Joseph E. Wedekind, Ph. D. - Related publications

Biochemistry University of Rochester, Rochester, NY 
x-ray crystallography, ncRNA structure, APOBEC3G
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Lemak S, Serbanescu MA, Khusnutdinova AN, Ruszkowski M, Beloglazova N, Xu X, Brown G, Cui H, Tan K, Joachimiak A, Cvitkovitch DG, Savchenko A, Yakunin AF. Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. The Journal of Biological Chemistry. 101251. PMID 34592310 DOI: 10.1016/j.jbc.2021.101251   
2021 Portillo X, Huang YT, Breaker RR, Horning DP, Joyce GF. Witnessing the structural evolution of an RNA enzyme. Elife. 10. PMID 34498588 DOI: 10.7554/eLife.71557   
2021 Cheng Y, Zhang S, Xu X, Chen SJ. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. The Journal of Physical Chemistry. B. PMID 34473508 DOI: 10.1021/acs.jpcb.1c04731   
2021 Zhou T, Wang H, Zeng C, Zhao Y. RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. Bmc Bioinformatics. 22: 428. PMID 34496744 DOI: 10.1186/s12859-021-04349-4   
2021 Phan HD, Lai LB, Zahurancik WJ, Gopalan V. The many faces of RNA-based RNase P, an RNA-world relic. Trends in Biochemical Sciences. PMID 34511335 DOI: 10.1016/j.tibs.2021.07.005   
2021 Alonso D, Mondragón A. Mechanisms of catalytic RNA molecules. Biochemical Society Transactions. 49: 1529-1535. PMID 34415304 DOI: 10.1042/BST20200465   
2021 Deng X, Wang S, Han Z, Gong W, Liu Y, Li C. Dynamics of binding interactions of TDP-43 and RNA:an equally weighted multiscale elastic network model study. Proteins. PMID 34599611 DOI: 10.1002/prot.26255   
2021 Krishnamohan A, Dodbele S, Jackman JE. Transient kinetic analysis for studying ionizations in RNA modification enzyme mechanisms. Methods in Enzymology. 658: 251-275. PMID 34517950 DOI: 10.1016/bs.mie.2021.07.002   
2021 Stoute J, Liu KF. CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes. Methods in Enzymology. 658: 419-434. PMID 34517957 DOI: 10.1016/bs.mie.2021.08.001   
2021 Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Expanding the binding specificity for RNA recognition by a PUF domain. Nature Communications. 12: 5107. PMID 34429425 DOI: 10.1038/s41467-021-25433-6   
2021 Hong X, Zheng J, Xie J, Tong X, Liu X, Song Q, Liu S, Liu S. RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. Rna Biology. 1-9. PMID 34663179 DOI: 10.1080/15476286.2021.1989200   
2021 Furuzono T, Murata A, Okuda S, Mizutani K, Adachi T, Nakatani K. Speeding drug discovery targeting RNAs: An iterative "RNA selection-compounds screening cycle" for exploring RNA-small molecule pairs. Bioorganic & Medicinal Chemistry. 36: 116070. PMID 33773376 DOI: 10.1016/j.bmc.2021.116070   
2021 Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Research. PMID 34634799 DOI: 10.1093/nar/gkab885   
2021 Das R, Russell R. How to Kinetically Dissect an RNA Machine. Biochemistry. PMID 34492193 DOI: 10.1021/acs.biochem.1c00392   
2021 Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers. e23476. PMID 34581432 DOI: 10.1002/bip.23476   
2021 Nakamura K, Nakao T, Mori T, Ohno S, Fujita Y, Masaoka K, Sakabayashi K, Mori K, Tobimatsu T, Sera T. Necessity of Flanking Repeats R1' and R8' of Human Pumilio1 Protein for RNA Binding. Biochemistry. PMID 34541851 DOI: 10.1021/acs.biochem.1c00445   
