mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo
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M. Fedor | Elisabeth M. Mahen | Peter Y. Watson | Joseph W. Cottrell | Martha J. Fedor | P. Y. Watson
[1] Kirsten L. Frieda,et al. Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers , 2008, Science.
[2] M. Ares,et al. Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.
[3] R. Breaker,et al. The structural and functional diversity of metabolite-binding riboswitches. , 2009, Annual review of biochemistry.
[4] J. Sambrook,et al. Molecular Cloning: A Laboratory Manual , 2001 .
[5] C. Pleij,et al. Self-induced structural switches in RNA. , 2002, Biochimie.
[6] S. Woodson. Recent insights on RNA folding mechanisms from catalytic RNA , 2000, Cellular and Molecular Life Sciences CMLS.
[7] M. Nomura,et al. Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly. , 2007, Molecular cell.
[8] D. Herschlag,et al. An RNA chaperone activity of non‐specific RNA binding proteins in hammerhead ribozyme catalysis. , 1994, The EMBO journal.
[9] K. J. Hertel,et al. Combinatorial Control of Exon Recognition* , 2008, Journal of Biological Chemistry.
[10] P. Romby,et al. Probing RNA structure and RNA-ligand complexes with chemical probes. , 2000, Methods in enzymology.
[11] S. Woodson,et al. Intracellular folding of the Tetrahymena group I intron depends on exon sequence and promoter choice. , 2004, RNA.
[12] C. Donahue,et al. Kinetics of hairpin ribozyme cleavage in yeast. , 1997, RNA.
[13] A. Lambowitz,et al. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. , 2007, Journal of molecular biology.
[14] X. Darzacq,et al. In vivo dynamics of RNA polymerase II transcription , 2007, Nature Structural &Molecular Biology.
[15] O. Uhlenbeck,et al. Keeping RNA happy. , 1995, RNA.
[16] N. Proudfoot,et al. Pause Sites Promote Transcriptional Termination of Mammalian RNA Polymerase II , 2006, Molecular and Cellular Biology.
[17] C. Martin,et al. Effects of solution conditions on the steady-state kinetics of initiation of transcription by T7 RNA polymerase. , 1994, Biochemistry.
[18] S. Lacadie,et al. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. , 2005, Molecular cell.
[19] M. Fedor,et al. Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. , 2005, Molecular cell.
[20] Duncan J. Smith,et al. "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. , 2008, Molecular cell.
[21] N. Sugimoto,et al. Stabilization of three-way junctions of DNA under molecular crowding conditions. , 2009, Journal of the American Chemical Society.
[22] T. C. Gluick,et al. Trimethylamine N-oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea. , 2003, Journal of the American Chemical Society.
[23] Tao Pan,et al. RNA folding during transcription. , 2006, Annual review of biophysics and biomolecular structure.
[24] M. Fedor,et al. Determination of intracellular RNA folding rates using self-cleaving RNAs. , 2009, Methods in enzymology.
[25] M. Belfort,et al. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. , 1994, Genes & development.
[26] C. Donahue,et al. The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics. , 2000, Journal of molecular biology.
[27] Changbong Hyeon,et al. Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. , 2008, Journal of the American Chemical Society.
[28] P. Babitzke,et al. RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction. , 2006, Molecular cell.
[29] Melissa J. Moore,et al. Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation , 2009, Cell.
[30] R. Montange,et al. Riboswitches: emerging themes in RNA structure and function. , 2008, Annual review of biophysics.
[31] E. Jankowsky,et al. RNA helicases--one fold for many functions. , 2007, Current opinion in structural biology.
[32] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[33] Huijue Jia,et al. Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones. , 2009, Journal of molecular biology.
[34] D. Crothers,et al. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. , 1973, Journal of molecular biology.
[35] Javier F. Cáceres,et al. RNA TURNOVER IN EUKARYOTES: ANALYSIS OF SPECIALIZED AND QUALITY CONTROL RNA DECAY PATHWAYS , 2008 .
[36] P. Bevilacqua,et al. A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. , 2002, Journal of molecular biology.
