| Year |
Citation |
Score |
| 2024 |
Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial motif noncoding RNA causes defects in sporulation and aggregation. Proceedings of the National Academy of Sciences of the United States of America. 121: e2318008121. PMID 38306478 DOI: 10.1073/pnas.2318008121 |
0.556 |
|
| 2023 |
Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Reports. 42: 113571. PMID 38096053 DOI: 10.1016/j.celrep.2023.113571 |
0.47 |
|
| 2023 |
Hamal Dhakal S, Kavita K, Panchapakesan SSS, Roth A, Breaker RR. 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage. Proceedings of the National Academy of Sciences of the United States of America. 120: e2307854120. PMID 37748066 DOI: 10.1073/pnas.2307854120 |
0.804 |
|
| 2023 |
Breaker RR, Harris KA, Lyon SE, Wencker FDR, Fernando CM. Evidence that OLE RNA is a component of a major stress-responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology. PMID 37469248 DOI: 10.1111/mmi.15129 |
0.448 |
|
| 2023 |
Mohsen MG, Breaker RR. In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers. Bio-Protocol. 13: e4775. PMID 37456339 DOI: 10.21769/BioProtoc.4775 |
0.834 |
|
| 2023 |
Narunsky A, Kavita K, Panchapakesan SSS, Fris ME, Breaker RR. A conserved uORF in the mRNA of species regulates operon expression. Microbial Genomics. 9. PMID 37233150 DOI: 10.1099/mgen.0.001019 |
0.814 |
|
| 2023 |
Salvail H, Breaker RR. Riboswitches. Current Biology : Cb. 33: R343-R348. PMID 37160088 DOI: 10.1016/j.cub.2023.03.069 |
0.546 |
|
| 2023 |
Sadeeshkumar H, Balaji A, Sutherland AG, Mootien S, Anthony KG, Breaker RR. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Analytical Biochemistry. 115047. PMID 36682579 DOI: 10.1016/j.ab.2023.115047 |
0.315 |
|
| 2023 |
Mohsen MG, Midy MK, Balaji A, Breaker RR. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Research. PMID 36617976 DOI: 10.1093/nar/gkac1218 |
0.844 |
|
| 2022 |
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes. Scientific Reports. 12: 19145. PMID 36352003 DOI: 10.1038/s41598-022-20695-6 |
0.307 |
|
| 2022 |
Lyon SE, Harris KA, Odzer NB, Wilkins SG, Breaker RR. Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function. The Journal of Biological Chemistry. 102674. PMID 36336078 DOI: 10.1016/j.jbc.2022.102674 |
0.535 |
|
| 2022 |
Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends in Biochemical Sciences. PMID 36150954 DOI: 10.1016/j.tibs.2022.08.009 |
0.81 |
|
| 2022 |
Sherlock ME, Higgs G, Yu D, Widner DL, White NA, Sudarsan N, Sadeeshkumar H, Perkins KR, Mirihana Arachchilage G, Malkowski SN, King CG, Harris KA, Gaffield G, Atilho RM, Breaker RR. Architectures and complex functions of tandem riboswitches. Rna Biology. 19: 1059-1076. PMID 36093908 DOI: 10.1080/15476286.2022.2119017 |
0.494 |
|
| 2022 |
Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine. Proceedings of the National Academy of Sciences of the United States of America. 119: e2120246119. PMID 35622895 DOI: 10.1073/pnas.2120246119 |
0.4 |
|
| 2022 |
Breaker RR. The Biochemical Landscape of Riboswitch Ligands. Biochemistry. 61: 137-149. PMID 35068140 DOI: 10.1021/acs.biochem.1c00765 |
0.483 |
|
| 2021 |
Roth A, Weinberg Z, Vanderschuren K, Murdock MH, Breaker RR. Natural circularly permuted group II introns in bacteria produce RNA circles. Iscience. 24: 103431. PMID 34901790 DOI: 10.1016/j.isci.2021.103431 |
0.313 |
|
| 2021 |
Brewer KI, Gaffield GJ, Puri M, Breaker RR. DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. Bioinformatics (Oxford, England). PMID 34524415 DOI: 10.1093/bioinformatics/btab624 |
0.492 |
|
| 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 |
0.669 |
|
| 2021 |
Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. Rna Biology. 1-16. PMID 33970790 DOI: 10.1080/15476286.2021.1917891 |
0.394 |
|
| 2021 |
Yang Y, Harris KA, Widner DL, Breaker RR. Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33619097 DOI: 10.1073/pnas.2020393118 |
0.544 |
|
| 2021 |
Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nature Chemical Biology. PMID 33495645 DOI: 10.1038/s41589-020-00713-2 |
0.512 |
|
| 2020 |
Salvail H, Balaji A, Yu D, Roth A, Breaker RR. Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria. Biochemistry. PMID 33236895 DOI: 10.1021/acs.biochem.0c00793 |
0.411 |
|
| 2020 |
Panchapakesan SSS, Corey L, Malkowski S, Higgs G, Breaker RR. A Second Riboswitch Class for the Enzyme Cofactor NAD. Rna (New York, N.Y.). PMID 33087526 DOI: 10.1261/rna.077891.120 |
0.591 |
|
| 2020 |
Malkowski S, Atilho R, Greenlee E, Weinberg C, Breaker RR. A rare bacterial RNA motif is implicated in the regulation of the gene whose encoded enzyme synthesizes phosphoribosylamine. Rna (New York, N.Y.). PMID 32843366 DOI: 10.1261/Rna.077313.120 |
0.656 |
|
| 2020 |
Breaker RR. Imaginary Ribozymes. Acs Chemical Biology. PMID 32687319 DOI: 10.1021/acschembio.0c00214 |
0.499 |
|
| 2020 |
Widner DL, Harris KA, Corey L, Breaker RR. OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE. The Journal of Biological Chemistry. PMID 32376692 DOI: 10.1074/Jbc.Ra120.012676 |