2021 Savita BK, Dalal V, Choudhary S, Gupta DN, Das N, Tomar S, Kumar P, Roy P, Sharma AK. Characterization of recombinant pumpkin 2S albumin and mutation studies to unravel potential DNA/RNA binding site. Biochemical and Biophysical Research Communications. 580: 28-34. PMID 34610489 DOI: 10.1016/j.bbrc.2021.09.076   
2021 Poudyal RR, Sieg JP, Portz B, Keating CD, Bevilacqua PC. RNA sequence and structure control assembly and function of RNA condensates. Rna (New York, N.Y.). PMID 34551999 DOI: 10.1261/rna.078875.121   
2021 Plavec Z, Pöhner I, Poso A, Butcher SJ. Virus structure and structure-based antivirals. Current Opinion in Virology. 51: 16-24. PMID 34564030 DOI: 10.1016/j.coviro.2021.09.005   
2021 Mukherjee P, Raghava Kurup R, Hundley HA. RNA immunoprecipitation to identify in vivo targets of RNA editing and modifying enzymes. Methods in Enzymology. 658: 137-160. PMID 34517945 DOI: 10.1016/bs.mie.2021.06.005   
2021 Schmidt A, Hanspach G, Hengesbach M. Structural dynamics govern substrate recruitment and catalytic turnover in H/ACA RNP pseudouridylation. Rna Biology. 18: 1300-1309. PMID 33111609 DOI: 10.1080/15476286.2020.1842984   
2021 Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. The Journal of Physical Chemistry. B. PMID 34694128 DOI: 10.1021/acs.jpcb.1c07288   
2021 Radecki P, Uppuluri R, Aviran S. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. Nar Genomics and Bioinformatics. 3: lqab073. PMID 34447931 DOI: 10.1093/nargab/lqab073   
2021 Zhang K, Frank AT. Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 34449236 DOI: 10.1021/acs.jpcb.1c05651   
2021 Höfler S, Lukat P, Blankenfeldt W, Carlomagno T. Eukaryotic Box C/D methylation machinery has two non-symmetric protein assembly sites. Scientific Reports. 11: 17561. PMID 34475498 DOI: 10.1038/s41598-021-97030-y   
2021 Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression. Molecular & Cellular Proteomics : McP. 100142. PMID 34478875 DOI: 10.1016/j.mcpro.2021.100142   
2021 Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, et al. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Research. PMID 34508350 DOI: 10.1093/nar/gkab724   
2021 Endo M, Kim JI, Shioi NA, Iwai S, Kuraoka I. endonuclease V is a ribonuclease specific for inosine-containing single-stranded RNA. Open Biology. 11: 210148. PMID 34665969 DOI: 10.1098/rsob.210148   
2021 Le Vay KK, Song EY, Ghosh B, Tang TD, Mutschler H. Enhanced ribozyme-catalyzed recombination and oligonucleotide assembly in peptide-RNA condensates. Angewandte Chemie (International Ed. in English). PMID 34569680 DOI: 10.1002/anie.202109267   
2021 Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. Wiley Interdisciplinary Reviews. Rna. e1688. PMID 34472205 DOI: 10.1002/wrna.1688   
2021 Hohmann KF, Blümler A, Heckel A, Fürtig B. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Nucleic Acids Research. PMID 34614185 DOI: 10.1093/nar/gkab876   
2021 Shin Y, Murakami KS. Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography. The Enzymes. 49: 305-314. PMID 34696836 DOI: 10.1016/bs.enz.2021.06.009   
2021 Hong S, Jeong D, Ryan J, Foo M, Tang X, Kim J. Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules. 11. PMID 34439849 DOI: 10.3390/biom11081182   
2021 Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs - switching atoms means shifting paradigms. Febs Letters. PMID 34468991 DOI: 10.1002/1873-3468.14188   
2021 Kim JM, Chun H. TAR RNA Mediated Folding of a Single-Arginine-Mutant HIV-1 Tat Protein within HeLa Cells Experiencing Intracellular Crowding. International Journal of Molecular Sciences. 22. PMID 34576162 DOI: 10.3390/ijms22189998   
