNA Folding and Function. PMCID: PMC4416989. (Medline) (PDF File) (Supporting Info)

225. Greenfeld, M., van de Meent, J-W., Pavlichin, D., Mabuchi, H., Wiggins, C.H., Gonzalez, R.L. Jr., Herschlag, D. (2015) BMC Bioinformatics 16, 1-4. Single-molecule Dataset (SMD): A Generalized Storage Format for Raw and Processed Single-molecule Data. PMCID: PMC4384321 (Medline) (PDF File) (Supporting Info)

224. Shah, N., Colbert, K.N., Enos, M.D., Herschlag, D., Weis, W.I. (2015) J. Biol. Chem. 290, 2175-2188. Three αSNAP and 10 ATP Molecules Are Used in SNARE Complex Disassembly by N-ethylmaleimide-sensitive Factor (NSF). PMCID: PMC4303669 (Medline) (PDF File)


223. Andrews, L., Zalatan, J., Herschlag, D. (2014) Biochemistry 53, 6811-6819. Probing the Origins of Catalytic Discrimination Between Phosphate and Sulfate Monoester Hydrolysis: Comparative Analysis of Alkaline Phosphatase and Protein Tyrosine Phosphatases. PMCID: PMC4222534. (Medline) (PDF File) (Supporting Info)

222. Gleitsman, K., Herschlag, D. (2014) RNA 20, 1732-1746. A Kinetic and Thermodynamic Framework for the Azoarcus Group I Ribozyme Reaction. PMCID: PMC4201826. (Medline) (PDF File) (Supporting Info)

221. Natarajan, A., Schwans, J.P., Herschlag, D. (2014) J. Am. Chem. Soc. 136, 7643-7654. Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site. PMCID: PMC4046884 (Medline) (PDF File) (Supplementary Info)

220. Khosla, C., Herschlag, D., Crane, D.E., Walsh, C.T. (2014) Biochemistry 53, 2875-2883. Assembly Line Polyketide Synthases: Mechanistic Insights and Unsolved Problems. PMCID: PMC4020578. (Medline) (PDF File

219. Shi, X.S., Bisaria, N., Benz-Moy, T., Bonilla, S., Pavlichin, D., Herschlag, D. (2014) J. Am. Chem. Soc. 136, 6643-6648. Roles of Long-range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme. PMCID: PMC4021564. (Medline) (PDF File) (Supporting Info)

218. Schwans, J.P., Hanoian, P., Lengerich, B., Sunden, F., Gonzalez, A., Tsai, Y., Hammes-Schiffer, S., Herschlag, D. (2014) Biochemistry 53, 2541-2555. Experimental and Computational Mutagenesis to Investigate the Positioning of a General Base within an Enzyme Active Site. PMCID: PMC4004248. (Medline) (PDF File) (Supporting Info)

217. Shi, X.S., Beauchamp, K.A., Harbury, P.A.B., Herschlag, D. (2014) Proc. Natl. Acad. Sci. U.S.A. 111, 1473-1480. From a Structural Average to the Conformational Ensemble of a DNA Bulge. PMCID: PMC3992658. (Medline) (PDF File) (Supporting Info)

216. Lipfert, J., Doniach, S., Das, R., Herschlag, D. (2014) Annu. Rev. Biochem. 83, 813-841 Understanding Nucleic Acid-Ion Interactions. PMCID: PMC4384882. (Medline) (PDF File)

215.  Giambasu, G., Luchko, T., Herschlag, D., York, D., Case, D. (2014) Biophys. J. 106, 883-894. Ion Counting from Explicit Solvent Simulations and 3D-RISM. PMCID: PMC3944826. (Medline) (PDF File) (Supporting Info


214. Wiersma-Koch, H.I., Sunden, F., Herschlag, D. (2013) Biochemistry 52, 9167-9176. Site-directed Mutagenesis to Map Interactions that Enhance Cognate and Limit Promiscuous Reaction of an Alkaline Phosphatase Superfamily Phosphodiesterase. PMCID: PMC4415882 (Medline) (PDF File) (Supporting Info)

213. Schwans, J., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D. (2013) Biochemistry 52, 7840-7855. Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase. PMCID: PMC3890242. (Medline) (PDF File) (Supporting Info)
        See also: Schwans, J.P., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D. (2018) Biochemistry Article ASAP. Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase. DOI: 10.1021/acs.biochem.8b00246. (PDF File)

212. Greenfeld, M., Herschlag, D. (2013) Methods in Molecular Enzymology 530, 281-297. Fluorescently Labeling Synthetic RNAs. PMID: 24034327. (Medline) (PDF File)

211. Porecha, R., Herschlag, D. (2013) Methods in Molecular Enzymology 530, 253-279. RNA Radiolabeling. PMID: 24034326. (Medline) (PDF File

210. Chen, J., Du Bois, J., Glenn, J., Herschlag, D., Khosla, C. (2013) ACS Chemical Biology 8, 1860-1861. The Stanford Institute for Chemical Biology. PMID: 24053754. (Medline) (PDF File

209. Nguyen, P., Shi, X.S., Sigurdson, S., Herschlag, D., Qin, P. (2013) ChemBioChem 14, 1720-1723. A Single-stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme. PMCID: PMC3817310. (Medline) (PDF File) (Supporting Info)

208. Schwans, J.P., Sunden, F., Lassila, J.K., Gonzalez, A., Tsai, Y., Herschlag, D. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 11308-11313. Use of Anion Aromatic Interactions to Position the General Base in the Ketosteroid Isomerase Active Site. PMCID: PMC3710852. (Medline) (PDF File) (Supporting Info)
        See also: Kosman, D. (2013) Faculty of 1000 Article Recommendation (Link)

207. Sigala, P.A., Fafarman, A.T., Schwans, J.P., Fried, S.D., Fenn, T.D., Caaveiro, J.M.M., Pybus, B., Ringe, D., Petsko, G., Boxer, S., Herschlag, D. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, E2552-E2561. Quantitative Dissection of Hydrogen Bond-mediated Proton Transfer in the Ketosteroid Isomerase Active Site. PMCID: PMC3710806. (Medline) (PDF File) (Supporting Info)

206. Andrews, L., Fenn, T., Herschlag, D. (2013) PLoS Biology 11, 1-18. Ground State Destabilization by Anionic Nucleophiles Contributes to the Activity of Phosphoryl Transfer Enzymes. PMCID: PMC3699461 (Medline) (PDF File
        See also: Hedstrom, L. (2013) Faculty of 1000 Article Recommendation (Link)

205. Shi, X.S., Herschlag, D., Harbury, P. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, E1444-E1451. The Structural Enzemble and Microscopic Elasticity of Freely Diffusing DNA by Direct Measurement of Fluctuations. PMCID: PMC3631670 (Medline) (PDF File) (Supporting Info)

204. Herschlag, D., Natarajan, A. (2013) Biochemistry 52, 2050-2067. Fundamental Challenges in Mechanistic Enzymology: Progress Toward Understanding the Rate Enhancements of Enzymes. PMCID: PMC3744632 (Medline) (PDF File)

203. Ruben, E.A., Schwans, J.P., Gonzalez, A., Tsai, Y., Herschlag, D. (2013) Biochemistry 52, 1074-1081. Ground State Destabilization from a Positioned General Base in the Ketosteroid Isomerase Active Site. PMCID: PMC3651043. (Medline) (PDF File) (Supporting Info)


202. Sim, A.Y.L., Lipfert, J., Herschlag, D., Doniach, S. (2012) Phys. Rev. E. 86, 021901. Salt Dependence of the Radius of Gyration and Flexibility of Single-Stranded DNA in Solution Probed by Small-Angle X-ray Scattering. PMID: 23005779. (Medline) (PDF File) (Supporting Info)

201. Forconi, M., Benz-Moy, T., Rule Gleitsman, K., Ruben, E., Metz, C., Herschlag, D. (2012) RNA 18, 1222-1229. Exploring Purine N7 Interactions via Atomic Mutagenesis: The Group I Ribozyme as a Case Study. PMCID: PMC3358644. (Medline) (PDF File) (Supporting Info)

200. Althoff, E.A., Wang, L., Jiang, L., Giger, L., Lassila, J.K., Wang, Z., Smith, M., Hari, S., Kast, P., Herschlag, D., Hilvert, D., Baker, D. (2012) Protein Science 5, 717-726. Robust Design and Optimization of Retroaldol Enzymes. PMICD: PMC3403469. (Medline) (PDF File) (Supporting Info)

