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Pan:Methods: Difference between revisions
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'''DM-tRNA-seq (demethylase tRNA-seq):''' | '''DM-tRNA-seq (demethylase tRNA-seq):''' | ||
''(Microbiome)'' Schwartz, M.H., H.P. Wang, J.N. Pan, W.C. Clark, S. Cui, M.J. Eckwahl, D.W. Pan, M. Parisien, S.M. Owens, B.L. Cheng, K. Martinez, J.B. Xu, E.B. Chang, Tao Pan*, A.M. Eren*: Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis, ''Nature Communications'' 9:5353, p.1-13 (2018). | ''(Microbiome)'' Schwartz, M.H., H.P. Wang, J.N. Pan, W.C. Clark, S. Cui, M.J. Eckwahl, D.W. Pan, M. Parisien, S.M. Owens, B.L. Cheng, K. Martinez, J.B. Xu, E.B. Chang, Tao Pan*, A.M. Eren*: Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis, ''Nature Communications'' 9:5353, p.1-13 (2018). | ||
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'''RNA modification:''' | '''RNA modification:''' | ||
''(m6A reader protein)'' Zhou, K.I., N. Liu & Tao Pan*: Identification of N6-methyladenosine reader proteins, ''Methods'' 126, 105-111 (2017). | ''(m6A reader protein)'' Zhou, K.I., N. Liu & Tao Pan*: Identification of N6-methyladenosine reader proteins, ''Methods'' 126, 105-111 (2017). | ||
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'''tRNA biology:''' | '''tRNA biology:''' | ||
''(tRNA microarray, misacylation)'' Schwartz*, M.H., Tao Pan*: Determining the fidelity of tRNA aminoacylation via microarrays, ''Methods'' 113, 27-33 (2017). | ''(tRNA microarray, misacylation)'' Schwartz*, M.H., Tao Pan*: Determining the fidelity of tRNA aminoacylation via microarrays, ''Methods'' 113, 27-33 (2017). | ||
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'''Co-transcriptional RNA folding | '''Co-transcriptional RNA folding''' | ||
''(Riboswitch)'' Perdrizet, G.A., I. Artsimovitch, R. Furman, T. R. Sosnick*, Tao Pan*: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, ''Proc. Natl. Acad. Sci. USA'' 109, 3323-3328 (2012). | ''(Riboswitch)'' Perdrizet, G.A., I. Artsimovitch, R. Furman, T. R. Sosnick*, Tao Pan*: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, ''Proc. Natl. Acad. Sci. USA'' 109, 3323-3328 (2012). | ||
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''(Ribozyme)'' 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). | ''(Ribozyme)'' 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). | ||
'''Tertiary RNA folding''' | |||
''(Metal ion in rate-liming step)'' 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). | |||
''(SAXS)'' Fang, X-W., K.L. Littrell, X-J. Yang, S.J. Henderson, S. Seifert, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: Mg2+-dependent compaction and folding of the yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by Small-angle X-ray scattering. Biochemistry 39, 11107-11113 (2000). | |||
''(Quantitative denaturation)'' Shelton, V., T.R. Sosnick* & Tao Pan*: The applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry 38, 16831-16839 (1999). | |||
''(Kinetic framework)'' Fang, X-W., Tao Pan* & T.R. Sosnick*: Mg2+-dependent folding of a large ribozyme without kinetic traps. Nature Str. Mol. Biol. 6, 1091-1095 (1999). | |||
''(Spectroscopy)'' Tao Pan* & T.R. Sosnick*: Intermediates and kinetic traps in the folding of a large ribozyme revealed by CD spectroscopy and catalytic activity. Nature Str. Mol. Biol. 4, 931-938 (1997). | |||
<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Press|Press]] | [[Pan:Publications|Publications]] | [[Pan:Methods|Methods]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]] | <font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Press|Press]] | [[Pan:Publications|Publications]] | [[Pan:Methods|Methods]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]] | ||
