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Thomas R. Cech - Related publications

Chemistry and Biochemistry University of Colorado, Boulder, Boulder, CO, United States 
RNA (ribozyme) catalysis
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. A Short Chemically-Modified dsRNA-Binding PNA (dbPNA) Inhibits Influenza Viral Replication by Targeting Viral RNA Panhandle Structure. Bioconjugate Chemistry. PMID 30721034 DOI: 10.1021/acs.bioconjchem.9b00039   
2019 Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nature Communications. 10: 990. PMID 30824702 DOI: 10.1038/s41467-019-08942-3   
2019 Strickland M, Catazaro J, Rajasekaran R, Strub MP, O'Hern C, Bermejo GA, Summers MF, Marchant J, Tjandra N. Long-range RNA structural information via a paramagnetically tagged reporter protein. Journal of the American Chemical Society. PMID 30652860 DOI: 10.1021/jacs.8b11384   
2019 Thomas C, Rusanov T, Hoang T, Augustin T, Kent T, Gaspar I, Pomerantz RT. One-step enzymatic modification of RNA 3' termini using polymerase θ. Nucleic Acids Research. PMID 30818397 DOI: 10.1093/nar/gkz029   
2019 Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brötzmann J, Staahl BT, Taylor KL, et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. PMID 30718774 DOI: 10.1038/s41586-019-0908-x   
2019 Halpert M, Liveanu V, Glaser F, Schuster G. The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities. Plant Molecular Biology. 99: 17-29. PMID 30511330 DOI: 10.1007/s11103-018-0799-5   
2019 Liu L, Li T, Song G, He Q, Yin Y, Lu JY, Bi X, Wang K, Luo S, Chen YS, Yang Y, Sun BF, Yang YG, Wu J, Zhu H, et al. Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome. Nucleic Acids Research. PMID 30698743 DOI: 10.1093/nar/gkz032   
2019 Gao J, Byrd AK, Zybailov BL, Marecki JC, Guderyon MJ, Edwards AD, Chib S, West KL, Waldrip ZJ, Mackintosh SG, Gao Z, Putnam AA, Jankowsky E, Raney KD. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chemical Communications (Cambridge, England). PMID 30855040 DOI: 10.1039/c8cc10091h   
2019 Dagil R, Ball NJ, Ogrodowicz RW, Hobor F, Purkiss AG, Kelly G, Martin SR, Taylor IA, Ramos A. IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties. Nucleic Acids Research. PMID 30864660 DOI: 10.1093/nar/gkz136   
2019 Krishna MS, Toh DK, Meng Z, Ong AAL, Wang Z, Lu Y, Xia K, Prabakaran M, Chen G. Sequence- and structure-specific probing of RNAs by short nucleobase-modified dsRNA-binding PNAs (dbPNAs) incorporating a fluorescent light-up uracil analog. Analytical Chemistry. PMID 30873827 DOI: 10.1021/acs.analchem.9b00280   
2019 Smail BA, Clifton BE, Mizuuchi R, Lehman N. Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms. Rna (New York, N.Y.). PMID 30670484 DOI: 10.1261/rna.068908.118   
2019 Richards J, Belasco JG. Obstacles to Scanning by RNase E Govern Bacterial mRNA Lifetimes by Hindering Access to Distal Cleavage Sites. Molecular Cell. PMID 30852060 DOI: 10.1016/j.molcel.2019.01.044   
2019 Bayfield MA, Vinayak J, Kerkhofs K, Mansouri-Noori F. La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates. Rna Biology. PMID 30777481 DOI: 10.1080/15476286.2019.1582955   
2019 Wang J, Hammond J, Johnson KA. Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes. Journal of Visualized Experiments : Jove. PMID 30774126 DOI: 10.3791/59021   
2019 Rani R, Yaseen AM, Malwade A, Sevilimedu A. An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe. Rna Biology. PMID 30794054 DOI: 10.1080/15476286.2019.1584026   
2019 Luige O, Murtola M, Ghidini A, Strömberg R. Further Probing of Cu-Dependent PNAzymes Acting as Artificial RNA Restriction Enzymes. Molecules (Basel, Switzerland). 24. PMID 30769777 DOI: 10.3390/molecules24040672   