0.628 |
|
| 2020 |
Yu D, Breaker RR. A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation. Rna (New York, N.Y.). PMID 32345632 DOI: 10.1261/Rna.075218.120 |
0.614 |
|
| 2020 |
Sherlock M, Breaker RR. Former Orphan Riboswitches Reveal Unexplored Areas of Bacterial Metabolism, Signaling and Gene Control Processes. Rna (New York, N.Y.). PMID 32165489 DOI: 10.1261/Rna.074997.120 |
0.478 |
|
| 2019 |
Perkins KR, Atilho RM, Moon MH, Breaker RR. Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-throughput Screen. Acs Chemical Biology. PMID 31609568 DOI: 10.1021/Acschembio.9B00713 |
0.327 |
|
| 2019 |
Malkowski SN, Spencer TCJ, Breaker RR. Evidence that the Motif is a Bacterial Riboswitch for the Ubiquitous Enzyme Cofactor NAD. Rna (New York, N.Y.). PMID 31467147 DOI: 10.1261/Rna.072538.119 |
0.594 |
|
| 2019 |
Harris KA, Odzer NB, Breaker RR. Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans. Molecular Microbiology. PMID 31461569 DOI: 10.1111/Mmi.14379 |
0.502 |
|
| 2019 |
Chen X, Mirihana Arachchilage G, Breaker RR. Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria. Rna (New York, N.Y.). PMID 31186369 DOI: 10.1261/Rna.071829.119 |
0.601 |
|
| 2019 |
Atilho RM, Mirihana Arachchilage G, Greenlee EB, Knecht KM, Breaker RR. A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer. Elife. 8. PMID 30950790 DOI: 10.7554/Elife.45210 |
0.576 |
|
| 2019 |
Stav S, Atilho RM, Mirihana Arachchilage G, Nguyen G, Higgs G, Breaker RR. Genome-wide discovery of structured noncoding RNAs in bacteria. Bmc Microbiology. 19: 66. PMID 30902049 DOI: 10.1186/S12866-019-1433-7 |
0.605 |
|
| 2019 |
Atilho RM, Arachchilage GM, Greenlee EB, Knecht KM, Breaker RR. Author response: A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer Elife. DOI: 10.7554/Elife.45210.020 |
0.32 |
|
| 2018 |
Atilho RM, Perkins KR, Breaker RR. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. Rna (New York, N.Y.). PMID 30287481 DOI: 10.1261/Rna.067975.118 |
0.487 |
|
| 2018 |
Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR. A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. Nucleic Acids Research. PMID 30085248 DOI: 10.1093/Nar/Gky709 |
0.597 |
|
| 2018 |
Sherlock ME, Sadeeshkumar H, Breaker RR. Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates. Biochemistry. PMID 30081631 DOI: 10.1021/Acs.Biochem.8B00617 |
0.641 |
|
| 2018 |
Harris KA, Breaker RR. Large Noncoding RNAs in Bacteria. Microbiology Spectrum. 6. PMID 29992899 DOI: 10.1128/Microbiolspec.Rwr-0005-2017 |
0.568 |
|
| 2018 |
Harris KA, Zhou Z, Peters ML, Wilkins SG, Breaker RR. A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex. Proceedings of the National Academy of Sciences of the United States of America. PMID 29915070 DOI: 10.1073/Pnas.1803191115 |
0.61 |
|
| 2018 |
Breaker RR. Riboswitches and Translation Control. Cold Spring Harbor Perspectives in Biology. PMID 29844057 DOI: 10.1101/Cshperspect.A032797 |
0.537 |
|
| 2018 |
Sherlock ME, Sudarsan N, Breaker RR. Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems. Proceedings of the National Academy of Sciences of the United States of America. PMID 29784782 DOI: 10.1073/Pnas.1720406115 |
0.597 |
|
| 2018 |
Sherlock ME, Sudarsan N, Stav S, Breaker RR. Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. Elife. 7. PMID 29504937 DOI: 10.7554/Elife.33908 |
0.631 |
|
| 2018 |
Breaker RR. RNA World theory Access Science. DOI: 10.1036/1097-8542.591330 |
0.382 |
|
| 2017 |
Greenlee EB, Stav S, Atilho RM, Brewer KI, Harris KA, Malkowski SN, Arachchilage GM, Perkins KR, Sherlock ME, Breaker RR. Challenges of Ligand Identification for the Second Wave of Orphan Riboswitch Candidates. Rna Biology. 0. PMID 29135333 DOI: 10.1080/15476286.2017.1403002 |
0.539 |
|
| 2017 |
Arachchilage GM, Sherlock ME, Weinberg Z, Breaker RR. SAM-VI RNAs Selectively Bind S-adenosylmethionine and Exhibit Similarities to SAM-III Riboswitches. Rna Biology. 0. PMID 29106323 DOI: 10.1080/15476286.2017.1399232 |
0.62 |
|
| 2017 |
Li S, Breaker RR. Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics. Bmc Genomics. 18: 785. PMID 29029611 DOI: 10.1186/S12864-017-4171-Y |
0.439 |
|
| 2017 |
Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Research. PMID 28977401 DOI: 10.1093/Nar/Gkx699 |
0.838 |
|
| 2017 |
Nelson JW, Breaker RR. The lost language of the RNA World. Science Signaling. 10. PMID 28611182 DOI: 10.1126/Scisignal.Aam8812 |
0.573 |
|
| 2017 |
Breaker RR, McCown P, Corbino K, Stav S, Sherlock M. Riboswitch Diversity and Distribution. Rna (New York, N.Y.). PMID 28396576 DOI: 10.1261/Rna.061234.117 |
0.571 |
|
| 2017 |
Reza Naghdi M, Smail K, Wang JX, Wade F, Breaker RR, Perreault J. Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database. Methods (San Diego, Calif.). PMID 28279853 DOI: 10.1016/J.Ymeth.2017.02.009 |
0.563 |
|
| 2017 |
Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR. Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proceedings of the National Academy of Sciences of the United States of America. PMID 28265071 DOI: 10.1073/Pnas.1619581114 |
