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

Jencks, W.P., Haber, M.T., Herschlag, D. and Nazaretian, K.L. (1986) J. Am. Chem. Soc. 108, 479-483. “Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on βnuc for Phosphoryl Transfer to Amines.” (PDF File)

Herschlag, D. and 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)

Herschlag, D. and 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)

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

Herschlag, D. and 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)

Herschlag, D. and 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)

Herschlag, D. and 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)

Herschlag, D. and 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)

Herschlag, D. and 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.” (Medline) (PDF File)

Herschlag, D. and Cech, T.R. (1990) Nature 344, 405-409. “DNA Cleavage Catalysed by the Ribozyme from Tetrahymena.”(Medline) (PDF File)

Herschlag, D. and Cech, T.R. (1990) Biochemistry 29, 10159-10171. “Catalysis of RNA Cleavage by the Tetrahymena thermophila Ribozyme. 1. Kinetic Description of the Reaction of an RNA Substrate Complementary to the Active Site.”(Medline) (PDF File)

Herschlag, D. and Cech, T.R. (1990) Biochemistry 29, 10172-10180. “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.”(Medline) (PDF File)

Herschlag, D., Piccirilli, J.A. and 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.” (Medline) (PDF File)

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.” (Medline) (PDF File)

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

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.” (Medline) (PDF File)

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

Legault, P., Herschlag, D., Celander, D.W. and 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.” (Medline) (PDF File)

Herschlag, D., Eckstein, F. and Cech, T.R. (1993) Biochemistry 32, 8299-8311. “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.” (Medline) (PDF File)

Herschlag, D., Eckstein, F. and Cech, T.R. (1993) Biochemistry 32, 8312-8321. “The Importance of Being Ribose at the Cleavage Site in the Tetrahymena Ribozyme Reaction.”(Medline) (PDF File)

Labow, B., Herschlag, D. and 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.”(Medline) (PDF File)

1993

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

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

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

1994

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

27. Herschlag, D. and 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.” (Medline) (PDF File)

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

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

30. Knitt, D.S., Narlikar, G.J. and Herschlag, D. (1994) Biochemistry 33, 13864-13879. “Dissection of the Role of the Conserved G•U Pair in Group I RNA Self-splicing.” (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)
    

1995

32. Narlikar, G.J., Gopalakrishnan, V., McConnell, T.S., Usman, N. and 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)

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

34. Hollfelder, F. and 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.” (Medline) (PDF File)

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

1996

36. Knitt, D.S. and Herschlag, D. (1996) Biochemistry 35, 1560-1570. “pH Dependencies of the Tetrahymena Ribozyme Reveal an Unconventional Origin of an Apparent pKa.” (Medline) (PDF File)

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

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

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

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

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

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

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

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

45. Shan, S. and 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.” (Medline) (PDF File)

1997

46. Narlikar, G.J., Khosla, M., Usman, N. and 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.”(Medline) (PDF File)

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

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

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

50. Peracchi, A., Beigelman, L., Scott, E.C., Uhlenbeck, O.C. and 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.” (Medline) (PDF File)

1998

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

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

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

54. Peracchi, A., Matulic-Adamic, J., Wang, S.L., Beigelman, L. and Herschlag, D. (1998) RNA 4, 1332-1346. “Structure-Function Relationships in the Hammerhead Ribozyme Probed by Base Rescue.” (Medline) (PDF File)

55. Peracchi, A., Beigelman, L., Karpeisky, A., Maloney, L. and 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.” (Medline) (PDF File)

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

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

1999

58. Shan, S. and Herschlag, D. (1999) “Hydrogen Bonding in Enzymatic Catalysis: Analysis of Energetic Contributions.” In Methods in Enzymology, Vol. 308, Schramm V.L. and Purich, D.L., eds. Academic Press, San Diego. pp. 246-276. (Medline) (PDF File)

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

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

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

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

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

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

65. Shan, S. and 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.” (Medline) (PDF File)

66. Shan, S., Narlikar, G.J. and 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.” (Medline) (PDF File)

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

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

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

70. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. and Herschlag, D. (1999) Biochemistry 43, 14363-14278. “Identification of the Hammerhead Ribozyme Metal Ion Binding Site Responsible for Rescue of the Deleterious Effect of a Cleavage Site Phosphorothioate.” (Medline) (PDF File)

71. Shan, S., Yoshida, A., Piccirilli, J. and Herschlag, D. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 12299-12304. “Three Metal Ions at the Active Site of the Tetrahymena Group I Ribozyme.” (Medline) (PDF File)

72. Narlikar, G.J., Bartley, L.E., Khosla, M. and 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.” (Medline) (PDF File)