2019 Zhou Z, Giles KE, Felsenfeld G. DNA·RNA triple helix formation can function as a -acting regulatory mechanism at the human locus. Proceedings of the National Academy of Sciences of the United States of America. PMID 30867287 DOI: 10.1073/pnas.1900107116   
2019 O'Hara JM, Marashi D, Morton S, Jaeger L, Grabow WW. Optimization of the Split-Spinach Aptamer for Monitoring Nanoparticle Assembly Involving Multiple Contiguous RNAs. Nanomaterials (Basel, Switzerland). 9. PMID 30845655 DOI: 10.3390/nano9030378   
2019 Bohnsack KE, Höbartner C, Bohnsack MT. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes. 10. PMID 30704115 DOI: 10.3390/genes10020102   
2019 Eason IR, Kaur HP, Alexander KA, Sukhodolets MV. Growth phase-specific changes in the composition of E. coli transcription complexes. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1109: 155-165. PMID 30785097 DOI: 10.1016/j.jchromb.2019.01.014   
2019 Zhang L, Vielle A, Espinosa S, Zhao R. RNAs in the spliceosome: Insight from cryoEM structures. Wiley Interdisciplinary Reviews. Rna. e1523. PMID 30729694 DOI: 10.1002/wrna.1523   
2019 Desfosses A, Milles S, Jensen MR, Guseva S, Colletier JP, Maurin D, Schoehn G, Gutsche I, Ruigrok RWH, Blackledge M. Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication. Proceedings of the National Academy of Sciences of the United States of America. PMID 30787192 DOI: 10.1073/pnas.1816417116   
2019 Wang X, N MPA, Jeon HJ, Lee Y, He J, Adhya S, Lim HM. Processing generates 3' ends of RNA masking transcription termination events in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America. PMID 30782818 DOI: 10.1073/pnas.1813181116   
2019 Zhang Y, Kleiner RE. A Metabolic Engineering Approach to Incorporate Modified Pyrimidine Nucleosides into Cellular RNA. Journal of the American Chemical Society. PMID 30735369 DOI: 10.1021/jacs.8b11449   
2019 Cruz-Gallardo I, Martino L, Kelly G, Atkinson RA, Trotta R, De Tito S, Coleman P, Ahdash Z, Gu Y, Bui TTT, Conte MR. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Research. PMID 30820564 DOI: 10.1093/nar/gkz144   
2019 Heller RC, Chung S, Crissy K, Dumas K, Schuster D, Schoenfeld TW. Engineering of a thermostable viral polymerase using metagenome-derived diversity for highly sensitive and specific RT-PCR. Nucleic Acids Research. PMID 30767012 DOI: 10.1093/nar/gkz104   
2019 Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Communications Biology. 2: 19. PMID 30652130 DOI: 10.1038/s42003-018-0271-8   
2019 Lang B, Armaos A, Tartaglia GG. RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. Nucleic Acids Research. 47: D601-D606. PMID 30445601 DOI: 10.1093/nar/gky967   
2019 Crabtree AM, Kizer EA, Hunter SS, Van Leuven JT, New DD, Fagnan MW, Rowley PA. A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from . Viruses. 11. PMID 30654470 DOI: 10.3390/v11010070   
2019 Skrajna A, Yang XC, Dominski Z. Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker. Journal of Visualized Experiments : Jove. PMID 30663646 DOI: 10.3791/58697   
2019 Pezone A, Zuchegna C, Tramontano A, Romano A, Russo G, de Rosa M, Vinciguerra M, Porcellini A, Gottesman ME, Avvedimento EV. RNA Stabilizes Transcription-Dependent Chromatin Loops Induced By Nuclear Hormones. Scientific Reports. 9: 3925. PMID 30850627 DOI: 10.1038/s41598-019-40123-6   
2019 Bahrami-Samani E, Xing Y. Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes. American Journal of Human Genetics. 104: 492-502. PMID 30827501 DOI: 10.1016/j.ajhg.2019.01.018   
2019 Lambert M, Benmoussa A, Provost P. Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA. Non-Coding Rna. 5. PMID 30720712 DOI: 10.3390/ncrna5010016   