199. Anthony, P.C., Sim, A.Y.L., Chu, V.B., Doniach, S., Block, S.M., Herschlag, D. (2012) J. Am. Chem. Soc. 134, 4607-4614. Electrostatics of Nucleic Acid Folding Under Conformational Constraint. PMCID: PMC33033965. (Medline) (PDF File) (Supporting Info)

198. Fredericksen, J.K., Li, N-S., Das, R., Herschlag, D., Piccirilli, J.A. (2012) RNA 18, 1123-1141. Metal Ion Rescue Revisited: Biochemical Detection of Site-bound Metal Ions Important for RNA Folding. PMCID: PMC3358636. (Medline) (PDF File) (Supporting Info)

197. Shi, X., Solomatin, S., Herschlag, D. (2012) J. Am. Chem. Soc. 134, 1910-1913. A Role for a Single-stranded Junction in RNA Catalysis by the Tetrahymena Group I Ribozyme. PMCID: PMC3277301. (Medline) (PDF File) (Supporting Info)

196. Greenfeld, M., Pavlichin, D.S., Mabuchi, H., Herschlag, D. (2012) PLoS One 7, e30024. Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data. PMCID: PMC3282690. (Medline) (PDF File) (Supporting Info)

195. Fafarman, A.T., Sigala, P.A., Schwans, J.P., Fenn, T.D., Herschlag, D., Boxer, S.G. (2012) Proc. Natl. Acad. Sci. U.S.A. 109, E299-E308. Quantitative, Directional Measurement of Electric Field Heterogeneity in the Active Site of Ketosteroid Isomerase. PMCID: PMC3277571. (Medline) (PDF File) (Supporting Info)


194. Schwans, J., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D. (2011) J. Am. Chem. Soc. 133, 20052-20055. Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase. PMCID: PMC3241876. (Medline) (PDF File) (Supporting Info)
           See also: Schwans, J., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D. (2016) J. Am. Chem. Soc. 138, 7801-7802. Correction to "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase." (Medline) (PDF File) (Supporting Info)

193. Sengupta, R.N., Yoshida, A., Herschlag, D., Piccirilli, J.A. (2011) ACS Chem. Biol. 7, 294-299. Thermodynamic Evidence for Negative Charge Stabilization by a Catalytic Metal Ion within an RNA Active Site. PMCID: PMC3707313. (Medline) (PDF File) (Supporting Info)

192. Bobyr, E., Lassila, J.K., Wiersma-Koch, H.I., Fenn, T.D., Lee, J.J., Nikolic-Hughes, I., Hodgson, K.O., Rees, D.C., Hedman, B., Herschlag, D. (2011)  J. Mol. Biol. 415, 102-117. High-resolution Analysis of Zn(II) Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography. PMCID: PMC3249517. (Medline) (PDF File) (Supporting Info)

191. Forconi, M., Schwans, J.P., Porecha, R.H., Sengupta, R.N., Piccirilli, J. A., Herschlag, D. (2011) Chemistry and Biology 18, 949-954. 2'-Fluoro Substituents Can Mimic Native 2'-Hydroxyls within Structured RNA. PMCID: PMC3167488. (Medline) (PDF File) (Supporting Info)

190. Benz-Moy, T.L., Herschlag, D. (2011) Biochemistry 50, 8733-8755. Structure-function Analysis from the Outside In: Long-range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles. PMCID: PMC3186870. (Medline) (PDF File) (Supporting Info)

189. Andrews, L., Deng, H., Herschlag, D. (2011) J. Am. Chem. Soc. 133, 11621-11631. Isotope-edited FTIR of Alkaline Phosphatase Resolves Paradoxical Ligand Binding Properties and Suggests a Role for Ground-state Destabilization. PMCID: PMC3152580. (Medline) (PDF File) (Supporting Info)

188. Greenfeld, M., Solomatin, S.V., Herschlag, D. (2011) J. Biol. Chem. 286, 19872-19879. Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA. PMCID: PMC3103363. (Medline) (PDF File) (Supporting Info)

187. Solomatin, S.V., Greenfeld, M, Herschlag, D. (2011) Nat. Struct. Mol. Biol. 18, 732-734. Implications of Molecular Heterogeneity for the Cooperativity of Biological Macromolecules. PMCID: PMC3109240. (Medline) (PDF File) (Supporting Info)

186. Forconi, M., Porecha, R.H., Piccirilli, J.A., Herschlag, D. (2011) J. Am. Chem. Soc.  133, 7791-7800. 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. PMCID: PMC3119543. (Medline) (PDF File) (Supporting Info)

185. Lassila, J.K., Zalatan, J.G., Herschlag, D. (2011) Annu. Rev. Biochem. 80, 669-702. Biological Phosphoryl Transfer Reactions: Understanding Mechanism and Catalysis. PMCID: PMC3418923. (Medline) (PDF File) (Supporting Info)


184. Hanoian, P., Sigala, P.A., Herschlag, D., Hammes-Schiffer, S. (2010) Biochemistry 49, 10339-10348. Hydrogen Bonding in the Active Site of Ketosteroid Isomerase: Electronic Inductive Effects and Hydrogen Bond Coupling. PMCID: PMC2996240. (Medline) (PDF File) (Supporting Info)

183. Riordan, D., Herschlag, D., Brown, P.O. (2010) Nucl. Acids Res. 39, 1501-1509. Identification of RNA Recognition Elements in the S. cerevisiae Transcriptome. PMCID: PMC3045596. (Medline) (PDF File) (Supporting Info)

182. Fafarman, A.T., Sigala, P.A., Herschlag, D., Boxer, S.G. (2010) J. Am. Chem. Soc. 132, 12811-12813. Decomposition of Vibrational Shifts of Nitriles into Electrostatic and Hydrogen Bonding Effects. PMCID: PMC2943212. (Medline) (PDF File) (Supporting Info)

181. Greenfeld, M., Herschlag, D. (2010) Methods Navigator: Cookbook for Biomedical Labs "Fluorescently Labeling Synthetic RNAs." (Medline) (PDF File)

180. Porecha, R., Herschlag, D. (2010) Methods Navigator: Cookbook for Biomedical Labs "RNA Radiolabeling." (Medline) (PDF File)

179. Wan, Y., Suh, H., Russell, R., Herschlag, D. (2010) J. Mol. Biol. Multiple Unfolding Events During Native Folding of the Tetrahymena Group I Ribozyme. PMCID: PMC2905490. (Medline) (PDF File) (Supporting Info)

178. Forconi, M., Sengupta, R.N., Piccirilli, J.A., Herschlag, D. (2010) Biochemistry 49, 2753-2762. A Rearrangement of the Guanosine-binding Site Establishes an Extended Network of Functional Interactions in the Tetrahymena Group I Ribozyme Active Site. PMCID: PMC2860537. (Medline) (PDF File

177. Lassila, J.K., Baker, D., Herschlag, D. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 4937-4942. Origins of Catalysis by Computationally Designed Retroaldolase Enzymes. PMCID: PMC2841948. (Medline) (PDF File) (Supporting Info)
        See also: Varani, G. (2010) Faculty of 1000 Article Recommendation (Link

176. Kraut, D.A., Sigala, P.A., Fenn, T.D., Herschlag, D. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 1960-1965. Dissecting the Paradoxical Effects of Hydrogen Bond Mutations in the Ketosteroid Isomerase Ozyanion Hole. PMCID: PMC2836627. (Medline) (PDF File) (Supporting Info)

175. Lipfert, J., Sim, A.Y.L., Herschlag, D., Doniach, S. (2010) RNA 16, 708-709. Dissecting Electrostatic Screening, Specific Ion Binding, and Ligand Binding in an Energetic Model for Glycine Riboswitch Folding. PMCID: PMC2844619. (Medline) (PDF File

174. Solomatin, S.V., Greenfeld, M., Chu, S., Herschlag, D. (2010) Nature 463, 681-684. Multiple Native States of an RNA Enzyme Reveal Persistent Ruggedness of an RNA Folding Landscape. PMCID: PMC2818749. (Medline) (PDF File) (Supporting Info)
        See also: Turner, D. (2011) Faculty of 1000 Article Recommendations (Link)
        See also:  Buchanan, M. (2010) Nature Physics  "When the Going Gets Tough" (Link)

173. Ali, M., Lipfert, J., Seifert, S., Herschlag, D., Doniach, S. (2010) J. Mol. Biol. 396, 153-165. The Ligand-free State of the TPP Riboswitch, A Partially Folded RNA Structure. PMCID: PMC2944767. (Medline) (PDF File) (Supporting Info)

172. Greenfeld, M., Herschlag, D. (2010) Methods in Enzymology 472, 205-220. Measuring the Energetic Coupling of Tertiary Contacts in RNA Folding Using Single Molecule Fluorescence Resonance Energy Transfer. (Medline) (PDF File)