0.541 |
|
| 2017 |
Breaker RR. Mechanistic Debris Generated by Twister Ribozymes. Acs Chemical Biology. PMID 28191925 DOI: 10.1021/Acschembio.7B00010 |
0.535 |
|
| 2017 |
Breaker RR, Atilho RM, Malkowski SN, Nelson JW, Sherlock ME. The Biology of Free Guanidine As Revealed by Riboswitches. Biochemistry. PMID 28060483 DOI: 10.1021/Acs.Biochem.6B01269 |
0.309 |
|
| 2016 |
Sherlock ME, Breaker RR. Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria. Biochemistry. PMID 28001372 DOI: 10.1021/acs.biochem.6b01271 |
0.522 |
|
| 2016 |
Sherlock ME, Malkowski SN, Breaker RR. Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. Biochemistry. PMID 28001368 DOI: 10.1021/Acs.Biochem.6B01270 |
0.66 |
|
| 2016 |
Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR. Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Molecular Cell. PMID 27989440 DOI: 10.1016/J.Molcel.2016.11.019 |
0.55 |
|
| 2016 |
Lünse CE, Weinberg Z, Breaker RR. Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers. Rna Biology. 0. PMID 27858507 DOI: 10.1080/15476286.2016.1251002 |
0.54 |
|
| 2016 |
Ruff KM, Muhammad A, McCown PJ, Breaker RR, Strobel SA. Singlet glycine riboswitches bind ligand as well as tandem riboswitches. Rna (New York, N.Y.). PMID 27659053 DOI: 10.1261/Rna.057935.116 |
0.436 |
|
| 2016 |
Li S, Hwang XY, Stav S, Breaker RR. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. Rna (New York, N.Y.). PMID 26843526 DOI: 10.1261/Rna.054890.115 |
0.646 |
|
| 2015 |
Li S, Lünse CE, Harris KA, Breaker RR. Biochemical analysis of hatchet self-cleaving ribozymes. Rna (New York, N.Y.). 21: 1845-51. PMID 26385510 DOI: 10.1261/Rna.052522.115 |
0.537 |
|
| 2015 |
Harris KA, Lünse CE, Li S, Brewer KI, Breaker RR. Biochemical analysis of pistol self-cleaving ribozymes. Rna (New York, N.Y.). 21: 1852-8. PMID 26385507 DOI: 10.1261/Rna.052514.115 |
0.531 |
|
| 2015 |
Blount KF, Megyola C, Plummer M, Osterman D, O'Connell T, Aristoff P, Quinn C, Chrusciel RA, Poel TJ, Schostarez HJ, Stewart CA, Walker DP, Wuts PG, Breaker RR. Novel Riboswitch-Binding Flavin Analog That Protects Mice against Clostridium difficile Infection without Inhibiting Cecal Flora. Antimicrobial Agents and Chemotherapy. 59: 5736-46. PMID 26169403 DOI: 10.1128/Aac.01282-15 |
0.375 |
|
| 2015 |
Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lünse CE, Breaker RR. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nature Chemical Biology. 11: 606-10. PMID 26167874 DOI: 10.1038/Nchembio.1846 |
0.549 |
|
| 2015 |
Nelson JW, Plummer MS, Blount KF, Ames TD, Breaker RR. Small molecule fluoride toxicity agonists. Chemistry & Biology. 22: 527-34. PMID 25910244 DOI: 10.1016/J.Chembiol.2015.03.016 |
0.736 |
|
| 2015 |
Nelson JW, Sudarsan N, Phillips GE, Stav S, Lünse CE, McCown PJ, Breaker RR. Control of bacterial exoelectrogenesis by c-AMP-GMP. Proceedings of the National Academy of Sciences of the United States of America. 112: 5389-94. PMID 25848023 DOI: 10.1073/Pnas.1419264112 |
0.396 |
|
| 2015 |
Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Molecular Cell. 57: 1088-98. PMID 25794617 DOI: 10.1016/J.Molcel.2015.02.009 |
0.711 |
|
| 2015 |
Kim PB, Nelson JW, Breaker RR. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Molecular Cell. 57: 317-28. PMID 25616067 DOI: 10.1016/J.Molcel.2015.01.001 |
0.409 |
|
| 2014 |
Breaker RR, Joyce GF. The expanding view of RNA and DNA function. Chemistry & Biology. 21: 1059-65. PMID 25237854 DOI: 10.1016/J.Chembiol.2014.07.008 |
0.631 |
|
| 2014 |
McCown PJ, Liang JJ, Weinberg Z, Breaker RR. Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. Chemistry & Biology. 21: 880-9. PMID 25036777 DOI: 10.1016/J.Chembiol.2014.05.015 |
0.379 |
|
| 2014 |
Furukawa K, Gu H, Breaker RR. In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP. Methods in Molecular Biology (Clifton, N.J.). 1111: 209-20. PMID 24549622 DOI: 10.1007/978-1-62703-755-6_15 |
0.397 |
|
| 2014 |
Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nature Chemical Biology. 10: 56-60. PMID 24240507 DOI: 10.1038/Nchembio.1386 |
0.834 |
|
| 2013 |
Li S, Smith KD, Davis JH, Gordon PB, Breaker RR, Strobel SA. Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 19018-23. PMID 24173035 DOI: 10.1073/Pnas.1310439110 |
0.336 |
|
| 2013 |
Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR. Riboswitches in eubacteria sense the second messenger c-di-AMP. Nature Chemical Biology. 9: 834-9. PMID 24141192 DOI: 10.1038/Nchembio.1363 |
0.518 |
|
| 2013 |
Roth A, Breaker RR. Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes. Cell. 153: 1417-8. PMID 23791167 DOI: 10.1016/J.Cell.2013.05.043 |
0.344 |
|
| 2013 |
Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. Journal of the American Chemical Society. 135: 9121-9. PMID 23679108 DOI: 10.1021/Ja403585E |
0.325 |
|
| 2013 |
Li S, Breaker RR. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Research. 41: 3022-31. PMID 23376932 DOI: 10.1093/Nar/Gkt057 |
0.615 |
|
| 2012 |
Breaker RR. Ancient, giant riboswitches at atomic resolution. Nature Structural & Molecular Biology. 19: 1208-9. PMID 23142981 DOI: 10.1038/Nsmb.2453 |