2019 Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Selectively Discriminates against 5'-Monophosphate RNA. Cell Reports. 26: 2019-2027.e4. PMID 30784585 DOI: 10.1016/j.celrep.2019.01.107   
2019 Jukam D, Limouse C, Smith OK, Risca VI, Bell JC, Straight AF. Chromatin-Associated RNA Sequencing (ChAR-seq). Current Protocols in Molecular Biology. e87. PMID 30786161 DOI: 10.1002/cpmb.87   
2019 Hazra D, Chapat C, Graille M. m⁶A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins. Genes. 10. PMID 30650668 DOI: 10.3390/genes10010049   
2019 Assis NG, Ribeiro RA, da Silva LG, Vicente AM, Hug I, Marques MV. Identification of Hfq-binding RNAs in Caulobacter crescentus. Rna Biology. PMID 30870072 DOI: 10.1080/15476286.2019.1593091   
2019 Furuhata Y, Kobayashi M, Maruyama R, Sato Y, Makino K, Michiue T, Yui H, Nishizawa S, Yoshimoto K. Programmable RNA Detection with a Fluorescent RNA Aptamer Using Optimized Three-way Junction Formation. Rna (New York, N.Y.). PMID 30745364 DOI: 10.1261/rna.069062.118   
2019 Scott DD, Francois-Moutal L, Kumirov VK, Khanna M. H, N and C backbone assignment of apo TDP-43 RNA recognition motifs. Biomolecular Nmr Assignments. PMID 30694439 DOI: 10.1007/s12104-018-09870-x   
2019 Ramanathan M, Porter DF, Khavari PA. Methods to study RNA-protein interactions. Nature Methods. 16: 225-234. PMID 30804549 DOI: 10.1038/s41592-019-0330-1   
2019 Muthmann N, Guez T, Vasseur JJ, Jaffrey SR, Debart F, Rentmeister A. Combining chemical synthesis and enzymatic methylation to access short RNAs with various 5' caps. Chembiochem : a European Journal of Chemical Biology. PMID 30768827 DOI: 10.1002/cbic.201900037   
2019 Adams MS, Znosko BM. Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions. Nucleic Acids Research. PMID 30698818 DOI: 10.1093/nar/gkz019   
2019 Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC. Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates. Nature Communications. 10: 490. PMID 30700721 DOI: 10.1038/s41467-019-08353-4   
2019 Kumarasinghe N, Moss WN. Analysis of a structured intronic region of the LMP2 pre-mRNA from EBV reveals associations with human regulatory proteins and nuclear actin. Bmc Research Notes. 12: 33. PMID 30658689 DOI: 10.1186/s13104-019-4070-1   
2019 Sampathi S, Acharya P, Zhao Y, Wang J, Stengel KR, Liu Q, Savona MR, Hiebert SW. The CDK7 inhibitor THZ1 alters RNA polymerase dynamics at the 5' and 3' ends of genes. Nucleic Acids Research. PMID 30805632 DOI: 10.1093/nar/gkz127   
2019 Ong AAL, Toh DK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. General recognition of U-G, U-A, and C-G pairs by double-stranded RNA-binding PNAs (dbPNAs) incorporated with an artificial nucleobase. Biochemistry. PMID 30775913 DOI: 10.1021/acs.biochem.8b01313   
2019 Almeida MV, de Jesus Domingues AM, Lukas H, Mendez-Lago M, Ketting RF. RppH can faithfully replace TAP to allow cloning of 5'-triphosphate carrying small RNAs. Methodsx. 6: 265-272. PMID 30788220 DOI: 10.1016/j.mex.2019.01.009   
2019 Sharma D, Sehgal P, Hariprakash J, Sivasubbu S, Scaria V. Methods for Annotation and Validation of Circular RNAs from RNAseq Data. Methods in Molecular Biology (Clifton, N.J.). 1912: 55-76. PMID 30635890 DOI: 10.1007/978-1-4939-8982-9_3   
2019 Yuan F, Bi Y, Siejka-Zielinska P, Zhou YL, Zhang XX, Song CX. Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. Chemical Communications (Cambridge, England). PMID 30723849 DOI: 10.1039/c9cc00274j   
2019 He Z, Ruan X, Liu X, Zheng J, Liu Y, Liu L, Ma J, Shao L, Wang D, Shen S, Yang C, Xue Y. FUS/circ_002136/miR-138-5p/SOX13 feedback loop regulates angiogenesis in Glioma. Journal of Experimental & Clinical Cancer Research : Cr. 38: 65. PMID 30736838 DOI: 10.1186/s13046-019-1065-7