171. Greenfeld, M., Herschlag, D. (2009) Methods in Enzymology 469, 375-389. Probing Nucleic Acid Ion-interactions with Buffer Exchange Atomic Emission Spectroscopy. PMID: 20946799. (Medline) (PDF File)

170. Shi, X.S., Herschlag, D. (2009) Methods in Enzymology 469, 289-302. Fluorescence Polarization Anisotropy to Measure RNA Dynamics. PMID: 20946795. (Medline) (PDF File)

169. Solomatin, S., Herschlag, D. (2009) Methods in Enzymology 469, 47-67. Methods of Site-specific Labeling of RNA with Fluorescent Dyes. PMID: 20946784. (Medline) (PDF File

168. Forconi, M., Herschlag, D. (2009) Methods in Enzymology 468, 311-333. Use of Phosphorothioates to Identify Sites of Metal Ion Binding in RNA. PMID: 20946776. (Medline) (PDF File)

167. Forconi, M., Herschlag, D. (2009) Methods in Enzymology 468, 91-106. Metal Ion-based RNA Cleavage as a Structural Probe. PMID: 20946766. (Medline) (PDF File)

166. Chu, V.B., Lipfert, J., Bai, Y., Pande, V.S., Doniach, S., Herschlag, D. (2009) RNA 15, 2195-2205. Do Conformational Biases of Simple Helical Junctions Influence RNA Folding Stability and Specificity? PMCID: PMC2779674. (Medline) (PDF File) (Supporting Info)
        See also: Luebke, K.J. (2010) Faculty of 1000 Article Recommendation (Link)

165. Henrickson, D.G., Hogan, D.J., McCullough, H.L., Myers, J.W., Herschlag, D., Ferrell, J.E., Brown, P.O. (2009) PLoS Biology 7, e1000238. Concordant Regulation of Translation and mRNA Decay for Hundreds of Targets of a Human microRNA. PMCID: PMC2766070. (Medline) (PDF File) (Supporting Info)

164. Forconi, M., Sengupta, R.N., Liu, M-C., Sartorelli, A.C., Piccirilli, J.A., Herschlag, D. (2009) Angew. Chem. Int. Ed. 48, 7171-7175. Structure and Function Converge to Identify a Hydrogen Bond in the Group I Ribozyme Active Site. PMCID: PMC2862986. (Medline) (PDF File) (Supporting Info)
        Selected as 'Hot Paper' by the Editors and highlighted in Nat. Chem. Biol. (2009) 5, 712.

163. Schwans, J.P., Kraut, D.A., Herschlag, D. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 14271-14275. Determining the Catalytic Role of Remote Substrate Binding Interactions in Ketosteroid Isomerase. PMCID: PMC2732871. (Medline) (PDF File) (Supporting Info)

162. Zalatan, J.G., Herschlag, D. (2009) Nature Chem. Biol. 5, 516-520. The Far Reaches of Enzymology. PMID: 19620986. (Medline) (PDF File)

161. Shi, X.S., Mollova, E., Pljevaljcic, G., Millar, D., Herschlag, D. (2009) J. Am. Chem. Soc. 131, 9571-9578. Probing the Dynamics of the P1 Helix within the Tetrahymena Group I Intron. PMICD: PMC2758093. (Medline) (PDF File) (Supporting Info)

160. Sigala, P.A., Caaveiro, J.M., Ringe, D., Petsko, G.A., Herschlag, D. (2009) Biochemistry 48, 6932-6939. Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site. PMCID: PMC3393856. (Medline) (PDF File) (Supporting Info)

159. Sigala, P.A., Tsuchida, M.A., Herschlag, D. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 9232-9237. Hydrogen Bond Dynamics in the Active Site of Photoactive Yellow Protein. PMCID: PMC2695108. (Medline) (PDF File) (Supporting Info)
        Biopolymers Research Highlights Volume 91/Number 9 iii

158. Kraut, D.A., Churchill, M.J., Dawson, P.E., Herschlag, D. (2009) ACS Chem. Biol. 4, 269-273. Evaluating the Potential for Halogen Bonding in the Oxyanion Hole of Ketosteroid Isomerase Using Unnatural Amino Acid Mutagenesis. PMCID: PMC2708088. (Medline) (PDF File)

157. Grant, G.P.G., Boyd, N., Herschlag, D., Qin, P.Z. (2009) J. Am. Chem. Soc. 131, 3136-3137. Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-directed Spin-labeling. PMCID: PMC2788000. (Medline) (PDF File) (Supporting Info)
        See also: Cafiso, D. (2009) Faculty of 1000 Article Recommendation (Link

156. Lipfert, J., Herschlag, D., Doniach, S. (2009) Methods in Molecular Biology 540, 141-159. Riboswitch Conformations Revealed by Small-angle X-ray Scattering. PMCID: PMC4393248. (Medline) (PDF File)

155. Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., Altman, R.B. (2009) RNA 15, 189-199. Coarse-grained Modeling of Large RNA Molecules with Knowledge-based Potentials and Structural Filters. PMCID: PMC2648710. (Medline) (PDF File) (Supporting Info)


154. Chu, V.B., Bai, Y., Lipfert, Y., Doniach, S., Herschlag, D. (2008) Curr. Opin. Chem. Biol. 12, 619-625. A Repulsive Field: Advances in the Electrostatics of the Ion Atmosphere. PMCID: PMC2976615. (Medline) (PDF File)

153. Lassila, J., Herschlag, D. (2008) Biochemistry 47, 12853-12859. Promiscuous Sulfatase Activity and Thio-effects in a Phosphodiesterase of the Alkaline Phosphatase Superfamily. PMCID: PMC2662379. (Medline) (PDF File)

152. Zalatan, J., Fenn, T.D., Herschlag, D. (2008) J. Mol. Biol. 384, 1174-1189. Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-site Metal Ion. PMCID: PMC2622731. (Medline) (PDF File) (Supporting Info)

151. Hogan, D., Riordan, D., Gerber, A., Herschlag, D., Brown, P.O. (2008) PLoS Biology 6, 2297-2313. Diverse RNA-binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System. PMCID: PMC2573929. (Medline) (PDF File
         See also: Marcotte, E.M. and Vogel, C. (2009) Faculty of 1000 Article Recommendation (Link)

150. Sigala, P., Kraut, D., Caaveiro, J., Pybus, B., Ruben, E., Ringe, D., Petsko, G., Herschlag, D. (2008) J. Am. Chem. Soc. 130, 13696-13708. Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole. PMCID: PMC2700827. (Medline) (PDF File) (Supporting Info)
        See also: Kirby, A.J., Hollfelder, F. (2008) Nature 456, 45-46. News and Views. Biochemistry: Enzymes Under the Nanoscope. (PDF File)

149. Laederach, A., Das, R., Vicens, Q., Pearlman, S., Brenowitz, M., Herschlag, D., Altman, R. (2008) Nature Protocols 3, 1395-1401. Semi-automated and Rapid Quantification of Nucleic Acid Footprinting and Structure Mapping Experiments. PMCID: PMC2652576. (Medline) (PDF File) (Supporting Info)

148. O'Brien, P., Lassila, J., Fenn, T., Zalatan, J., Herschlag, D. (2008) Biochemistry 47, 7663-7672. Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in E. coli Alkaline Phosphatase. PMCID: PMC2587100. (Medline) (PDF File)

147. Chu, V.B., Herschlag, D. (2008) Curr. Opin. Struc. Biol. 18, 305-314. Unwinding RNA's Secrets: Advances in the Biology, Physics, and Modeling of Complex RNAs. PMCID: PMC2574980. (Medline) (PDF File)

146. Forconi, M., Lee, J., Piccirilli, J., Herschlag, D. (2008) Biochemistry 47, 6883-6893. Functional Identification of Ligands for a Catalytic Metal Ion in Group I Introns. PMCID: PMC2758101. (Medline) (PDF File) (Supporting Info)

145. Bai, Y., Chu, V.B., Lipfert, J., Pande, V.S., Herschlag, D., Doniach, S. (2008) J. Am. Chem. Soc. 130, 12334-12341. Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble. PMCID: PMC3167486. (Medline) (PDF File) (Supporting Info)
        See also: Baker, N. (2008) Faculty of 1000 Article Recommendation (Link

144. Mueller-Planitz, F., Herschlag, D. (2008) J. Biol. Chem. 283, 17463-17476. Coupling between ATP Binding and DNA Cleavage by DNA Topoisomerase II: A Unifying Kinetic and Structural Mechanism. PMCID: PMC2427340. (Medline) (PDF File) (Supporting Info)