0.342 |
|
| 2012 |
Breaker RR, Conklin DS, Gold L, Söll D, Montimurro JS, Agris PF. RNA science and its applications-a look toward the future: Albany, NY USA, November 3-4, 2011. Rna Biology. 9: 1050-3. PMID 22858674 DOI: 10.4161/Rna.21209 |
0.517 |
|
| 2012 |
Pedrolli DB, Matern A, Wang J, Ester M, Siedler K, Breaker R, Mack M. A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis. Nucleic Acids Research. 40: 8662-73. PMID 22740651 DOI: 10.1093/Nar/Gks616 |
0.339 |
|
| 2012 |
Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker RR. Identification of ligand analogues that control c-di-GMP riboswitches. Acs Chemical Biology. 7: 1436-43. PMID 22646696 DOI: 10.1021/Cb300138N |
0.441 |
|
| 2012 |
Wallace JG, Zhou Z, Breaker RR. OLE RNA protects extremophilic bacteria from alcohol toxicity. Nucleic Acids Research. 40: 6898-907. PMID 22561371 DOI: 10.1093/Nar/Gks352 |
0.555 |
|
| 2012 |
Gu H, Furukawa K, Breaker RR. Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate. Analytical Chemistry. 84: 4935-41. PMID 22519888 DOI: 10.1021/Ac300415K |
0.519 |
|
| 2012 |
Breaker RR. New insight on the response of bacteria to fluoride. Caries Research. 46: 78-81. PMID 22327376 DOI: 10.1159/000336397 |
0.304 |
|
| 2012 |
McCown PJ, Winkler WC, Breaker RR. Mechanism and distribution of glmS ribozymes. Methods in Molecular Biology (Clifton, N.J.). 848: 113-29. PMID 22315066 DOI: 10.1007/978-1-61779-545-9_8 |
0.787 |
|
| 2012 |
Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. Widespread genetic switches and toxicity resistance proteins for fluoride. Science (New York, N.Y.). 335: 233-5. PMID 22194412 DOI: 10.1126/Science.1215063 |
0.773 |
|
| 2012 |
Breaker RR. Riboswitches and the RNA world. Cold Spring Harbor Perspectives in Biology. 4. PMID 21106649 DOI: 10.1101/Cshperspect.A003566 |
0.597 |
|
| 2011 |
Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Research. 21: 1929-43. PMID 21994249 DOI: 10.1101/Gr.112516.110 |
0.5 |
|
| 2011 |
Chen AG, Sudarsan N, Breaker RR. Mechanism for gene control by a natural allosteric group I ribozyme. Rna (New York, N.Y.). 17: 1967-72. PMID 21960486 DOI: 10.1261/Rna.2757311 |
0.465 |
|
| 2011 |
Breaker RR. Prospects for riboswitch discovery and analysis. Molecular Cell. 43: 867-79. PMID 21925376 DOI: 10.1016/J.Molcel.2011.08.024 |
0.583 |
|
| 2011 |
Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. Plos Computational Biology. 7: e1002031. PMID 21573207 DOI: 10.1371/Journal.Pcbi.1002031 |
0.544 |
|
| 2011 |
McCown PJ, Roth A, Breaker RR. An expanded collection and refined consensus model of glmS ribozymes. Rna (New York, N.Y.). 17: 728-36. PMID 21367971 DOI: 10.1261/Rna.2590811 |
0.494 |
|
| 2011 |
Meyer MM, Hammond MC, Salinas Y, Roth A, Sudarsan N, Breaker RR. Challenges of ligand identification for riboswitch candidates. Rna Biology. 8: 5-10. PMID 21317561 DOI: 10.4161/Rna.8.1.13865 |
0.81 |
|
| 2011 |
Ames TD, Breaker RR. Bacterial aptamers that selectively bind glutamine. Rna Biology. 8: 82-9. PMID 21282981 DOI: 10.4161/Rna.8.1.13864 |
0.849 |
|
| 2011 |
Weinberg Z, Breaker RR. R2R--software to speed the depiction of aesthetic consensus RNA secondary structures. Bmc Bioinformatics. 12: 3. PMID 21205310 DOI: 10.1186/1471-2105-12-3 |
0.572 |
|
| 2011 |
Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR. Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Molecular Microbiology. 79: 21-34. PMID 21166891 DOI: 10.1111/J.1365-2958.2010.07439.X |
0.87 |
|
| 2010 |
Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (New York, N.Y.). 329: 845-8. PMID 20705859 DOI: 10.1126/Science.1190713 |
0.81 |
|
| 2010 |
Ames TD, Rodionov DA, Weinberg Z, Breaker RR. A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chemistry & Biology. 17: 681-5. PMID 20659680 DOI: 10.1016/J.Chembiol.2010.05.020 |
0.864 |
|
| 2010 |
Block KF, Hammond MC, Breaker RR. Evidence for widespread gene control function by the ydaO riboswitch candidate. Journal of Bacteriology. 192: 3983-9. PMID 20511502 DOI: 10.1128/Jb.00450-10 |
0.859 |
|
| 2010 |
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biology. 11: R31. PMID 20230605 DOI: 10.1186/Gb-2010-11-3-R31 |
0.645 |
|
| 2010 |
Breaker RR. RNA switches out in the cold. Molecular Cell. 37: 1-2. PMID 20129048 DOI: 10.1016/J.Molcel.2009.12.032 |
0.528 |
|
| 2010 |
Breaker RR. RNA second messengers and riboswitches: Relics from the RNA world? Microbe. 5: 13-20. DOI: 10.1128/microbe.5.13.1 |
0.471 |
|
| 2010 |
Ames TD, Breaker RR. Bacterial Riboswitch Discovery and Analysis The Chemical Biology of Nucleic Acids. 433-454. DOI: 10.1002/9780470664001.ch20 |
0.724 |
|
| 2009 |
Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature. 462: 656-9. PMID 19956260 DOI: 10.1038/Nature08586 |
0.595 |
|
| 2009 |
Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Structural basis of ligand binding by a c-di-GMP riboswitch. Nature Structural & Molecular Biology. 16: 1218-23. PMID 19898477 DOI: 10.1038/Nsmb.1702 |
0.76 |
|
| 2009 |