2021 Singh O, Venugopal PP, Mathur A, Chakraborty D. Temperature-Dependent Conformational Evolution of SARS CoV-2 RNA Genome Using Network Analysis. The Journal of Physical Chemistry. B. PMID 34524834 DOI: 10.1021/acs.jpcb.1c05795   
2021 Hagen T, Laski A, Brümmer A, Pruška A, Schlösser V, Cléry A, Allain FH, Zenobi R, Bergmann S, Hall J. Inosine Substitutions in RNA Activate Latent G-Quadruplexes. Journal of the American Chemical Society. PMID 34520206 DOI: 10.1021/jacs.1c05214   
2021 Ding P, Kharytonchyk S, Kuo N, Cannistraci E, Flores H, Chaudhary R, Sarkar M, Dong X, Telesnitsky A, Summers MF. 5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34493679 DOI: 10.1073/pnas.2112475118   
2021 Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. Wiley Interdisciplinary Reviews. Rna. e1694. PMID 34553495 DOI: 10.1002/wrna.1694   
2021 Martinez NM, Schaening-Burgos C, Gilbert WV. Pseudouridine site assignment by high-throughput in vitro RNA pseudouridylation and sequencing. Methods in Enzymology. 658: 277-310. PMID 34517951 DOI: 10.1016/bs.mie.2021.06.026   
2021 Wei Y, Yang Z, Zong C, Wang B, Ge X, Tan X, Liu X, Tao Z, Wang P, Ma C, Wan Y, Li J. Trans  Single-Stranded DNA Cleavage Via CRISPR/Cas14a1 Activated by Target RNA without Destruction. Angewandte Chemie (International Ed. in English). PMID 34553468 DOI: 10.1002/anie.202110384   
2021 Pyle JD, Whelan SPJ. Isolation of reconstructed functional ribonucleoprotein complexes of Machupo virus. Journal of Virology. JVI0105421. PMID 34432522 DOI: 10.1128/JVI.01054-21   
2021 Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chemical Communications (Cambridge, England). PMID 34590632 DOI: 10.1039/d1cc04383h   
2021 Tac HA, Koroglu M, Sezerman U. RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines. Functional & Integrative Genomics. PMID 34529170 DOI: 10.1007/s10142-021-00805-9   
2021 Dai W, Li A, Yu NJ, Nguyen T, Leach RW, Wühr M, Kleiner RE. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nature Chemical Biology. PMID 34556860 DOI: 10.1038/s41589-021-00874-8   
2021 Aoyama JJ, Raina M, Storz G. Synthetic dual-function RNA reveals features necessary for target regulation. Journal of Bacteriology. JB0034521. PMID 34460309 DOI: 10.1128/JB.00345-21   
2021 Rapisarda A, Bargiela A, Llamusi B, Pont I, Estrada-Tejedor R, Garcia-España E, Artero R, Perez-Alonso M. Defined D-hexapeptides bind CUG repeats and rescue phenotypes of myotonic dystrophy myotubes in a Drosophila model of the disease. Scientific Reports. 11: 19417. PMID 34593893 DOI: 10.1038/s41598-021-98866-0   
2021 Johnson KA, Dangerfield T. Mechanisms of inhibition of viral RNA replication by nucleotide analogs. The Enzymes. 49: 39-62. PMID 34696838 DOI: 10.1016/bs.enz.2021.07.001   
2021 Dwivedi VD, Singh A, El-Kafraway SA, Alandijany TA, Faizo AA, Bajrai LH, Kamal MA, Azhar EI. Mechanistic insights into the Japanese encephalitis virus RNA dependent RNA polymerase protein inhibition by bioflavonoids from Azadirachta indica. Scientific Reports. 11: 18125. PMID 34518560 DOI: 10.1038/s41598-021-96917-0   
2021 Feng X, Yang S, Zhang Y, Zhiyuan C, Tang K, Li G, Yu H, Leng J, Wang Q. , Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean. Frontiers in Plant Science. 12: 690973. PMID 34567023 DOI: 10.3389/fpls.2021.690973