Pan:Publications

2007-2010:

• Saikia, M., Y. Fu, M. Pavon-Eternod, C. He & Tao Pan*: Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs, RNA, in press (2010).

• Tuller, T., A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, Tao Pan, O. Dahan, I. Furman & Y. Pilpel: An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation, Cell 141, 344-354 (2010).

• Baird, N.J., H-P. Gong, S.S. Zaheer, K.F. Freed, Tao Pan* & T.R. Sosnick*: Extended structures in RNA folding intermediates are due to non-native interactions rather than electrostatic repulsion, J. Mol. Biol. 397, 1298-1306 (2010).

• Geslain, R. & Tao Pan*: Functional analysis of human tRNA isodecoders, J. Mol. Biol. 396, 821-831 (2010).

• Pavon-Eternod, M., M. Wei, Tao Pan* & Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA 16, 267-273 (2010).

• Netzer, N., J.M. Goodenbour, A. David, K.A. Dittmar, R.B. Jones, J.R. Schneider, D. Boone, E.M. Eves, M.R. Rosner, J.S. Gibbs, A. Embry, B. Dolan, S. Das, H. Hickman, P. Berglund, J.R. Bennink, J.W. Yewdell*, Tao Pan*: Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity, Nature 462, 522-526 (2009).

• Wong, T.N. & Tao Pan: RNA Folding during Transcription: Protocols and Studies. Methods in Enzymology 468, 167-193 (2009).

• Pavon-Eternod, M., S. Gomes, R. Geslain, Q. Dai, M. R. Rosner* & Tao Pan*: tRNA Over-expression in Breast Cancer and Functional Consequences, Nucl. Acids Res. 37, 7268-7280 (2009).

• Zaborske, J.M., J. Narasimhan, L. Jiang, S.A. Wek, K.A. Dittmar, F. Freimoser, Tao Pan* & R.C. Wek*: Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p, J. Biol. Chem. 284, 25254-25267 (2009).

• Zhou, Y., J.M. Goodenbour, L.A. Godley, A. Wickrema* & Tao Pan*: High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Biochem. Biophys. Res. Comm. 385, 160-164 (2009).

• Dai, Q., M. Saikia, N-S. Li, Tao Pan* & J.A. Piccirilli*: Efficient Chemical Synthesis of AppDNA by Adenylation of Immobilized DNA-5-monophosphate, Organic Letters 11, 1067-1070 (2009).

• Qu, X-H., G. J. Smith, K.T. Lee, T. R. Sosnick, Tao Pan & N. F. Scherer: Single-Molecule Non-equilibrium Periodic Mg2+-concentration Jump Experiments Reveal Details of the Early Folding Pathways of a Large RNA, Proc. Natl. Acad. Sci. USA 105, 6602-6607 (2008).

• Smith, G.J., K.T. Lee, X-H. Qu, Z. Xie, J. Pesic, T.R. Sosnick, Tao Pan & N.F. Scherer: Discrete single molecule dynamics suggest relatively simple but rugged structure for a large collapsed-state RNA, J. Mol. Biol. 378, 941-951 (2008).

• Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan* & J.A. Piccirilli*: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007).

• Baird, N.J., X.-W. Fang, N. Srividya, Tao Pan & T. R. Sosnick: Folding of a universal ribozyme, the RNase P RNA. Q. Rev. Biophys. 40, 113-161 (2007). Review.

• Wong, T., T.R. Sosnick* & Tao Pan*: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007).

Selected older publications:

• Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).

• Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli* & Tao Pan*: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006).

• Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).

• Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006). Review.

• Baird NJ, Westhof E, Qin H, Pan T*, Sosnick TR*. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 352:712-22 (2005).

• Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-7 (2005).

• Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).

• Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).

• Dittmar KA, Mobley EM, Radek AJ, Pan T. Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol. 337:31-47 (2004).

• Krasilnikov AS, Yang X, Pan T, Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-4 (2003).

• Fang, X-W., P. Thiyagarajan, T.R. Sosnick* & Tao Pan*: The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523 (2002).

• Fang, X-W., B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98, 4355-4360 (2001).

• Tao Pan*, I. Artsimovitch, X-W. Fang, R. Landick & T.R. Sosnick*: Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. USA 96, 9545-9550 (1999).

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