143. Sattin, B.D., Zhao, W., Travers, K., Chu, S., Herschlag, D. (2008) J. Am. Chem. Soc. 130, 6085-6087. Direct Measurement of Tertiary Contact Cooperativity in RNA Folding. PMCID: PMC2835547. (Medline) (PDF File) (Supporting Info)
        See also: Gonzalez, R.L. (2008) Nat. Chem. Biol. 4, 451-452. News and Views. Navigating the RNA Folding Landscape.  (PDF File)

142. Hendrickson, D.G., Hogan, D.J., Herschlag, D., Ferrell, J.E., Brown, P.O. (2008) PLoS One 3, e2126. Systematic Identification of mRNAs Recruited to RISC by Specific microRNAs and Corresponding Changes in Transcript Abundance. PMCID: PMC2330160. (Medline) (PDF File) (Supporting Info)
        See also: Rio, D. (2009) Faculty of 1000 Article Recommendation (Link)

141. Das, R., Kudaravalli, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B., Herschlag, D. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 4144-4149. Structural Interference of Native and Partially Folded RNA by High-throughput Contact Mapping. PMCID: PMC2393762. (Medline) (PDF File) (Supporting Info)
        See also: Lehman, N. and Burton, A. (2008) Faculty of 1000 Article Recommendation (Link)


140. Bai, Y., Greenfeld, M., Travers, K., Chu, V.B., Lipfert, J., Doniach, S., Herschlag, D. (2007) J. Am. Chem. Soc. 129, 14981-14988. Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids. PMCID: PMC3167487. (Medline) (PDF File) (Supporting Info)
        See also: Egli, M. (2008) Faculty of 1000 Article Recommendation (Link)

139. Sigala, P.A., Fafarman, A.T., Bogard, P.E., Boxer, S.G., Herschlag, D. (2007) J. Am. Chem. Soc. 129, 12104-12105. Do Ligand Binding and Solvent Exclusion Alter the Electrostatic Character within the Oxyanion Hole of an Enzymatic Active Site? PMCID: PMC3171184. (Medline) (PDF File) (Supporting Info)
        See also: Matthews, R., Licht, S.S. (2007) Faculty of 1000 Article Recommendation (Link

138. Forconi, M., Piccirilli, J.A., Herschlag, D. (2007) RNA 13, 1656-1667. Modulation of Individual Steps in Group I Intron Catalysis by a Peripheral Metal Ion. PMCID: PMC1986806. (Medline) (PDF File

137. Chu, V.B., Bai, Y., Lipfert, J., Herschlag, D., Doniach, S. (2007) Biophys. J. 9, 3202-3209. Evaluation of Ion Binding to DNA Duplexes Using a Size-modified Poisson-Boltzmann Theory. PMCID: PMC2025650. (Medline) (PDF File) (Supporting Info)

136. Zalatan, J.G., Catrina, I., Mitchell, R., Grzyska, P.K., O'Brien, P.J., Herschlag, D., Hengge, A.C. (2007) J. Am. Chem. Soc. 129, 9789-9798. Kinetic Isotope Effects for Alkaline Phosphatase Reactions: Implications for the Role of Active Site Metal Ions in Catalysis. PMCID: PMC3171187. (Medline) (PDF File) (Supporting Info)

135. Travers, K., Boyd, N., Herschlag, D. (2007) RNA 13, 1205-1213. Low Specificity of Metal Ion Binding in the Metal Ion Core of a Folded RNA. PMCID: PMC1924890. (Medline) (PDF File

134. Mueller-Planitz, F., Herschlag, D. (2007) Nucleic Acids Res. 35, 3764-3773. DNA Topoisomerase II Selects DNA Cleavage Sites Based on Reactivity Rather than Binding Affinity. PMCID: PMC1920260. (Medline) (PDF File) (Supporting Info)

133. Karbstein, K., Lee, J., Herschlag, D. (2007) Biochemistry 46, 4861-4875. Probing the Role of a Secondary Structure Element at the 5'-and 3'-Splice Sites in Group I Intron Self-splicing: The L-16 Scal Ribozyme Reveals a New Role of the G-U Pair in Self-splicing. PMCID: PMC2597287. (Medline) (PDF File) (Supporting Info)

132. Catrina, I., O'Brien, P., Purcell, J., Nikolic-Hughes, I., Zalatan, J.G., Hengge, A.C., Herschlag, D. (2007) J. Am. Chem. Soc. 129, 5760-5765. Probing the Origin of the Compromised Catalysis of E. coli Alkaline Phosphatase in its Promiscuous Sulfatase Reaction. PMCID: PMC2532492. (Medline) (PDF File)

131. Lee, T.H., Lapidus, L.J., Zhao, W., Travers, K.J., Herschlag, D., Chu, S. (2007) Biophys. J. 92, 3275-3283. Measuring the Folding Transition Time of Single RNA Molecules. PMCID: PMC1852359. (Medline) (PDF File)
        See also: Gruebele, M. and Ebbinghaus, S. (2009) Faculty of 1000 Article Recommendation (Link)

130. Lipfert, J., Chu, V.B., Bai, Y., Herschlag, D., Doniach, S. (2007) J. Appl. Crystallogr. 40, 235-239. Low Resolution Models for Nucleic Acids from Small-angle X-ray Scattering with Applications to Electrostatic Modeling. (PDF File)

129. Lipfert, J., Das, R., Chu, V.B., Kudaravalli, M., Boyd, N., Herschlag, D., Doniach, S. (2007) J. Mol. Biol. 365, 1393-1406. Structural Transitions and Thermodynamics of a Glycerine-dependent Riboswitch from Vibrio cholerae. PMCID: PMC1941672. (Medline) (PDF File) (Supporting Info)
         See also: Egli, M. (2007) Faculty of 1000 Article Recommendation (Link)


128. Woodside, M.T., Anthony, P.C., Behnke-Parks, W., Larizadeh, K., Herschlag, D., Block, S.M. (2006) Science 314, 1001-1004. Direct Measurement of the Full, Sequence-dependent Folding Landscape of a Nucleic Acid. PMCID: PMC2656380. (Medline) (PDF File) (Supporting Info)

127. Fierke, C.A., Herschlag, D. (2006) Curr. Opin. Chem. Biol. 10, 453-454. The Wide Reach of Enzymology: From Bioorganic Chemistry to Chemical Biology and Beyond. Editorial Overview. (PDF File)

126. Russell, R., Das, R., Suh, H., Travers, K., Laederach, A., Engelhardt, M., Herschlag, D. (2006) J. Mol. Biol.  363, 531-544. The Paradoxical Behavior of a Highly Structured Misfolded Intermediate in RNA Folding. PMID: 16963081. (Medline) (PDF File

125. Mueller-Planitz, F., Herschlag, D. (2006) J. Biol. Chem.  281, 23395-23404. Interdomain Communication in DNA Topoisomerase II: DNA Binding and Enzyme Activation. PMID: 16782968. (Medline) (PDF File) (Supporting Info)

124. Zalatan, J.G., Fenn, T.D., Brunger, A.T., Herschlag, D. (2006) Biochemistry 45, 9788-9803. Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase: Implications for Mechanism and Evolution. PMID: 1689310. (Medline) (PDF File) (Supporting Info)

123. Woodside, M.T., Behnke-Parks, W.M., Larizadeh, K., Travers, K., Herschlag, D., Block, S.M. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 6190-6195. Nanomechanical Measurements of the Sequence-dependent Folding Landscapes of Single Nucleic Acid Hairpins. PMCID: PMC1458853. (Medline) (PDF File) (Supporting Info)

122. Kraut, D.A., Sigala, P.A., Pybus, B., Liu, C.W., Ringe, D., Petsko, G.A., Herschlag, D. (2006) PLoS Biology 4, e99. Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole. PMCID: PMC1413570. (Medline) (PDF File) (Supporting Info)

121. Gerber, A.P., Luschnig, S., Krasnow, M.A., Brown, P.O., Herschlag, D. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 4487-4492. Genome-wide Identification of mRNAs Associated with the Translational Regulator PUMILIO in Drosophilia melanogaster. PMCID: PMC1400586. (Medline) (PDF File) (Supporting Info)
        See also: Gavis, E. (2006) Faculty of 1000 Article Recommendation (Link)

120. Zalatan, J.G., Herschlag, D. (2006) J. Am. Chem. Soc. 128, 1293-1303. Alkaline Phosphatase Mono- and Di-esterase Reactions: Comparative Transition State Analysis. PMCID: PMC2538955. (Medline) (PDF File) (Supporting Info)