[37] M. Fedor,et al. The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. , 1999, Journal of molecular biology.
[38] D. K. Treiber,et al. Exposing the kinetic traps in RNA folding. , 1999, Current opinion in structural biology.
[39] D. Herschlag,et al. Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. , 2008, Current opinion in structural biology.
[40] R. Sikorski,et al. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.
[41] T. Pan,et al. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. , 1999, Journal of molecular biology.
[42] D. Herschlag,et al. Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A. Preface. , 2009, Methods in enzymology.
[43] Christina Waldsich,et al. RNA folding in vivo. , 2002, Current opinion in structural biology.
[44] L. Armengol,et al. Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility , 2008, BMC Genomics.
[45] S. Woodson,et al. Effect of transcription on folding of the Tetrahymena ribozyme. , 2003, RNA.
[46] David E Draper,et al. Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. , 2007, Journal of Molecular Biology.
[47] Huan‐Xiang Zhou,et al. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. , 2008, Annual review of biophysics.
[48] R. Green,et al. RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli. , 2004, RNA.
[49] N. Sugimoto,et al. Molecular crowding effects on structure and stability of DNA. , 2008, Biochimie.
[50] Tao Pan,et al. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures , 2007, Proceedings of the National Academy of Sciences.
[51] D. Lilley,et al. Folding of the adenine riboswitch. , 2006, Chemistry & biology.
[52] R. Ellis,et al. Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001, Current opinion in structural biology.
[53] R. Batey,et al. Structures of regulatory elements in mRNAs. , 2006, Current opinion in structural biology.
[54] N. Sugimoto,et al. The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. , 2004, Journal of the American Chemical Society.
[55] M. Fedor. Tertiary structure stabilization promotes hairpin ribozyme ligation. , 1999, Biochemistry.
[56] S. Woodson,et al. RNA folding and ribosome assembly. , 2008, Current opinion in chemical biology.
[57] D M Crothers,et al. Kinetics of an RNA conformational switch. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[58] M. Fedor,et al. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. , 1995, Biochemistry.
[59] J. van Duin,et al. Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? , 1995, RNA.
[60] O. Uhlenbeck,et al. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[61] D. Herschlag. RNA Chaperones and the RNA Folding Problem (*) , 1995, The Journal of Biological Chemistry.
[62] N. Tanner,et al. The DEAD-box protein family of RNA helicases. , 2006, Gene.
[63] R. Konrat,et al. RNA Chaperones, RNA Annealers and RNA Helicases , 2007, RNA biology.
[64] M. Fedor,et al. Hairpin ribozymes with four-way helical junctions mediate intracellular RNA ligation. , 2001, Journal of molecular biology.
[65] S. Woodson,et al. Loop dependence of the stability and dynamics of nucleic acid hairpins , 2007, Nucleic acids research.
[66] J Andrew Berglund,et al. The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing , 2009, Proceedings of the National Academy of Sciences.
[67] A. Lambowitz,et al. DEAD-box proteins unwind duplexes by local strand separation. , 2007, Molecular cell.
[68] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[69] T. Rouault. The role of iron regulatory proteins in mammalian iron homeostasis and disease , 2006, Nature chemical biology.
[70] M. Fedor,et al. Kinetic analysis of ribozyme-substrate complex formation in yeast. , 2004, RNA.
[71] I. Tinoco,et al. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications. , 1995, Nucleic acids research.
[72] E. Androphy,et al. Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes , 2006, Nucleic acids research.
[73] E. Sontheimer,et al. Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.
[74] C. Yanofsky,et al. Evolution of bacterial trp operons and their regulation. , 2008, Current opinion in microbiology.
[75] D. Bentley,et al. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. , 2005, Current opinion in cell biology.
[76] D. Crothers,et al. The kinetics of ligand binding by an adenine-sensing riboswitch. , 2005, Biochemistry.
[77] Dongrong Wen,et al. Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment , 2008, BMC Genomics.
[78] R. Russell. RNA misfolding and the action of chaperones. , 2008, Frontiers in bioscience : a journal and virtual library.
[79] D. Porschke,et al. Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. , 1974, Biophysical chemistry.