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Fedor Lab Publications

Research Publications

Ruminski D.J., Watson P.Y., Mahen E.M., Fedor M.J. (2016) A DEAD-box RNA Helicase Promotes Thermodynamic Equilibration of Kinetically Trapped RNA Structures In Vivo. RNA, 22, 416-427.

Viladoms, J. and Fedor, M.J. (2012) The glmS Ribozyme Cofactor is a General Acid-Base Catalyst J. Am. Chem. Soc.134(46), 19043-19049 PMID:23113700

Watson, P.Y., Fedor, M.J. (2012) The ydaO Motif is an ATP-sensing Riboswitch in Bacillus subtilis. Nature Chem. Biol., 8(12), 963-965 PMID:23086297

Viladoms, J., Scott, L.G. and Fedor, M.J. (2011) An Active-site Guanine Participates in glmS Ribozyme Catalysis in its Protonated State. J. Am. Chem. Soc., 133, 18388-18396. PMCID:PMC3212626

Watson, P.Y. and Fedor, M.J. (2011) The glmS Riboswitch Integrates Signals from Activating and Inhibitory Metabolites In Vivo, Nat. Struct. Molec. Biol., 18, 359-363. PMID: 21317896 PMCID: PMC3075592

Cottrell, J.W., Scott, L.G., and Fedor, M.J. (2011) The pH Dependence of Hairpin Ribozyme Catalysis Reflects Ionization of an Active Site Adenine. J. Biol. Chem. 286, 17658-17664. PMID: 21454684 PMCID: PMC3093841

Mahen E.M., Watson P.Y., Cottrell J.W., and Fedor, M.J. (2010) mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo. PLoS Biol 8(2): e1000307. doi:10.1371/journal.pbio.1000307. PMID: 20161716 PMCID: PMC2817708

Liu, L., Cottrell, J. W., Scott, L. G., and Fedor, M. J. (2009) Direct Measurement of the Ionization State of an Essential Guanine in the Hairpin Ribozyme. Nat. Chem. Biol. 5(5): 351-7. PMCID: PMC2670934 PMID: 19330013

Cottrell, J. W., Kuzmin, Y. I., and Fedor, M. J. (2007) Functional Analysis of Hairpin Ribozyme Active Site Architecture. J. Biol. Chem. 282(18): 13498-507. PMID: 17351263

Da Costa, C .P., Fedor, M. J., and Scott, L. (2007) 8-Azaguanine Reporter of Purine Ionization States in Structured RNAs. J. Am. Chem. Soc. 129(11): 3426-32. PMID: 17326637

Mahen, E. M., Harger, J. W., Calderon, E. M., and Fedor, M. J. (2005) Kinetics and Thermodynamics make Different Contributions to RNA Folding in Vitro and in Yeast. Molecular Cell 19(1): 27-37. PMID: 15989962

Kuzmin, Y. I., Da Costa, C. P., Cottrell, J. W., and Fedor, M. J. (2005) Role of an Active Site Adenine in Hairpin Ribozyme Catalysis. J. Mol. Biol. 349(5): 989-1010. PMID: 15907933

Kuzmin, Y. I., Da Costa, C. P., and Fedor, M. J. (2004) Role of an Active Site Guanine in Hairpin Ribozyme Catalysis Probed by Exogenous Nucleobase Rescue. J. Mol. Biol. 340(2): 233-251. PMID: 15201049

Yadava, R. S., Mahen, E. M., and Fedor, M. J. (2004) Kinetic Analysis of Ribozyme-Substrate Complex Formation in Yeast. RNA 10(5): 863-879. PMID: 15100441

Lebruska, L. L, Kuzmine, I. I., and Fedor, M. J. (2002) Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis. Chem. Biol. 9(4): 465-473. PMID: 11983335

Yadava, R. S., Choi, A. J., Lebruska, L. L., and Fedor, M. J. (2001) Hairpin Ribozymes with Four-way Helical Junctions Mediate Intracellular RNA Ligation. J. Mol. Biol. 309(4): 893-902. PMID: 11399066

Donahue, C. P., Yadava, R. S., Nesbitt, S. M., and Fedor, M. J. (2000) The Kinetic Mechanism of the Hairpin Ribozyme in Vivo: Influence of RNA Helix Stability on Intracellular Cleavage Kinetics. J. Mol. Biol. 295(3): 693-707. PMID: 10623557

Fedor, M. J. (1999) Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation. Biochemistry 38(34): 11040-11050. PMID: 10460159

Nesbitt, S. M., Erlacher, H. A., and Fedor, M. J. (1999) The Internal Equilibrium of the Hairpin Ribozyme: Temperature, Ion and pH Effects. J. Mol. Biol. 286(4): 1009-1024. PMID: 10047478

Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) An Unusual pH-independent and Metal-ion-independent Mechanism for Hairpin Ribozyme Catalysis. Chem. Biol. 4(8): 619-630. PMID: 9281529

Donahue, C. P. and Fedor, M. J. (1997) Kinetics of Hairpin Ribozyme Cleavage in Yeast. RNA 3(9): 961-973. PMID: 9292496

Hegg, L. A. and Fedor, M. J. (1995) Kinetics and Thermodynamics of Intermolecular Catalysis by Hairpin Ribozymes. Biochemistry 34(48): 15813-15828. PMID: 7495813