119. Hougland, J., Piccirilli, J., Forconi, M., Lee, J., Herschlag, D. (2005) RNA World 3rd Edition How the Group I Intron Works: A Case Study of RNA Structure and Function. Gesteland, R.F., Cech, T.R., Atkins, J.F., Editors. Cold Spring Harbor Laboratory Press, New York. 133-205. (PDF File)

118. Johnson, T.H., Tijerina, P., Chadee, A.B., Herschlag, D., Russell, R. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 10176-10181. Structural Specificity Conferred by a Group I RNA Peripheral Element. PMCID: PMC1177367. (Medline) (PDF File) (Supporting Info)
        See also: Westhof, E. (2005) Faculty of 1000 Article Recommendation (Link)

117. Das, R., Travers, K., Bai, Y., Herschlag, D. (2005) J. Am. Chem. Soc. 127, 8272-8273. Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core. PMCID: PMC2538950. (Medline) (PDF File) (Supporting Info)
        See also: Luebke, K.J. (2005) Faculty of 1000 Article Recommendation (Link

116. Nikolic-Hughes, I., O'Brien, P.J., Herschlag, D. (2005) J. Am. Chem. Soc. 127, 9314-9315. Alkaline Phosphatase Catalysis is Ultrasensitive to Charge Sequestered Between the Active Site Zinc Ions. PMID: 15984827. (Medline) (PDF File) (Supporting Info)

115. Forconi, M., Herschlag, D. (2005) J. Am. Chem. Soc. 127, 6160-6161. Promiscuous Catalysis by the Tetrahymena Group I Ribozyme. PMID: 15853307. (Medline) (PDF File) (Supporting Info)
        See also: Luebke, K.J. (2005) Faculty of 1000 Article Recommendation (Link)

114. Hougland, J.L., Kravchuk, A.V., Herschlag, D., Piccirilli, J.A. (2005) PLoS Biology 3, e277. Functional Identification of a Catalytic Metal Ion Binding Site within RNA. PMCID: PMC1184590. (Medline) (PDF File) (Supporting Info)

113. Arava, Y., Boas, F.E., Brown, P.O., Herschlag, D. (2005) Nucleic Acids Res. 33, 2421-2432. Dissecting Eukaryotic Translation and Its Control By Ribosome Density Mapping. PMCID: PMC1087779. (Medline) (PDF File) (Supporting Info)

112. Bai, Y., Das, R., Millet, I.S., Herschlag, D., Doniach, S. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 1035-1040. Probing Counterion Modulated Repulsion and Attraction Between Nucleic Acid Duplexes in Solution. PMCID: PMC545826. (Medline) (PDF File) (Supporting Info)
        See also: Stivers, J. (2005) Faculty of 1000 Article Recommendation (Link)

111. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., Altman, R.B. (2005) RNA 11, 344-354. SAFA: Semi-Automated Footprinting Analysis Software for High-throughput Quantification of Nucleic Acid Footprinting Experiments. PMCID: PMC545826. (Medline) (PDF File) (Supporting Info)


110. Andresen, K., Das, R., Park, H.Y., Smith, H., Kwok, L.W., Lamb, J.S., Kirkland, E.J., Herschlag, D., Finkelstein, K.D., Pollack, L. (2004) Physical Review Letters 93, 248103-1 - 248103-1. Spatial Distribution of Competing Ions Around DNA in Solution. PMID: 15697865. (Medline) (PDF File)

109. Karbstein, K., Tang, K-H., Herschlag, D. (2004) RNA 10, 1730-1739. A Base Triple in the Tetrahymena Group I Core Affects the Reaction Equilibrium via a Threshold Effect. PMCID: PMC1370661. (Medline) (PDF File

108. Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., Chance, M. (2004)  J. Mol. Biol. 343, 1195-1206. Principles of RNA Compaction: Insights From the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations. PMID: 15491606. (Medline) (PDF File)

107. Nikolic-Hughes, I., Rees, D.C., Herschlag, D. (2004) J. Am. Chem. Soc. 126, 11814-11819. Do Electrostatic Interactions with Positively Charged Active Site Groups Tighten the Transition State for Enzymatic Phosphoryl Transfer? PMID: 15382915. (Medline) (PDF File)

106. Gerber, A.P., Herschlag, D., Brown, P.O. (2004) PLoS Biology 2, 342-354. Extensive Association of Functionality and Cytotopically Related mRNAs with Puf-family RNA-binding Proteins in Yeast. PMCID: PMC368173. (Medline) (PDF File) (Supporting Info)
         See also: Bahler, J. (2005) Faculty of 1000 Article Recommendation (Link)


105. Shepard, K.A., Gerber, A.P., Jambhekar, A., Takizawa, P.A., Herschlag, D., Brown, P.O., DeRisi, J.L., Vale, R.D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 11429-11434. Widespread Cytoplasmic mRNA Transport in S. cerevisiae: Identification of 20 New Bud-localized Transcripts Using DNA Microarray Analysis. PMCID: PMC208774. (Medline) (PDF File) (Supporting Info)
        See also: Long, R. (2012) Faculty of 1000 Article Recommendation (Link)

104. Das, R., Kwok, L.W., Millet, I.S., Bai, Y., Mills, T.T., Jacob, J., Maskel, G.S., Seifert, S., Simon, M.G.J., Thiyagarajan, P., Doniach, S., Pollack, L., Herschlag, D. (2003) J. Mol. Biol. 332, 311-319. The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena Ribozyme. PMID: 12948483. (Medline) (PDF File)
        See also: Hall, K. (2003) Faculty of 1000 Article Recommendation (Link)

103. Peck, M.L., Herschlag, D. (2003) RNA 9, 1180-1187. Adenosine 5'-O-(3-thio) Triphosphate (ATPS) Is a Substrate for the Nucleotide Hydrolysis and RNA Unwinding Activities of Eukaryotic Translation Initiation Factor eIF4A. PMCID: PMC1370482. (Medline) (PDF File)
           See also: Lorsch, J. (2003) Faculty of 1000 Article Recommendation (Link)

102. Das, R., Mills, T.T., Kwok, L.W., Maskel, G.S., Millett, I.S., Doniach, S., Finkelstein, K.D., Herschlag, D., Pollack, L. (2003) Physical Review Letters 90, 188103-1 - 188103-4. The Counterion Distribution Around DNA Probed by Solution X-ray Scattering. PMID: 12786045. (Medline) (PDF File)

101. Kraut, D.A., Carroll, K.S., Herschlag, D. (2003) Annu. Rev. Biochem. 72, 517-571. Challenges in Enzyme Mechanism and Energetics. PMID: 12704087. (Medline) (PDF File)

100. Bartley, L.E., Zhuang, X., Das, R., Chu, S., Herschlag, D. (2003) J. Mol. Biol. 328, 1011-1026. Exploration of the Transition State for Tertiary Structure Formation between an RNA Helix and a Large Structured RNA. PMID: 12729738. (Medline) (PDF File) (Supporting Info)
        See also: Silverman, S. (2003) Faculty of 1000 Article Recommendation (Link)

99. Arava, Y., Wang, Y., Storey, J.D., Liu, C.L., Brown, P., Herschlag, D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 3889-3894. Genome-wide Analysis of mRNA Translation Profiles in Saccharmyces cerevisiae. PMCID: PMC153018. (Medline) (PDF File
        See also: Lorsch, J. (2003) Faculty of 1000 Article Recommendation (Link)

98. Karbstein, K., Herschlag, D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 2300-2305. Extraordinarily Slow Binding of Guanosine to the Tetrahymena Group I Ribozyme. PMCID: PMC151335. (Medline) (PDF File) (Supporting Info)


97. Cheng, H., Nikolic-Hughes, I., Wang, J.H., Deng, H., O'Brien, P.J., Wu, L., Zhang, Z.Y., Herschlag, D., Callender, R. (2002) J. Am. Chem. Soc. 124, 11295-11306. Environmental Effects on Phosphoryl Group Bonding Probed by Vibrational Spectroscopy: Implications for Understanding Phosphoryl Transfer and Enzymatic Catalysis. PMID: 12236744. (Medline) (PDF File)

96. Karbstein, K., Carroll, K.S., Herschlag, D. (2002) Biochemistry 41, 11171-11183. Probing the Tetrahymena Ribozyme Reaction in Both Directions. PMID: 12220182. (Medline) (PDF File) (Supporting Info)

95. Wang, Y., Liu, C.L., Storey, J.D., Tibshirani, R.J., Herschlag, D., Brown, P.O. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 5860-5865. Precision and Functional Specificity in mRNA Decay. PMCID: PMC122867. (Medline) (PDF File

94. Shan, S., Herschlag, D. (2002) RNA 8, 861-872. Dissection of a Metal Ion Mediated Conformational Change in Tetrahymena Ribozyme Catalysis. PMCID: PMC1370303. (Medline) (PDF File

