Ronald R. Breaker - Publications

Affiliations: 
Molecular, Cellular and Developmental Biology Yale University, New Haven, CT 
Area:
non-coding RNA
Website:
http://bbs.yale.edu/people/ronald_breaker-2.profile

192 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.4
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  0.4
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  0.4
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  0.32
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  0.84
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  0.84
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  0.4
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  0.64
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  1
2017 Nelson JW, Breaker RR. The lost language of the RNA World. Science Signaling. 10. PMID 28611182 DOI: 10.1126/scisignal.aam8812  0.4
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  0.76
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  0.32
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  0.64
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  0.4
2016 Sherlock ME, Breaker RR. Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria. Biochemistry. PMID 28001372 DOI: 10.1021/acs.biochem.6b01271  0.4
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  0.4
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  0.4
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  0.64
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  0.64
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  1
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  0.4
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  1
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  0.64
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  1
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  1
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  1
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  1
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: 606-610. DOI: 10.1038/nchembio.1846  1
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  1
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  1
2014 Nelson JW, Zhou Z, Breaker RR. Gramicidin D enhances the antibacterial activity of fluoride. Bioorganic & Medicinal Chemistry Letters. 24: 2969-71. PMID 24857543 DOI: 10.1016/j.bmcl.2014.03.061  1
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  1
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  1
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  1
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  1
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  1
2013 Gu H, Breaker RR. Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products. Biotechniques. 54: 337-43. PMID 23750543 DOI: 10.2144/000114009  1
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  1
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  1
2012 Breaker RR. Ancient, giant riboswitches at atomic resolution. Nature Structural & Molecular Biology. 19: 1208-9. PMID 23142981 DOI: 10.1038/nsmb.2453  1
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  1
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  1
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  1
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  1
2012 Li S, Breaker RR. Fluoride enhances the activity of fungicides that destabilize cell membranes. Bioorganic & Medicinal Chemistry Letters. 22: 3317-22. PMID 22460034 DOI: 10.1016/j.bmcl.2012.03.006  1
2012 Breaker RR. New insight on the response of bacteria to fluoride. Caries Research. 46: 78-81. PMID 22327376 DOI: 10.1159/000336397  1
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  1
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  1
2012 Breaker RR. Riboswitches and the RNA world. Cold Spring Harbor Perspectives in Biology. 4. PMID 21106649 DOI: 10.1101/cshperspect.a003566  1
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  1
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  1
2011 Breaker RR. Prospects for riboswitch discovery and analysis. Molecular Cell. 43: 867-79. PMID 21925376 DOI: 10.1016/j.molcel.2011.08.024  1
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  1
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  1
2011 Wallace JG, Breaker RR. Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125. Letters in Applied Microbiology. 52: 430-2. PMID 21362000 DOI: 10.1111/j.1472-765X.2011.03017.x  1
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  1
2011 Ames TD, Breaker RR. Bacterial aptamers that selectively bind glutamine. Rna Biology. 8: 82-9. PMID 21282981 DOI: 10.4161/rna.V.I.13864  1
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  1
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  1
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  1
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  1
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  1
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  1
2010 Breaker RR. RNA switches out in the cold. Molecular Cell. 37: 1-2. PMID 20129048 DOI: 10.1016/j.molcel.2009.12.032  1
2010 Ames TD, Breaker RR. Bacterial Riboswitch Discovery and Analysis The Chemical Biology of Nucleic Acids. 433-454. DOI: 10.1002/9780470664001.ch20  1
2010 Breaker RR. RNA second messengers and riboswitches: Relics from the RNA world? Microbe. 5: 13-20.  1
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  1
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  1
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  1
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  1
2009 Breaker RR. Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiology. 4: 771-3. PMID 19722830 DOI: 10.2217/fmb.09.46  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Breaker RR. Complex riboswitches. Science (New York, N.Y.). 319: 1795-7. PMID 18369140 DOI: 10.1126/science.1152621  1
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  1
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  1
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  1
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  1
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  1