Poiata E, Meyer MM, Ames TD, Breaker RR. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. Rna (New York, N.Y.). 15: 2046-56. PMID 19776155 DOI: 10.1261/Rna.1824209 |
0.8 |
|
| 2009 |
Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. Design and antimicrobial action of purine analogues that bind Guanine riboswitches. Acs Chemical Biology. 4: 915-27. PMID 19739679 DOI: 10.1021/Cb900146K |
0.705 |
|
| 2009 |
Link KH, Breaker RR. Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Therapy. 16: 1189-201. PMID 19587710 DOI: 10.1038/Gt.2009.81 |
0.562 |
|
| 2009 |
Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. Bmc Genomics. 10: 268. PMID 19531245 DOI: 10.1186/1471-2164-10-268 |
0.844 |
|
| 2009 |
Link KH, Breaker RR. In vitro selection of glmS ribozymes. Methods in Molecular Biology (Clifton, N.J.). 540: 349-64. PMID 19381572 DOI: 10.1007/978-1-59745-558-9_25 |
0.52 |
|
| 2009 |
Hammond MC, Wachter A, Breaker RR. A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nature Structural & Molecular Biology. 16: 541-9. PMID 19377483 DOI: 10.1038/Nsmb.1588 |
0.769 |
|
| 2009 |
Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Finding non-coding RNAs through genome-scale clustering. Journal of Bioinformatics and Computational Biology. 7: 373-88. PMID 19340921 DOI: 10.1142/S0219720009004126 |
0.444 |
|
| 2009 |
Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Annual Review of Biochemistry. 78: 305-34. PMID 19298181 DOI: 10.1146/Annurev.Biochem.78.070507.135656 |
0.606 |
|
| 2009 |
Lee ER, Blount KF, Breaker RR. Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. Rna Biology. 6: 187-94. PMID 19246992 DOI: 10.4161/Rna.6.2.7727 |
0.707 |
|
| 2009 |
Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ. Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environmental Microbiology. 11: 230-8. PMID 19125817 DOI: 10.1111/J.1462-2920.2008.01758.X |
0.306 |
|
| 2008 |
Boese BJ, Corbino K, Breaker RR. In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification. Nucleosides, Nucleotides & Nucleic Acids. 27: 949-66. PMID 18696364 DOI: 10.1080/15257770802257903 |
0.87 |
|
| 2008 |
Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science (New York, N.Y.). 321: 411-3. PMID 18635805 DOI: 10.1126/Science.1159519 |
0.785 |
|
| 2008 |
Wang JX, Breaker RR. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 86: 157-68. PMID 18443629 DOI: 10.1139/O08-008 |
0.418 |
|
| 2008 |
Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Molecular Cell. 29: 691-702. PMID 18374645 DOI: 10.1016/J.Molcel.2008.01.012 |
0.793 |
|
| 2008 |
Regulski EE, Breaker RR. In-line probing analysis of riboswitches. Methods in Molecular Biology (Clifton, N.J.). 419: 53-67. PMID 18369975 DOI: 10.1007/978-1-59745-033-1_4 |
0.865 |
|
| 2008 |
Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna (New York, N.Y.). 14: 822-8. PMID 18369181 DOI: 10.1261/Rna.988608 |
0.851 |
|
| 2008 |
Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Molecular Microbiology. 68: 918-32. PMID 18363797 DOI: 10.1111/J.1365-2958.2008.06208.X |
0.87 |
|
| 2008 |
Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. Rna (New York, N.Y.). 14: 685-95. PMID 18305186 DOI: 10.1261/Rna.937308 |
0.622 |
|
| 2008 |
Kim JN, Breaker RR. Purine sensing by riboswitches. Biology of the Cell / Under the Auspices of the European Cell Biology Organization. 100: 1-11. PMID 18072940 DOI: 10.1042/Bc20070088 |
0.707 |
|
| 2007 |
Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biology. 8: R239. PMID 17997835 DOI: 10.1186/Gb-2007-8-11-R239 |
0.758 |
|
| 2007 |
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. The Plant Cell. 19: 3437-50. PMID 17993623 DOI: 10.1105/Tpc.107.053645 |
0.458 |
|
| 2007 |
Kim JN, Roth A, Breaker RR. Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proceedings of the National Academy of Sciences of the United States of America. 104: 16092-7. PMID 17911257 DOI: 10.1073/Pnas.0705884104 |
0.748 |
|
| 2007 |
Boese BJ, Breaker RR. In vitro selection and characterization of cellulose-binding DNA aptamers. Nucleic Acids Research. 35: 6378-88. PMID 17881365 DOI: 10.1093/Nar/Gkm708 |
0.815 |
|
| 2007 |
Link KH, Guo L, Ames TD, Yen L, Mulligan RC, Breaker RR. Engineering high-speed allosteric hammerhead ribozymes. Biological Chemistry. 388: 779-86. PMID 17655496 DOI: 10.1515/Bc.2007.105 |
0.81 |
|
| 2007 |
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research. 35: 4809-19. PMID 17621584 DOI: 10.1093/Nar/Gkm487 |
0.868 |
|
| 2007 |
Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. Plos Computational Biology. 3: e126. PMID 17616982 DOI: 10.1371/Journal.Pcbi.0030126 |
0.753 |
|
| 2007 |
Cheah MT, Wachter A, Sudarsan N, Breaker RR. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature. 447: 497-500. PMID 17468745 DOI: 10.1038/Nature05769 |
0.613 |
|
| 2007 |
Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nature Structural & Molecular Biology. 14: 308-17. PMID 17384645 DOI: 10.1038/Nsmb1224 |
0.863 |
|
| 2007 |
Welz R, Breaker RR. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. Rna (New York, N.Y.). 13: 573-82. PMID 17307816 DOI: 10.1261/Rna.407707 |