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

74. O’Brien, P. and 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)

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

2000

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

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

78. Admiraal, S.J. and 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)

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

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

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

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

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

2001

84. Admiraal, S.J., Meyer, P., Schneider, B., Deville-Conne, D., Janin, J. and 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.” (Medline) (PDF File)

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

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

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

88. Russell, R. and 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.” (Medline) (PDF File)

89. Peluso, P., Shan, S., Nock, S., Herschlag, D. and Walter, P. (2001) Biochemistry 40, 15224-15233. “Role of SRP RNA in the GTPase Cycles of Fth and FtsY.” (Medline) (PDF File)

2002

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

91. O’Brien, P. and Herschlag, D. (2002) Biochemistry 41, 3207-3225. “Alkaline Phosphatase Revisited: The Hydrolysis of Alkyl Phosphates.” (Medline) (PDF File)

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. and Pollack, L. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 4266-4271. “Rapid Compaction During RNA Folding.” (Medline) (PDF File)

93. Sorin, E.J., Engelhardt, M.A., Herschlag, D. and Pande, V.S. (2002) J. Mol. Biol. 317, 493-506. “RNA Simulations: Probing Hairpin Unfolding and the Dynamics of a GNRA Tetraloop.” (Medline) (PDF File)

94. Shan, S. and Herschlag, D. (2002) RNA 8, 861-872. “Dissection of a Metal Ion Mediated Conformational Change in Tetrahymena Ribzoyme Catalysis.” (Medline) (PDF File)

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

96. Karbstein, K., Carroll, K.S. and Herschlag, D. (2002) Biochemistry 41, 11171-83. “Probing the Tetrahymena Ribozyme Reaction in Both Directions.” (Medline) (PDF File)

97. Cheng, H., Nikolic-Hughes, I., Wang, J.H., Deng, H., O’Brien, P.J., Wu, L., Zhang, Z.Y., Herschlag, D. and 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.” (Medline) (PDF File)

2003

98. Karbstein, K. and Herschlag, D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 2300-2305. “Extraordinarily Slow Binding of Guanosine to the Tetrahymena Group 1 Ribozyme.” (Medline) (PDF File)

99. Arava, Y., Wang, Y., Storey, J.D., Liu, C.L., Brown, P. and Herschlag, D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 3889-3894. “Genome-wide Analysis of mRNA Translation Profiles in Saccharomyces cerevisiae.” (Medline) (PDF File)

100. Bartley, L.E., Zhuang, X., Das, R., Chu, S. and 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.” (Medline) (PDF File)

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

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

103. Peck, M.L. and 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.” (Medline) (PDF File)

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. and 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.” (Medline) (PDF File)

105. Shepard, K.A., Gerber, A.P., Jambhekar, A., Takizawa, P.A., Herschlag, D., Brown, P.O., DeRisi, J.L. and 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.” (Medline) (PDF File)

2004

106. Gerber, A.P., Herschlag, D. and Brown, P.O. (2004) PLoS Biology 2, 342-354. “Extensive Association of Functionally and Cytotopically Related mRNAs with Puf-family RNA-binding Proteins in Yeast.” (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?” (Medline) (PDF File)

108. Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D. and 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.” (Medline) (PDF File)

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

110. Andresen, K., Das, R., Park, H.Y., Smith, H., Kwok, L.W., Lamb, J.S., Kirkland, E.J., Herschlag, D., Finkelstein, K.D. and Pollack, L. (2004) Physical Review Letters 93, 248103-1 - 248103-4. “Spatial Distribution of Competing Ions Around DNA in Solution.” (Medline) (PDF File)

2005

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

112. Bai, Y., Das, R., Millet, I.S., Herschlag, D. and 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.” (Medline) (PDF File)

113. Arava, Y., Boas, F.E., Brown, P.O. and Herschlag, D. (2005) Nucleic Acids Research 33, 2421-2432 “Dissecting Eukaryotic Translation and Its Control By Ribosome Density Mapping.” (Medline) (PDF File)

114. Hougland, J.L., Kravchuk, A.V., Herschlag, D. and Piccirilli, J.A. (2005) PLoS Biology 3 e277 “Functional Identification of a Catalytic Metal Ion Binding Site Within RNA.” (Medline) (PDF File)

115. Forconi, M. and Herschlag, D. (2005) J. Am. Chem. Soc. 127, 6160-6161 “Promiscuous Catalysis by the Tetrahymena Group I Ribozyme.”(Medline) (PDF File)

116. Nikolic-Hughes, I., O'Brien, P.J. and Herschlag, D. (2005) J. Am. Chem. Soc. 127, 9314–9315 “Alkaline Phosphatase Catalysis Is Ultrasensitive to Charge Sequestered Between the Active Site Zinc Ions.” (Medline) (PDF File)