2007 Stern E, Wagner R, Sigworth FJ, Breaker R, Fahmy TM, Reed MA. Importance of the Debye screening length on nanowire field effect transistor sensors. Nano Letters. 7: 3405-9. PMID 17914853 DOI: 10.1021/nl071792z  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2007 Barrick JE, Breaker RR. The power of riboswitches. Scientific American. 296: 50-7. PMID 17186833  1
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  1
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  1
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  1
2006 Blount KF, Breaker RR. Riboswitches as antibacterial drug targets. Nature Biotechnology. 24: 1558-64. PMID 17160062 DOI: 10.1038/nbt1268  1
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  1
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  1
2006 Lim J, Grove BC, Roth A, Breaker RR. Characteristics of ligand recognition by a glmS self-cleaving ribozyme. Angewandte Chemie (International Ed. in English). 45: 6689-93. PMID 16986193 DOI: 10.1002/anie.200602534  1
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  1
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  1
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  1
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  1
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  1
2006 Kim J, Breaker R. Riboswitches: Regulators of modern and ancient metabolism Biochemist. 28: 11-15.  1
2005 Breaker RR. Gene expression control: harnessing RNA switches. Gene Therapy. 12: 725-6. PMID 19202632 DOI: 10.1038/sj.gt.3302461  1
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  1
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  1
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  0.4
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature. 432: 838-45. PMID 15602549 DOI: 10.1038/nature03195  1
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  1
2004 Mandal M, Breaker RR. Gene regulation by riboswitches. Nature Reviews. Molecular Cell Biology. 5: 451-63. PMID 15173824 DOI: 10.1038/nrm1403  1
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  1
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  1
2004 Sreedhara A, Li Y, Breaker RR. Ligating DNA with DNA. Journal of the American Chemical Society. 126: 3454-60. PMID 15025472 DOI: 10.1021/ja039713i  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2001 Breaker RR. Selection for catalytic function with nucleic acids. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 9.4. PMID 18428882 DOI: 10.1002/0471142700.nc0904s00  1
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  1
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  1
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  1
2001 Jose AM, Soukup GA, Breaker RR. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Research. 29: 1631-7. PMID 11266567  1
2001 Li Y, Breaker RR. In vitro selection of kinase and ligase deoxyribozymes. Methods (San Diego, Calif.). 23: 179-90. PMID 11181037 DOI: 10.1006/meth.2000.1119  1
2000 Breaker RR. Tech.Sight. Molecular biology. Making catalytic DNAs. Science (New York, N.Y.). 290: 2095-6. PMID 11187837 DOI: 10.1126/science.290.5499.2095  1
2000 Koizumi M, Breaker RR. Molecular recognition of cAMP by an RNA aptamer. Biochemistry. 39: 8983-92. PMID 10913311 DOI: 10.1021/bi000149n  1
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  1
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  1
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  1
2000 Li Y, Liu Y, Breaker RR. Capping DNA with DNA. Biochemistry. 39: 3106-14. PMID 10715132 DOI: 10.1021/bi992710r  1
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  1
1999 Li Y, Liu Y, Breaker RR. In vitro selection of deoxyribozymes with DNA capping activity. Nucleic Acids Symposium Series. 237-8. PMID 10780467  1
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  1
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  1
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  1
1999 Kurz M, Breaker RR. In vitro selection of nucleic acid enzymes. Current Topics in Microbiology and Immunology. 243: 137-58. PMID 10453642  1
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  1
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  1
1999 Breaker RR. Catalytic DNA: in training and seeking employment. Nature Biotechnology. 17: 422-3. PMID 10331790 DOI: 10.1038/8588  1
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  1
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  1
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  1
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  1
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  1
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  1
1998 Iverson BL, Breaker RR. Be careful what you wish for Trends in Biotechnology. 16: 52-53. DOI: 10.1016/S0167-7799(98)01131-7  1
1997 Breaker RR. In Vitro Selection of Catalytic Polynucleotides. Chemical Reviews. 97: 371-390. PMID 11848875  1
1997 Breaker RR. DNA aptamers and DNA enzymes. Current Opinion in Chemical Biology. 1: 26-31. PMID 9667831  1
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  1
1997 Tang J, Breaker RR. Rational design of allosteric ribozymes. Chemistry & Biology. 4: 453-9. PMID 9224568  1
1997 Breaker RR. DNA enzymes Nature Biotechnology. 15: 427-431. PMID 9131619  1
1996 Carmi N, Shultz LA, Breaker RR. In vitro selection of self-cleaving DNAs Chemistry and Biology. 3: 1039-1046. PMID 9000012  1
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  1
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  1
1995 Breaker RR, Joyce GF. Self-incorporation of coenzymes by ribozymes. Journal of Molecular Evolution. 40: 551-8. PMID 7643406 DOI: 10.1007/BF00160500  1
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  1
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  1
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  1
1994 Breaker RR, Banerji A, Joyce GF. Continuous in vitro evolution of bacteriophage RNA polymerase promoters. Biochemistry. 33: 11980-6. PMID 7522554  1
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  1
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  1
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  1
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  1
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  1
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