0.527 |
|
| 2007 |
Barrick JE, Breaker RR. The power of riboswitches. Scientific American. 296: 50-7. PMID 17186833 DOI: 10.1038/Scientificamerican0107-50 |
0.699 |
|
| 2007 |
Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR. Antibacterial lysine analogs that target lysine riboswitches. Nature Chemical Biology. 3: 44-9. PMID 17143270 DOI: 10.1038/Nchembio842 |
0.568 |
|
| 2007 |
Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes Plos Computational Biology. 3: 1212-1223. DOI: 10.1371/journal.pcbi.0030126 |
0.651 |
|
| 2006 |
Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR. Identification of a large noncoding RNA in extremophilic eubacteria. Proceedings of the National Academy of Sciences of the United States of America. 103: 19490-5. PMID 17164334 DOI: 10.1073/Pnas.0607493103 |
0.765 |
|
| 2006 |
Blount KF, Breaker RR. Riboswitches as antibacterial drug targets. Nature Biotechnology. 24: 1558-64. PMID 17160062 DOI: 10.1038/Nbt1268 |
0.449 |
|
| 2006 |
Blount K, Puskarz I, Penchovsky R, Breaker R. Development and application of a high-throughput assay for glmS riboswitch activators Rna Biology. 3: 77-81. PMID 17114942 DOI: 10.4161/Rna.3.2.3102 |
0.362 |
|
| 2006 |
Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. Tandem riboswitch architectures exhibit complex gene control functions. Science (New York, N.Y.). 314: 300-4. PMID 17038623 DOI: 10.1126/Science.1130716 |
0.861 |
|
| 2006 |
Link KH, Guo L, Breaker RR. Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection. Nucleic Acids Research. 34: 4968-75. PMID 16982640 DOI: 10.1093/Nar/Gkl643 |
0.482 |
|
| 2006 |
Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature. 441: 1167-71. PMID 16728979 DOI: 10.1038/Nature04740 |
0.649 |
|
| 2006 |
Roth A, Nahvi A, Lee M, Jona I, Breaker RR. Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. Rna (New York, N.Y.). 12: 607-19. PMID 16484375 DOI: 10.1261/Rna.2266506 |
0.756 |
|
| 2006 |
Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. Molecular-recognition characteristics of SAM-binding riboswitches. Angewandte Chemie (International Ed. in English). 45: 964-8. PMID 16381055 DOI: 10.1002/Anie.200503198 |
0.682 |
|
| 2006 |
Roth A, Welz R, Breaker RR. Riboswitches: Natural Metabolite-binding RNAs Controlling Gene Expression The Aptamer Handbook: Functional Oligonucleotides and Their Applications. 191-207. DOI: 10.1002/3527608192.ch8 |
0.537 |
|
| 2005 |
Breaker RR. Gene expression control: harnessing RNA switches. Gene Therapy. 12: 725-6. PMID 19202632 DOI: 10.1038/Sj.Gt.3302461 |
0.549 |
|
| 2005 |
Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chemistry & Biology. 12: 1325-35. PMID 16356850 DOI: 10.1016/J.Chembiol.2005.10.007 |
0.437 |
|
| 2005 |
Penchovsky R, Breaker RR. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnology. 23: 1424-33. PMID 16244657 DOI: 10.1038/Nbt1155 |
0.602 |
|
| 2005 |
Wickiser JK, Cheah MT, Breaker RR, Crothers DM. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry. 44: 13404-14. PMID 16201765 DOI: 10.1021/Bi051008U |
0.496 |
|
| 2005 |
Winkler WC, Breaker RR. Regulation of bacterial gene expression by riboswitches. Annual Review of Microbiology. 59: 487-517. PMID 16153177 DOI: 10.1146/Annurev.Micro.59.030804.121336 |
0.795 |
|
| 2005 |
Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biology. 6: R70. PMID 16086852 DOI: 10.1186/Gb-2005-6-8-R70 |
0.869 |
|
| 2005 |
Tucker BJ, Breaker RR. Riboswitches as versatile gene control elements. Current Opinion in Structural Biology. 15: 342-8. PMID 15919195 DOI: 10.1016/J.Sbi.2005.05.003 |
0.63 |
|
| 2005 |
Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. Rna (New York, N.Y.). 11: 774-84. PMID 15811922 DOI: 10.1261/Rna.7286705 |
0.769 |
|
| 2005 |
Wickiser JK, Winkler WC, Breaker RR, Crothers DM. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell. 18: 49-60. PMID 15808508 DOI: 10.1016/J.Molcel.2005.02.032 |
0.812 |
|
| 2005 |
Zivarts M, Liu Y, Breaker RR. Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Research. 33: 622-31. PMID 15681614 DOI: 10.1093/Nar/Gki182 |
0.505 |
|
| 2004 |
Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chemistry & Biology. 11: 1729-41. PMID 15610857 DOI: 10.1016/J.Chembiol.2004.11.018 |
0.476 |
|
| 2004 |
Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature. 432: 838-45. PMID 15602549 DOI: 10.1038/Nature03195 |
0.466 |
|
| 2004 |
Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (New York, N.Y.). 306: 275-9. PMID 15472076 DOI: 10.1126/Science.1100829 |
0.834 |
|
| 2004 |
Mandal M, Breaker RR. Gene regulation by riboswitches. Nature Reviews. Molecular Cell Biology. 5: 451-63. PMID 15173824 DOI: 10.1038/Nrm1403 |
0.849 |
|
| 2004 |
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proceedings of the National Academy of Sciences of the United States of America. 101: 6421-6. PMID 15096624 DOI: 10.1073/Pnas.0308014101 |
0.85 |
|
| 2004 |
Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 428: 281-6. PMID 15029187 DOI: 10.1038/Nature02362 |
0.842 |
|
| 2004 |