117. Das, R., Travers, K., Bai, Y. and Herschlag, D. (2005) J. Am. Chem. Soc. 127, 8272-8273 “Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core.” (Medline) (PDF File)
     See also: Faculty of 1000, 21 June 2005 http://www.f1000biology.com/article/id/1011707
     

118. Johnson, T.H., Tijerina, P., Chadee, A.B., Herschlag, D. and Russell, R. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 10176-10181 “Structural Specificity Conferred by a Group I RNA Peripheral Element.” (Medline) (PDF File)

119. Hougland, J., Piccirilli, J., Forconi, M., Lee, J. and 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. and Atkins, J.F., Editors. Cold Spring Harbor Laboratory Press, New York. pp. 133-205. (PDF File)

2006

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

121. Gerber, A.P., Luschnig, S., Krasnow, M.A., Brown, P.O. and 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 Drosophila melanogaster." (Medline) (PDF File)

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

123. Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 6190-6195 "Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins." (Medline) (PDF File)

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

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

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

127. Fierke, C.A. and 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)

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

2007

129. Lipfert, J., Das, R., Chu, V.B., Kudaravalli, M., Boyd, N., Herschlag, D. and Doniach, S. (2007) J. Mol. Biol. 365, 1393-406 “Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae.” (Medline) (PDF File)
     
     
130. Lipfert, J., Chu, V.B., Bai, Y., Herschlag, D. and Doniach, S. (2007) Journal of Applied Crystallography 40, 235-239 “Low Resolution Models for Nucleic Acids from Small-Angle X-ray Scattering with Applications to Electrostatic Modeling.” (PDF File)
     
     
131. Lee, T.H., Lapidus, L.J., Zhao, W., Travers, K.J., Herschlag, D. and Chu, S. (2007) Biophysical Journal 92, 3275-83. “Measuring the Folding Transition Time of Single RNA Molecules.” (Medline) (PDF File)
     See also: Faculty of 1000 Biology, 30 Jan. 2009 http://www.f1000biology.com/article/id/1147123
     
     
132. Catrina, I., O'Brien, Purcell, J., Nikolic-Hughes, I., Zalatan, J.G., Hengge, A.C., and 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.” (Medline) (PDF File)
     
     
133. Karbstein, K., Lee, J. and 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 ScaI Ribozyme Reveals a New Role of the G•U Pair in Self-splicing.” (Medline) (PDF File)
     
     
134. Mueller-Planitz, F., and Herschlag, D. (2007) Nucleic Acids Research 35, 3764-3773. “DNA Topoisomerase II Selects DNA Cleavage Sites Based on Reactivity Rather than Binding Affinity.” (Medline) (PDF File)
     
     
135. Travers, K., Boyd, N. and Herschlag, D. (2007) RNA 13, 1205-1213. “Low Specificity of Metal Ion Binding in the Metal Ion Core of a Folded RNA.” (Medline) (PDF File)
     
     
136. Zalatan, J.G., Catrina, I., Mitchell, R., Grzyska, P.K., O'Brien, P.J., Herschlag, D. and 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.” (Medline) (PDF File)
     
     
137. Chu, V.B., Bai, Y., Lipfert, J., Herschlag, D. and Doniach, S. (2007) Biophysical Journal “Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory.” (Medline) (PDF File)
     
     
138. Forconi, M., Piccirilli, J.A. and Herschlag, D.  (2007) RNA 13, 1656-1667. “Modulation of Individual Steps in Group I Intron Catalysis by a Peripheral Metal Ion.” (Medline) (PDF File)
     
     
139. Sigala, P.A., Fafarman, A.T., Bogard, P.E., Boxer, S.G. and 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?” (Medline) (PDF File)
     See also: Faculty of 1000 Biology, 16 Oct. 2007                  http://www.f1000biology.com/article/id/1091226/evaluation
     
     
140. Bai, Y., Travers, K., Chu, V.B., Lipfert, J., Doniach, S. and Herschlag, D. (2007) J. Am. Chem. Soc. 29, 14981-14988. “ Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids.” (Medline) (PDF File)
     
     2008
     
141. Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B. and Herschlag, D. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 4144-4149. “Structural Inference of Native and Partially Folded RNA by High-Throughput Contact Mapping."(Medline) (PDF File)
     

     See also: SeparationsNow.com, April 2008 http://www.separationsnow.com/coi/cda/detail.cda?id=18511&type=Feature&chId=2&page=1
     Faculty of 1000 Biology, 17 Sept. 2008 http://www.f1000biology.com/article/id/1119588/evaluation
     

142. Hendrickson, D.G., Hogan, D.J., Herschlag, D. Ferrell, J.E. and Brown, P.O. (2008) PloS One 3(5):e2126. “Systematic Identification of mRNAs Recruited to RISC by Specific microRNAs and Corresponding Changes in Transcript Abundance.” (Medline) (PDF File)
     