93. Sorin, E.J., Engelhardt, M.A., Herschlag, D., Pande, V.S. (2002) J. Mol. Biol. 317, 493-596. RNA Simulations: Probing Hairpin Unfolding and the Dynamics of a GNRA Tetraloop. PMID: 11955005. (Medline) (PDF File) (Supporting Info)

92. Russell, R., Millett, I.S., Tate, M.W., Kwok, L.W., Nakatani, B., Gruner, S.M., Mochrie, S.G.J., Pande, V., Doniach, S., Herschlag, D., Pollack, L. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 4266-4271. Rapid Compaction During RNA Folding. PMCID: PMC123637. (Medline) (PDF File) (Supporting Info)
        See also: Lehman, N. (2002) Faculty of 1000 Article Recommendation (Link)

91. O'Brien, P., Herschlag, D. (2002) Biochemistry 41, 3207-3225. Alkaline Phosphatase Revisited: The Hydrolysis of Alkyl Phosphates. PMID: 1186460. (Medline) (PDF File) (Supporting Info)

90. Russell, R., Zhaung, X., Babcock, H.P., Millett, I.S., Doniach, S., Chu, S., Herschlag, D. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 155-160. Exploring the Folding Landscape of a Structured RNA. PMCID: PMC117531. (Medline) (PDF File) (Supporting Info)


89. Peluso, P., Shan, S., Nock, S., Herschlag, D., Walter, P. (2001) Biochemistry 40, 15224-15233. Role of SRP RNA in the GTPase Cycles of Fth and FtsY. PMID: 11735405. (Medline) (PDF File
        See also: Freymann, D. (2002) Faculty of 1000 Article Recommendation (Link)

88. Russell, R., Herschlag, D. (2001) J. Mol. Biol. 308, 839-851. Probing the Folding Landscape of the Tetrahymena Ribozyme: Commitment to Form the Native Conformation Is Late in the Folding Pathway. PMID: 11352576. (Medline) (PDF File) (Supporting Info)

87. O'Brien, P., Herschlag, D. (2001) Biochemistry 40, 5691-5699. Functional Interrelationships in the Alkaline Phosphatase Superfamily: Phosphodiesterase Activity of E. coli Alkaline Phosphatase. PMID: 11341834. (Medline) (PDF File

86. Shan, S., Kravchuk, A.V., Piccirilli, J.A., Herschlag, D. (2001) Biochemistry 40, 5161-5171. Defining the Catalytic Metal Ion Interactions in the Tetrahymena Ribozyme Reaction. PMID: 11318638. (Medline) (PDF File) (Supporting Info)

85. O'Rear, J., Wang, S., Feig, A.L., Uhlenbeck, O.C., Herschlag, D. (2001) RNA 7, 537-545. Comparison of the Hammerhead Cleavage Reactions Stimulated by Monovalent and Divalent Cations. PMCID: PMC1370107. (Medline) (PDF File)

84. Admiraal, S.J., Meyer, P., Schneider, B., Deville-Conne, D., Janin, J., Herschlag, D. (2001) Biochemistry 40, 403-413. Chemical Rescue of Phosphoryl Transfer in a Cavity Mutant of Nucleoside Diphosphate Kinase: Implications for Site-directed Mutagenesis. PMID: 11148034. (Medline) (PDF File)


83. Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D., Chu, S. (2000) Science 288, 2048-2051. A Single Molecule Study of RNA Catalysis and Folding. PMID: 10856219. (Medline) (PDF File)

82. Shan, S., Herschlag, D. (2000) RNA 6, 795-813. An Unconventional Origin of Metal Ion Rescue and Inhibition in the Tetrahymena roup I Ribozyme Reaction. PMCID: PMC1369959. (Medline) (PDF File

81. Russell, R., Millett, I.S., Doniach, S., Herschlag, D. (2000) Nat. Struc. Biol. 5, 367-370. Small Angle X-ray Scattering Reveals a Compact Intermediate in RNA Folding. PMID: 10802731. (Medline) (PDF File

80. Peluso, P., Herschlag, D., Freymann, D.M., Johnson, A.E., Walter, P. (2000) Science 288, 1640-1643. Role of 4.5S RNA in Assembly of the Bacterial Signal Recognition Particle with Its Receptor. PMID: 10834842. (Medline) (PDF File

79. Narlikar, G.J., Bartley, L.E., Herschlag, D. (2000) Biochemistry 39, 6183-6189. Use of Duplex Rigidity for Stability and Specificity in RNA Tertiary Structure. PMID: 10821693. (Medline) (PDF File

78. Admiraal, S.J., Herschlag, D. (2000) J. Am. Chem. Soc. 122, 2145-2148. The Substrate-assisted General Base Catalysis Model for Phosphate Monoester Hydrolysis: Evaluation Using Reactivity Comparisons. (PDF File)

77. Engelhardt, M.A., Doherty, E.A., Knitt, D.S., Doudna, J.A., Herschlag, D. (2000) Biochemistry 39, 2639-2651. The P5abc Peripheral Element Facilitates Preorganization of the Tetrahymena Group I Ribozyme for Catalysis. PMID: 10704214. (Medline) (PDF File)

76. Yoshida, A., Shan, S., Herschlag, D., Piccirilli, J. (2000) Chemistry and Biology 7, 85-96. The Role of the Cleavage Site 2'-Hydroxyl in the Tetrahymena Group I Ribozyme Reaction. PMID: 10662698. (Medline) (PDF File


75. Lorsch, J., Herschlag, D. (1999) EMBO 18, 6705-6717. Kinetic Dissection of Fundamental Processes of Eukaryotic Translation Initiation In Vitro. PMCID: PMC117133. (Medline) (PDF File

74. O'Brien, P., Herschlag, D. (1999) J. Am. Chem. Soc. 121, 11022-11023. Does the Active Site Arginine Change the Nature of the Transition State for Alkaline Phosphatase-catalyzed Phosphoryl Transfer? (PDF File)

73. Gerton, J., Herschlag, D., Brown, P. (1999) J. Biol. Chem. 274, 33480-33487. Stereospecificity of Reactions Catalyzed by HIV-1 Integrase. PMID: 10559232. (Medline) (PDF File

72. Narlikar, G.J., Bartley, L.E., Khosla, M., Herschlag, D. (1999) Biochemistry 38, 14192-14204. 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. PMID: 10571993. (Medline) (PDF File

71. Shan, S., Yoshida, A., Piccirilli, J., Herschlag, D. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 12290-12304. Three Metal Ions at the Active Site of the Tetrahymena Group I Ribozyme. PMCID: PMC22911. (Medline) (PDF File

70. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L., Herschlag, D. (1999) Biochemistry 43, 14363-14378. Identification of the Hammerhead Ribozyme Metal Ion Binding Site Responsible for Rescue of the Deleterious Effect of a Cleavage Site Phosphorothioate. PMID: 10572011. (Medline) (PDF File) (Supporting Info)

69. Zhang, Y.L., Hollfelder, F., Gordon, S.J., Chen, L., Keng, Y.F., Wu, L., Herschlag, D., Zhang, Z.Y. (1999) Biochemistry 38, 12111-12123. Impaired Transition State Complementarity in the Hydrolysis of O-Arylphosphorothioates by Protein-tyrosine Phosphatases. PMID: 10508416. (Medline) (PDF File)

68. Russell, R., Herschlag, D. (1999) J. Mol. Biol. 291, 1155-1167. New Pathways in Folding of the Tetrahymena Group I RNA Enzyme. PMID: 10518951. (Medline) (PDF File

67. Peck, M., Herschlag, D. (1999) RNA 5, 1210-1221. Effects of Olionucleotide Length and Atomic Composition on Stimulation of the ATPase Activity of Translation Initiation Factor eIF4A. PMCID: PMC1369844. (Medline) (PDF File)

66. Shan, S., Narlikar, G.J., Herschlag, D. (1999) Biochemistry 38, 10976-10988. Protonated 2'-Aminoguanosine as a Probe for the Electrostatic Environment of the Active Site of the Tetrahymena Group I Ribozyme. PMID: 10460152. (Medline) (PDF File)

65. Shan, S., Herschlag, D. (1999) Biochemistry 38, 10958-10975. Probing the Role of Metal Ions in RNA Catalysis: Kinetic and Thermodynamic Characterization of Metal Ion Interaction with the 2'-Moiety of the Guanosine Nucleophile in the Tetrahymena Group I Ribozyme. PMID: 10460151. (Medline) (PDF File