Roth A, Breaker RR. Selection in vitro of allosteric ribozymes. Methods in Molecular Biology (Clifton, N.J.). 252: 145-64. PMID 15017047 DOI: 10.1385/1-59259-746-7:145 |
0.535 |
|
| 2004 |
Mandal M, Breaker RR. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Structural & Molecular Biology. 11: 29-35. PMID 14718920 DOI: 10.1038/Nsmb710 |
0.874 |
|
| 2004 |
Nahvi A, Barrick JE, Breaker RR. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Research. 32: 143-50. PMID 14704351 DOI: 10.1093/Nar/Gkh167 |
0.862 |
|
| 2003 |
Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes & Development. 17: 2688-97. PMID 14597663 DOI: 10.1101/Gad.1140003 |
0.624 |
|
| 2003 |
Winkler WC, Breaker RR. Genetic control by metabolite-binding riboswitches. Chembiochem : a European Journal of Chemical Biology. 4: 1024-32. PMID 14523920 DOI: 10.1002/Cbic.200300685 |
0.769 |
|
| 2003 |
Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nature Structural Biology. 10: 701-7. PMID 12910260 DOI: 10.1038/Nsb967 |
0.883 |
|
| 2003 |
Breaker RR, Emilsson GM, Lazarev D, Nakamura S, Puskarz IJ, Roth A, Sudarsan N. A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. Rna (New York, N.Y.). 9: 949-57. PMID 12869706 DOI: 10.1261/Rna.5670703 |
0.777 |
|
| 2003 |
Emilsson GM, Nakamura S, Roth A, Breaker RR. Ribozyme speed limits. Rna (New York, N.Y.). 9: 907-18. PMID 12869701 DOI: 10.1261/Rna.5680603 |
0.554 |
|
| 2003 |
Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell. 113: 577-86. PMID 12787499 DOI: 10.1016/S0092-8674(03)00391-X |
0.829 |
|
| 2003 |
Lazarev D, Puskarz I, Breaker RR. Substrate specificity and reaction kinetics of an X-motif ribozyme. Rna (New York, N.Y.). 9: 688-97. PMID 12756327 DOI: 10.1261/Rna.2600503 |
0.793 |
|
| 2003 |
Sudarsan N, Barrick JE, Breaker RR. Metabolite-binding RNA domains are present in the genes of eukaryotes. Rna (New York, N.Y.). 9: 644-7. PMID 12756322 DOI: 10.1261/Rna.5090103 |
0.748 |
|
| 2002 |
Winkler WC, Cohen-Chalamish S, Breaker RR. An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences of the United States of America. 99: 15908-13. PMID 12456892 DOI: 10.1073/Pnas.212628899 |
0.748 |
|
| 2002 |
Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 419: 952-6. PMID 12410317 DOI: 10.1038/Nature01145 |
0.873 |
|
| 2002 |
Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR. Genetic control by a metabolite binding mRNA. Chemistry & Biology. 9: 1043. PMID 12323379 DOI: 10.1016/S1074-5521(02)00224-7 |
0.79 |
|
| 2002 |
Emilsson GM, Breaker RR. Deoxyribozymes: new activities and new applications. Cellular and Molecular Life Sciences : Cmls. 59: 596-607. PMID 12022469 DOI: 10.1007/S00018-002-8452-4 |
0.313 |
|
| 2002 |
Breaker RR. Engineered allosteric ribozymes as biosensor components. Current Opinion in Biotechnology. 13: 31-9. PMID 11849955 DOI: 10.1016/S0958-1669(02)00281-1 |
0.424 |
|
| 2001 |
Carmi N, Breaker RR. Characterization of a DNA-cleaving deoxyribozyme. Bioorganic & Medicinal Chemistry. 9: 2589-600. PMID 11557347 DOI: 10.1016/S0968-0896(01)00035-9 |
0.334 |
|
| 2001 |
Soukup GA, DeRose EC, Koizumi M, Breaker RR. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. Rna (New York, N.Y.). 7: 524-36. PMID 11345431 DOI: 10.1017/S1355838201002175 |
0.535 |
|
| 2001 |
Seetharaman S, Zivarts M, Sudarsan N, Breaker RR. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nature Biotechnology. 19: 336-41. PMID 11283591 DOI: 10.1038/86723 |
0.514 |
|
| 2001 |
Jose AM, Soukup GA, Breaker RR. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Research. 29: 1631-7. PMID 11266567 DOI: 10.1093/Nar/29.7.1631 |
0.597 |
|
| 2000 |
Koizumi M, Breaker RR. Molecular recognition of cAMP by an RNA aptamer. Biochemistry. 39: 8983-92. PMID 10913311 DOI: 10.1021/Bi000149N |
0.565 |
|
| 2000 |
Soukup GA, Breaker RR. Allosteric nucleic acid catalysts. Current Opinion in Structural Biology. 10: 318-25. PMID 10851196 DOI: 10.1016/S0959-440X(00)00090-7 |
0.449 |
|
| 2000 |
Tang J, Breaker RR. Structural diversity of self-cleaving ribozymes. Proceedings of the National Academy of Sciences of the United States of America. 97: 5784-9. PMID 10823936 DOI: 10.1073/Pnas.97.11.5784 |
0.493 |
|
| 2000 |
Soukup GA, Emilsson GA, Breaker RR. Altering molecular recognition of RNA aptamers by allosteric selection. Journal of Molecular Biology. 298: 623-32. PMID 10788325 DOI: 10.1006/Jmbi.2000.3704 |
0.826 |
|
| 2000 |
Li Y, Liu Y, Breaker RR. Capping DNA with DNA. Biochemistry. 39: 3106-14. PMID 10715132 DOI: 10.1021/Bi992710R |
0.302 |
|
| 1999 |
Koizumi M, Kerr JN, Soukup GA, Breaker RR. Allosteric ribozymes sensitive to the second messengers cAMP and cGMP. Nucleic Acids Symposium Series. 275-6. PMID 10780486 |
0.301 |
|
| 1999 |
Soukup GA, Breaker RR. Relationship between internucleotide linkage geometry and the stability of RNA. Rna (New York, N.Y.). 5: 1308-25. PMID 10573122 DOI: 10.1017/S1355838299990891 |
0.566 |
|
| 1999 |
Soukup GA, Breaker RR. Nucleic acid molecular switches. Trends in Biotechnology. 17: 469-76. PMID 10557159 DOI: 10.1016/S0167-7799(99)01383-9 |