     
143. Sattin, B.D., Zhao, W., Travers, K., Chu, S. and Herschlag, D. (2008) J. Am. Chem. Soc. 130, 6085-6087. “Direct Measurement of Tertiary Contact Cooperativity in RNA Folding." (Medline) (PDF File)
     See also: “Navigating the RNA folding landscape” Nature Chemical Biology 4, 451 - 452 (2008). http://www.nature.com/nchembio/journal/v4/n8/full/nchembio0808-451.html
     
     
144. Mueller-Planitz, F. and 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.” (Medline) (PDF File)
     
     
145. Bai, Y., Chu, V.B., Lipfert, J., Pande, V.S., Herschlag, D. and 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.” (Medline) (PDF File)
     

     See also: Faculty of 1000 Biology, Dec 2008
     http://www.f1000biology.com/article/id/1128869
     

146. Forconi, M., Lee, J., Lee, J., Piccirilli, J., and Herschlag, D. (2008) Biochemistry 47, 6883-6894 “Functional Identification of Ligands for a Catalytic Metal Ion in Group I Introns.” (Medline) (PDF File)
     
     
147. Chu, V.B. and Herschlag, D. (2008) Curr. Opin. Struc. Biol. 18, 305-314. “Unwinding RNA’s Secrets: Advances in the Biology, Physics, and Modeling of Complex RNAs.”  (Medline) (PDF File)
     
     
148. O'Brien, P., Lassila, J., Fenn, T., Zalatan, J. and 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.” (Medline) (PDF File)
     
     
149. Laederach, A., Das, R., Vicens, Q, Pearlman, S, Brenowitz, M., Herschlag, D., and Altman, R. (2008) Nature Protocols 3, 1395-1401.Click here to read “Semi-automated and Rapid Quantification of Nucleic Acid Footprinting and Structure Mapping Experiments.” (Medline) (PDF File)
     
     
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.”(Medline) (PDF File)
     

     See also: Nature 2008, 456, 45-47.
     http://www.nature.com/nature/journal/v456/n7218/full/456045a.html
     
     

151. Hogan, D., Riordan, D., Gerber, A., Herschlag, D. and Brown, P. (2008) PloS Biology 6, 2297-2313. “Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System.” (Medline) (PDF File)
     
     
152. Zalatan, J., Fenn, T. D., Herschlag, D. (2008) J. Mol. Biol. 384, 1174-1189. “Comparative Enzymology the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active Site Metal Ion.” (Medline) (PDF File)
     
     
153. Lassila, J. and Herschlag, D. (2008) Biochemistry 47, 12853–12859. “Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily.” (Medline) (PDF File)
     
     
154. Chu, V.B., Bai, Y., Lipfert, Y., Doniach, S. and Herschlag, D. (2008) Curr. Opin. Chem. Biol. 12, 619-625. “A Repulsive Field: Advances in the Electrostatics of the Ion Atmosphere.” (Medline) (PDF File)
     
     2009
     
     
155. Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D. and
     Altman, R.B. (2009) RNA 15, 189-199. “Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.” (Medline) (PDF File)
     
     
156. Lipfert, J., Herschlag, D. and Doniach, S. (2009) Methods in Molecular Biology 540, 141-159 “Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering.” (Medline) (PDF File)
     
     
157. Grant, G.P.G., Boyd, N., Herschlag, D. and 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.” (Medline) (PDF File)
     See also: Faculty of 1000 Biology, Feb 2009
     http://www.f1000biology.com/article/id/1156905/evaluation
     
     
158. Kraut, D. A., Churchill, M.J., Dawson, P.E. and 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.” (Medline) (PDF File)
     
     
159. Sigala, P.A., Tsuchida, M. A., and Herschlag, D. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 9232-9237 “Hydrogen Bond Dynamics in the Active Site of Photoactive Yellow Protein.” (Medline) (PDF File)
     Biopolymers Research Highlights Volume 91 / Number 9 iii
     
     
160. Sigala, P.A., Caaveiro, J. M. M., Ringe, D., Petsko, G. A. and Herschlag D. (2009) Biochemistry “Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site.” DOI: 10.1021/bi900713j (Medline) (PDF File)
     
     
161. Shi, X., Mollova, E., Pljevaljcic, G., Millar, D. and Herschlag, D. (2009) J. Am. Chem. Soc. “Probing the Dynamics of the P1 Helix within the Tetrahymena Group I Intron.” In press (Medline) (PDF File)
     
     
162. Zalatan, J.G. and Herschlag, D. (2009) Nature Chem. Biol. “The Far Reaches of Enzymology.” In press