64. Admiraal, S.J., Herschlag, D. (1999) J. Am. Chem. Soc. 121, 5837-5845. Catalysis of Phosphoryl Transfer from ATP by Amine Nucleophiles. PMID: 10200157. (Medline) (PDF File

63. Admiraal, S.J., Schneider, B., Meyer, P., Janin, J., Veron, M., Deville-Bonne, D., Herschlag, D. (1999) Biochemistry 38, 4701-4711. Nucleophilic Activation by Positioning in Phosphoryl Transfer Catalyzed by Nucleoside Diphosphate Kinase. PMID: 10200157. (Medline) (PDF File

62. O'Brien, P., Herschlag, D. (1999) Chemistry and Biology 6, R91-R105. Catalytic Promiscuity and the Evolution of New Enzymatic Activities. PMID: 10099128. (Medline) (PDF File

61. Doherty, E.A., Herschlag, D., Doudna, J.A. (1999) Biochemistry 38, 2982-2990. Assembly of an Exceptionally Stable RNA Tertiary Interface in a Group I Ribozyme. PMID: 10074350. (Medline) (PDF File

60. Korber, P., Zander, T., Herschlag, D., Bardwell, J.C.A. (1999) J. Biol. Chem. 274, 249-256. A New Heat Shock Protein that Binds Nucleic Acids. PMID: 9867837. (Medline) (PDF File

59. Russell, R., Herschlag, D. (1999) RNA 5, 158-166. Specificity from Steric Restrictions in the Guanosine Binding Pocket of a Group I Ribozyme. PMCID: PMC1369748. (Medline) (PDF File

58. Shan, S., Herschlag, D. (1999) Methods Enzymol. 308, 246-276. Hydrogen Bonding in Enzymatic Catalysis: Analysis of Energetic Contributions. PMID: 10507008. (Medline) (PDF File)


57. O'Brien, P., Herschlag, D. (1998) J. Am. Chem. Soc. 120, 12369-12370. Sulfatase Activity of E. coli Alkaline Phosphatase Demonstrates a Functional Linke to Arylsulfatases, an Evolutionarily Related Enzyme Family. (PDF File

56. Herschlag, D. (1998) Nature 395, 548-549. Ribozyme Crevices and Catalysis (News and Views). PMID: 9783578. (Medline) (PDF File

55. Peracchi, A., Beigelman, L., Karpeisky, A., Maloney, L., Herschlag, D. (1998) Biochemistry 37, 14765-14775. A Core Folding Model for Catalysis by the Hammerhead Ribozyme Accounts for its Extraordinary Sensitivity to Abasic Mutations. PMID: 9778351. (Medline) (PDF File)

54. Peracchi, A., Matulic-Adamic, J., Wang, S.L., Beielman, L., Herschlag, D. (1998) RNA 4, 1332-1346. Structure-function Relationships in the Hammerhead Ribozyme Proved by Base Rescue. PMCID: PMC1369707. (Medline) (PDF File

53. Narlikar, G.J., Herschlag, D. (1998) Biochemistry  37, 9902-9911. Direct Demonstration of the Catalytic Role of Binding Interactions in Enzymatic Reactions. PMID: 9665695. (Medline) (PDF File

52. Lorsch, J.R., Herschlag, D. (1998) Biochemistry 37, 2194-2206. The DEAD Box Protein of eIF4A. 2. A Cycle of Nucleotide and RNA-dependent Conformational Changes. PMID: 9485365. (Medline) (PDF File

51. Lorsch, J.R., Herschlag, D. (1998) Biochemistry 37, 2180-2193. The DEAD Box Protein eIF4A. 1. A Kinetic and Thermodynamic Framework Reveals Coupled Binding of RNA Nucleotide. PMID: 9485364. (Medline) (PDF File


50. Peracchi, A., Beigelman, L., Scott, E.C., Uhlenbeck, O.C., Herschlag, D. (1997) J. Biol. Chem.  272, 26822-26826. Involvement of a Specific Metal Ion in the Transition of the Hammerhead Ribozyme to Its Catalytic Conformation. PMID: 9341112. (Medline) (PDF File

49. Hertel, K.J., Peracchi, A., Uhlenbeck, O.C., Herschlag, D. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 8497-8502. Use of Intrinsic Binding Energy for Catalysis by an RNA Enzyme. PMCID: PMC22973. (Medline) (PDF File)

48. McConnell, T.S., Herschlag, D., Cech, T.R. (1997) Biochemistry 36, 8293-8303. The Effects of Divalent Metal Ions on Individual Steps of the Tetrahymena Ribozyme Reaction. PMID: 9204875. (Medline) (PDF File

47. Narlikar, G.J., Herschlag, D. (1997) Annu. Rev. Biochem. 66, 19-59. Mechanistic Aspects of Enzymatic Catalysis: Lessons from Comparison of RNA and Protein Enzymes. PMID: 9242901. (Medline) (PDF File

46. Narlikar, G.J., Khosla, M., Usman, N., Herschlag, D. (1997)  Biochemistry 36, 2465-2477. Quantitating Tertiary Binding Energies of 2' Hydroxyl Groups on the P1 Duplex of the Tetrahymena Ribozyme: Intrinsic Binding Energy in an RNA Enzyme. PMID: 9054551. (Medline) (PDF File) (Supporting Info)

45. Shan, S., Herschlag, D. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 14474-14479. The Change in Hydrogen Bond Strength Accompanying Charge Rearrangement: Implications for Enzymatic Catalysis. PMCID: PMC26157. (Medline) (PDF File

44. Peracchi, A., Beigelman, L., Usman, N., Herschlag, d. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 11522-11527. Rescue of Abasic Hammerhead Ribozymes by Exogenous Addition of Specific Bases. PMCID: PMC38090. (Medline) (PDF File

43. Narlikar, G.J., Herschlag, D. (1996) Nat. Struc. Biol. 3, 701-710. Isolation of a Local Tertiary Folding Transition in the Context of a Globally Folded RNA. PMID: 8756329. (Medline) (PDF File)


42. Maegley, K.A., Admiraal, S.J., Herschlag, D. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 8160-8166. Ras-catalyzed Hydrolysis of GTP: Insights from Model Studies. PMID: 8710841. (Medline) (PDF File

41. Shan, S., Herschlag, D. (1996) J. Am. Chem. Soc. 118, 5515-5518. Energetic Effects of Multiple Hydrogen Bonds. Implications for Enzymatic Catalysis. (PDF File)

40. Hertel, K.J., Herschlag, D., Uhlenbeck, O.C. (1996) EMBO J. 15, 3751-3757. Specificity of Hammerhead Ribozyme Cleavage. PMCID: PMC452045. (Medline) (PDF File

39. Cech, T.R., Herschlag, D. (1996) Group I Ribozymes: Substrate Recognition, Catalytic Strategies and Comparative Mechanistic Analysis. In Nucleic Acids and Molecular BiologySpecial Issue on RNA Catalysis, Vol. 10, Eckstein, F., Lilley, D.M.J., Editors. Springer-Verlag, Berline, pp 1-17. (PDF File)

38. Mei, R., Herschlag, D. (1996) Biochemistry 35, 5796-5809. Mechanistic Investigations of a Ribozyme Derived from the Tetrahymena roup I Intron. Insights into Catalysis and the Second Step of Self-Splicing. PMID: 8639540. (Medline) (PDF File

37. Shan, S., Loh, S., Herschlag, D. (1996)  Science 272, 97-101. The Energetics of Hydrogen Bonds in Model Systems. Implications for Enzymatic Catalysis. PMID: 8600542. (Medline) (PDF File

36. Knitt, D.S., Herschlag, D. (1996) Biochemistry 35, 1560-1570. pH Dependencies of the Tetrahymena Ribozyme Reveal an unvonventional Origin of an Apparent pKa. PMID: 8634287. (Medline) (PDF File)


35. Admiraal, S.J., Herschlag, D. (1995) Chemistry and Biology 2, 729-739. Mapping the Transition State for ATP Hydrolysis. Implications for Enzymatic Catalysis. PMID: 9383480. (Medline) (PDF File)

34. Hollfelder, F., Herschlag, D. (1995) Biochemistry 34, 12255-12264. The Nature of the Transition State for Enzyme-catalyzed Phosphoryl Transfer. Hydrolysis of O-Arylphosphorothioates by Alkaline Phosphatase. PMID: 7547968. (Medline) (PDF File)

33. Herschlag, D. (1995) J. Biol. Chem. 270, 20871-20874. RNA Chaperones and the RNA Folding Problem. PMID: 754662. (Medline) (PDF File)

32. Narlikar, G.J., Gopalakrishnan, V., McConnell, T.S., Usman, N., Herschlag, D. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 3668-3672. Use of Binding Energy by an RNA Enzyme for Catalysis by Positioning and Substrate Destabilization. (Medline) (PDF File