Fedor, M. J. and Uhlenbeck, O. C. (1992) Kinetics of Intermolecular Cleavage by Hammerhead Ribozymes. Biochemistry 31(48): 12042-12054. PMID: 1280996

Fedor, M. J. and Uhlenbeck, O. C. (1990) Substrate Sequence Effects on "Hammerhead" RNA Catalytic Efficiency. Proc. Natl. Acad. Sci. 87(5): 1668-1672. PMID: 1689847

Uhlenbeck O. C., Dahm, S. C., Ruffner, D. E., and Fedor, M. J. (1989) Structure and Mechanism of the Hammerhead Self-cleaving Domain. Nucleic Acids Symp. Ser. 21: 95-96. PMID: 2481843

Fedor, M. J. and Kornberg, R. D. (1989) Upstream Activating Sequence-Dependent Alteration of Chromatin Structure and Transcription Activation of the Yeast GAL1-GAL10 Genes. Mol. Cell. Biol. 9: 1721-1732. PMID: 2657404

Fedor, M. J., Lue, N. F., and Kornberg, R. D. (1988) Statistical Positioning of Nucleosomes by Specific Protein-Binding to an Upstream Activating Sequence in Yeast. J. Mol. Biol. 204: 109-127. PMID: 3063825

Fedor, M. J. and Daniell, E. (1983) DNase I Cleavage of Adenoviral Nucleoprotein. Nucleic Acids Res. 11: 4417-4434. PMID: 6306591

Fedor, M. J. and Daniell, E. (1983) Ionic and Nonionic Interactions in Adenoviral Nucleoprotein Complexes. J. Virol. 47: 370-375. PMID: 6620457

Daniell, E. and Fedor, M. J. (1982) Transcription of Adenovirus Cores In Vitro: Major RNA Products Differ from those made from a DNA Template. Proc. Natl. Acad. Sci. 79: 1834-1838. PMID: 6952232

Daniell, E., Burg, J. L., and Fedor, M. J. (1982) DNA and Histone Synthesis in Butyrate-Inhibited BSC-1 Cells infected with SV40. Virology 116: 196-206. PMID: 6278707

Fedor, M.J. (1982) Structure and Function of Adenovirus Chromatin. Ph.D. Dissertation. University of California, Berkeley.

Daniell, E., Groff, D.E., and Fedor, M. J. (1981) Adenovirus Chromatin Structure at Different Stages of Infection. Mol. Cell. Biol. 1: 1094-1105. PMID: 7346714

Fedor, M. J. and Daniell, E. (1980) Acetylation of Histone-like Proteins of Adenovirus Type 5. J. Virol. 35: 637-643. PMID: 7420537


Watson, P. Y. and Fedor, M. J. (2009) Determination of Intracellular RNA Folding Rates Using Self-Cleaving RNAs. Methods Enzymol. 468: 259-286.

Fedor, M. J. (2009) Comparative Enzymology and Structural Biology of RNA Self-Cleavage. Annu. Rev. Biophys. 38: 271-299. PMID: 19416070  E-print

Fedor, M. J. (2008) Alternative Splicing Minireview Series: Combinatorial Control Facilitates Splicing Regulation of Gene Expression and Enhances Genome Diversity. J. Biol. Chem. 283: 1209-1210. PMID: 18024424

Fedor, M. J. and Williamson, J. R. (2005) The catalytic diversity of RNAs. Solicited review. Nat. Rev. Mol. Cell Biol. 6(5): 399-412. PMID: 15956979

Fedor, M. J. (2004) Determination of Kinetic Parameters for Hammerhead and Hairpin Ribozymes. In Catalytic Nucleic Acid Enzymes. Methods Mol. Biol. 252: 19-32. PMID: 15017040

Fedor, M. J. (2002) The Catalytic Mechanism of the Hairpin Ribozyme. Biochem. Soc. Trans. 30(6): 1109-1115. PMID: 12440984

Fedor, M. J. and Westhof, E. (2002) Ribozymes: The First 20 Years. Meeting Report. Mol. Cell 10(4): 703-704. PMID: 12419214

Fedor, M. J. (2002) The Role of Metal Ions in RNA Catalysis. Curr. Opin. Struct. Biol. 12(3): 289-295. PMID: 12127446

Fedor, M. J. (2002) RNA Biochemistry From A to Z. Book review. Cell 109: 20-22.

Fedor, M. J. (2000) Structure and Function of the Hairpin Ribozyme. J. Mol. Biol. 297(2): 269-291. PMID: 10715200

Fedor, M. J., Donahue, C. P. and Nesbitt, S. M. (2000) Hairpin Ribozyme Activity In Vitro and In Vivo. In Ribozymes. Technology and Applications (R. K. Gaur and G. Krupp, Eds.) Eaton Publishing, Natick, MA.

Fedor, M. J. (1998) Ribozymes. Current Biology 8(13): R441-R443.

Fedor, M. J. (1997) Capturing a Speeding Locomotive. Book Review. Cell 88: 589-592.

Fedor, M. J. (1994) A Slippery Grip. News and Views. Nat. Struct. Biol. 1(5): 267-269. PMID: 7545070

Fedor, M. J. (1992) Chromatin Structure and Gene Expression. Curr. Opin. Cell Biol. 4(3): 436-443. PMID: 1497914