0.368 |
|
| 1999 |
Koizumi M, Soukup GA, Kerr JN, Breaker RR. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Structural Biology. 6: 1062-71. PMID 10542100 DOI: 10.1038/14947 |
0.587 |
|
| 1999 |
Soukup GA, Breaker RR. Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. Structure (London, England : 1993). 7: 783-91. PMID 10425680 DOI: 10.1016/S0969-2126(99)80102-6 |
0.518 |
|
| 1999 |
Li Y, Breaker RR. Deoxyribozymes: new players in the ancient game of biocatalysis. Current Opinion in Structural Biology. 9: 315-23. PMID 10361095 DOI: 10.1016/S0959-440X(99)80042-6 |
0.395 |
|
| 1999 |
Soukup GA, Breaker RR. Engineering precision RNA molecular switches. Proceedings of the National Academy of Sciences of the United States of America. 96: 3584-9. PMID 10097080 DOI: 10.1073/Pnas.96.7.3584 |
0.565 |
|
| 1999 |
Li Y, Breaker RR. Phosphorylating DNA with DNA. Proceedings of the National Academy of Sciences of the United States of America. 96: 2746-51. PMID 10077582 DOI: 10.1073/Pnas.96.6.2746 |
0.344 |
|
| 1999 |
Li Y, Breaker RR. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2γ-hydroxyl group Journal of the American Chemical Society. 121: 5364-5372. DOI: 10.1021/Ja990592P |
0.564 |
|
| 1998 |
Tang J, Breaker RR. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acids Research. 26: 4214-21. PMID 9722642 DOI: 10.1093/Nar/26.18.4214 |
0.435 |
|
| 1998 |
Roth A, Breaker RR. An amino acid as a cofactor for a catalytic polynucleotide. Proceedings of the National Academy of Sciences of the United States of America. 95: 6027-31. PMID 9600911 DOI: 10.1073/Pnas.95.11.6027 |
0.473 |
|
| 1998 |
Carmi N, Balkhi SR, Breaker RR. Cleaving DNA with DNA. Proceedings of the National Academy of Sciences of the United States of America. 95: 2233-7. PMID 9482868 DOI: 10.1073/Pnas.95.5.2233 |
0.302 |
|
| 1997 |
Breaker RR. DNA aptamers and DNA enzymes. Current Opinion in Chemical Biology. 1: 26-31. PMID 9667831 DOI: 10.1016/S1367-5931(97)80105-6 |
0.389 |
|
| 1997 |
Tang J, Breaker RR. Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. Rna (New York, N.Y.). 3: 914-25. PMID 9257650 |
0.48 |
|
| 1997 |
Tang J, Breaker RR. Rational design of allosteric ribozymes. Chemistry & Biology. 4: 453-9. PMID 9224568 DOI: 10.1016/S1074-5521(97)90197-6 |
0.558 |
|
| 1996 |
Carmi N, Shultz LA, Breaker RR. In vitro selection of self-cleaving DNAs Chemistry and Biology. 3: 1039-1046. PMID 9000012 DOI: 10.1016/S1074-5521(96)90170-2 |
0.301 |
|
| 1996 |
Breaker RR. Are engineered proteins getting competition from RNA? Current Opinion in Biotechnology. 7: 442-448. PMID 8768905 DOI: 10.1016/S0958-1669(96)80122-4 |
0.569 |
|
| 1995 |
Breaker RR, Joyce GF. A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity. Chemistry & Biology. 2: 655-60. PMID 9383471 DOI: 10.1016/1074-5521(95)90028-4 |
0.629 |
|
| 1995 |
Breaker RR, Joyce GF. Self-incorporation of coenzymes by ribozymes. Journal of Molecular Evolution. 40: 551-8. PMID 7643406 DOI: 10.1007/Bf00160500 |
0.694 |
|
| 1995 |
Schwartz ME, Breaker RR, Asteriadis GT, Gough GR. A universal adapter for chemical synthesis of DNA or RNA on any single type of solid support Tetrahedron Letters. 36: 27-30. DOI: 10.1016/0040-4039(94)02161-4 |
0.322 |
|
| 1994 |
Breaker RR, Joyce GF. A DNA enzyme that cleaves RNA. Chemistry & Biology. 1: 223-9. PMID 9383394 DOI: 10.1016/1074-5521(94)90014-0 |
0.643 |
|
| 1994 |
Chakrabarti AC, Breaker RR, Joyce GF, Deamer DW. Production of RNA by a polymerase protein encapsulated within phospholipid vesicles. Journal of Molecular Evolution. 39: 555-9. PMID 7528810 DOI: 10.1007/Bf00160400 |
0.676 |
|
| 1994 |
Breaker RR, Banerji A, Joyce GF. Continuous in vitro evolution of bacteriophage RNA polymerase promoters. Biochemistry. 33: 11980-6. PMID 7522554 DOI: 10.1021/Bi00205A037 |
0.716 |
|
| 1994 |
Breaker RR, Joyce GF. Inventing and improving ribozyme function: rational design versus iterative selection methods. Trends in Biotechnology. 12: 268-75. PMID 7519862 DOI: 10.1016/0167-7799(94)90138-4 |
0.564 |
|
| 1994 |
Breaker RR, Joyce GF. Emergence of a replicating species from an in vitro RNA evolution reaction. Proceedings of the National Academy of Sciences of the United States of America. 91: 6093-7. PMID 7517040 DOI: 10.1073/Pnas.91.13.6093 |
0.728 |
|
| 1993 |
Breaker RR, Gough GR, Gilham PT. Synthesis and properties of adenosine oligonucleotide analogues containing methylene groups in place of phosphodiester 5'-oxygens. Biochemistry. 32: 9125-8. PMID 8396423 |
0.56 |
|
| 1992 |
Schwartz ME, Breaker RR, Asteriadis GT, deBear JS, Gough GR. Rapid synthesis of oligoribonucleotides using 2′-O-(o-nitrobenzyloxymethyl)-protected monomers Bioorganic and Medicinal Chemistry Letters. 2: 1019-1024. DOI: 10.1016/S0960-894X(00)80610-1 |
0.314 |
|
| 1990 |
Breaker RR, Gough GR, Gilham PT. Polynucleotide phosphorylase forms polymers from an ADP analog in which the 5' oxygen is replaced by a methylene group. Nucleic Acids Research. 18: 3085-6. PMID 2349124 DOI: 10.1093/Nar/18.10.3085 |
0.565 |
|
| Show low-probability matches. |