31. Herschlag, D. (1994) J. Am. Chem. Soc. 116, 11631-11635. Ribonuclease Revisited: Catalysis Via the Classical General Acid-Base Mechanism or a Triester-like Mechanism? (PDF File)

30. Knitt, D.S., Narlikar, G.J., Herschlag, D. (1994) Biochemistry 33, 13864-13879. Dissection of the Role of the Conserved G-U Pair in Group I RNA Self-Splicing. PMID: 7947795. (Medline) (PDF File)

29. Coetzee, T., Herschlag, D., Belfort, M. (1994) Genes & Development 8, 1575-1588. Escherichia Coli Proteins, Includin Ribosomal Protein S12 Facilitate In Vitro Splicing of Phage T4 Introns by Acting as RNA Chaperones. PMID: 7958841. (Medline) (PDF File

28. Herschlag, D., Khosla, M., Tsuchihashi, Z., Karpel, R.L. (1994) EMBO J. 13, 2913-2924. An RNA Chaperone Activity of Nonspecific RNA Binding Proteins in Hammerhead Ribozyme Catalysis. PMCID: PMC395173. (Medline) (PDF File

27. Herschlag, D., Khosla, M. (1994) Biochemistry 33, 5291-5297. Comparison of pH Dependencies of the Tetrahymena Ribozyme Reactions with RNA 2'-Substituted and Phosphorothioate Substrates Reveals a Rate-limiting Conformational Step. PMID: 8172903. (Medline) (PDF File)

26. Hertel, K.J., Herschlag, D., Uhlenbeck, O.C. (1994) Biochemistry 33, 3374-3385. A Kinetic and Thermodynamic Framework for the Hammerhead Ribozyme Reaction. PMID: 8136375. (Medline) (PDF File)


25. Tsuchihashi, Z., Khosla, M., Herschlag, D. (1993) Science 262, 99-102. Protein Enhancement of Hammerhead Ribozyme Catalysis. PMID: 7692597. (Medline) (PDF File

24. McConnell, T.S., Cech, T.R., Herschlag, D. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8362-8366. Guanosine Binding to the Tetrahymena Ribozyme: Thermodynamic Coupling with Oligonucleotide Binding. PMCID: PMC47356. (Medline) (PDF File)

23. Herschlag, D., Johnson, F.B. (1993) Genes & Development 7, 173-179. Synergism in Transcriptional Activation: A Kinetic View. PMID: 8436289. (Medline) (PDF File)

The above publications are as an Independent Investigator (7/92-Present)

22. Labow, B., Herschlag, D., Jencks, W.P. (1993) Biochemistry 32, 8737-8741. Catalysis of the Hydrolysis of Phosphorylated Pyridines by Alkaline Phosphatase Has Little or No Dependence on the pKa of the Leaving Group. PMID: 8395879. (Medline) (PDF File)

21. Herschlag, D., Eckstein, F., Cech, T.R. (1993) Biochemistry 32, 8312-3221. The Importance of Being Ribose at the Cleavage Site in the Tetrahymena Ribozyme Reaction. PMID: 7688573. (Medline) (PDF File)

20. Herschlag, D., Eckstein, F., Cech, T.R. (1993) Biochemistry 32, 8312-8321. The Importance of299-8311. 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. PMID: 7688572. (Medline) (PDF File)

19. Legault, P., Herschlag, D., Celander, D.W., Cech, T.R. (1992) Nucleic Acids Res. 20, 6613-6619. Mutations at the Guanosine-binding Site of the Tetrahymena Ribozyme Also Affect Site-specific Hydrolysis. PMCID: PMC334578. (Medline) (PDF File)

18. Cech, T.R., Herschlag, D., Piccirilli, J.A., Pyle, A.M. (1992) J. Biol. Chem. 267, 17479-17482. RNA Catalysis by a Group I Ribozyme. Developing a Model for Transition State Stabilization. PMID: 1381347. (Medline) (PDF File

17. Herschlag, D. (1992) Biochemistry 31, 1386-1399. Evidence for Processivity and Two-Step Binding of the RNA Substrate From Studies of J1/2 Mutants of the Tetrahymena Ribozyme. PMID: 1736996. (Medline) (PDF File)

16. Young, B., Herschlag, D., Cech, T.R. (1991) Cell 67, 1007-1019. Mutations in a Nonconserved Sequence of the Tetrahymena Ribozyme Increase Activity and Specificity. PMID: 1959129. (Medline) (PDF File

15. Herschlag, D. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 6921-6925. Implications of Ribozyme Kinetics for Targeting the Cleavage of Specific RNA Molecules In Vivo: More Isn't Always Better. PMCID: PMC52205. (Medline) (PDF File

14. Herschlag, D., Piccirilli, J.A., Cech, T.R. (1991) Biochemistry 30, 4844-4854. Ribozyme-catalyzed and Non-enzymatic Reactions of Phosphate Diesters: Rate Effects upon Substitution of Sulfur for a Non-bridging Phosphoryl Oxygen Atom. PMID: 2036355. (Medline) (PDF File

13. Herschlag, D., Cech, T.R. (1990) Biochemistry 29, 10172-10180. Catalysis of RNA Cleavage by the Tetrahymena thermophilia Ribozyme. 2. Kinetic Description of the Reaction of an RNA Substrate that Forms a Mismatch at the Active Site. PMID: 2271646. (Medline) (PDF File)

12. Herschlag, D., Cech, T.R. (1990) Biochemistry 29, 10159-10171. Catalysis of RNA Cleavage by the Tetrahymena thermophilia Ribozyme. 1. Kinetic Description of the Reaction of RNA Substrate Complementary to the Active Site. PMID: 2271645. (Medline) (PDF File)

11. Herschlag, D., Cech, T.R. (1990) Nature 344, 405-409. DNA Cleavage Catalyzed by the Ribozyme from Tetrahymena. PMID: 1690858. (Medline) (PDF File)

10. Herschlag, D., Jencks, W.P. (1990) Biochemistry  29, 5172-5179. Catalysis of the Hydrolysis of Phosphorylated Pyridines by Mg(OH)+: A Possible Model for Enzymatic Phosphoryl Transfer. PMID: 2378873. (Medline) (PDF File)

9. Herschlag, D., Jencks, W.P. (1990) J. Am. Chem. Soc. 112, 1951-1956. Nucleophiles of High Reactivity in Phosphoryl Transfer Reactions: Effect Compounds and Fluoride Ion. (PDF File)

8. Herschlag, D., Jencks, W.P. (1990) J. Am. Chem. Soc. 112, 1942-1950. The Effect of Mg2+, Hydrogen Bonding and Steric Factors on Rate and Equilibrium Constants for Phosphoryl Transfer between Carboxylate Ions and Pyridines. (PDF File)

7. Herschlag, D., Jencks, W.P. (1989) J. Am. Chem. Soc. 111, 7587-7596. Phosphoryl Transfer to Oxyanions: The Nature of the Transition State and Electrostatic Repulsion. (PDF File)

6. Herschlag, D., Jencks, W.P. (1989) J. Am. Chem. Soc. 111, 7579-7586. Evidence That Metaphosphate is Not an Intermediate in Solvolysis Reactions in Aqueous Solution. (PDF File)

5. Herschlag, D. (1988) Bioorganic Chemistry 16, 62-96. The Role of Induced Fit and Conformational Changes of Enzymes in Specificity and Catalysis. (PDF File)

4. Herschlag, D., Jencks, W.P. (1987) J. Am. Chem. Soc.  109, 4665-4674. The Effect of Divalent Metal Ions on the Rate and Transition State Structure of Phosphoryl Transfer Reactions. (PDF File)

3. Herschlag, D., Jencks, W.P. (1986) J. Am. Chem. Soc.  108, 7938-7946. Pyrophosphate Formation from Acetyl Phosphate and Orthophosphate Anions in Concentrated Aqueous Salt Solutions Does Not Provide Evidence for a Metaphosphate intermediate. (PDF File)

2. Jencks, W.P., Haber, M.T., Herschlag, D., Nazaretian, K.L. (1986) J. Am. Chem. Soc.  108, 479-483. Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation of Bnuc for Phosphoryl Transfer to Amines. PMID: 22175464. (Medline) (PDF File)

1. Herschlag, D., Stevens, E.S., Gander, J.E. (1983) Int. J. Peptide. Prot. Res. 22, 16-20. Galactofuranosyl-containing Glycopeptide of Penicillium charlesii: Cavuum Ultraviolet Circular Dichroism. PMID: 6224750. (Medline) (PDF File)