Ronald Breaker

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Poiata Elena; Meyer Michelle M; Ames Tyler D; Breaker Ronald R
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.
Link K H; Breaker R R
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches.
Breaker Ronald R
Riboswitches: from ancient gene-control systems to modern drug targets.

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All Publications

2009: Poiata Elena; Meyer Michelle M; Ames Tyler D; Breaker Ronald R
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.
RNA (New York, N.Y.) 2009;15(11):2046-56.
2009: Link K H; Breaker R R
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches.
Gene therapy 2009;16(10):1189-201.
2009: Breaker Ronald R
Riboswitches: from ancient gene-control systems to modern drug targets.
Future microbiology 2009;4():771-3.
2009: Hammond Ming C; Wachter Andreas; Breaker Ronald R
A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.
Nature structural & molecular biology 2009;16(5):541-9.
2009: Tseng Huei-Hun; Weinberg Zasha; Gore Jeremy; Breaker Ronald R; Ruzzo Walter L
Finding non-coding RNAs through genome-scale clustering.
Journal of bioinformatics and computational biology 2009;7(2):373-88.
2009: Lee Elaine R; Blount Kenneth F; Breaker Ronald R
Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression.
RNA biology 2009;6(2):187-94.
2009: Tripp H James; Schwalbach Michael S; Meyer Michelle M; Kitner Joshua B; Breaker Ronald R; Giovannoni Stephen J
Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11.
Environmental microbiology 2009;11(1):230-8.
2009: Meyer Michelle M; Ames Tyler D; Smith Daniel P; Weinberg Zasha; Schwalbach Michael S; Giovannoni Stephen J; Breaker Ronald R
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
BMC genomics 2009;10():268.
2009: Link Kristian H; Breaker Ronald R
In vitro selection of glmS ribozymes.
Methods in molecular biology (Clifton, N.J.) 2009;540():349-64.
2009: Roth Adam; Breaker Ronald R
The structural and functional diversity of metabolite-binding riboswitches.
Annual review of biochemistry 2009;78():305-34.
2008: Boese B J; Corbino K; Breaker R R
In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification.
Nucleosides, nucleotides & nucleic acids 2008;27(8):949-66.
2008: Sudarsan N; Lee E R; Weinberg Z; Moy R H; Kim J N; Link K H; Breaker R R
Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
Science (New York, N.Y.) 2008;321(5887):411-3.
2008: Weinberg Zasha; Regulski Elizabeth E; Hammond Ming C; Barrick Jeffrey E; Yao Zizhen; Ruzzo Walter L; Breaker Ronald R
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
RNA (New York, N.Y.) 2008;14(5):822-8.
2008: Regulski Elizabeth E; Moy Ryan H; Weinberg Zasha; Barrick Jeffrey E; Yao Zizhen; Ruzzo Walter L; Breaker Ronald R
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
Molecular microbiology 2008;68(4):918-32.
2008: Wang Joy Xin; Breaker Ronald R
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.
Biochemistry and cell biology = Biochimie et biologie cellulaire 2008;86(2):157-68.
2008: Meyer Michelle M; Roth Adam; Chervin Stephanie M; Garcia George A; Breaker Ronald R
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria.
RNA (New York, N.Y.) 2008;14(4):685-95.
2008: Wang Joy Xin; Lee Elaine R; Morales Dianali Rivera; Lim Jinsoo; Breaker Ronald R
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling.
Molecular cell 2008;29(6):691-702.
2008: Breaker Ronald R
Complex riboswitches.
Science (New York, N.Y.) 2008;319(5871):1795-7.
2008: Kim Jane N; Breaker Ronald R
Purine sensing by riboswitches.
Biology of the cell / under the auspices of the European Cell Biology Organization 2008;100(1):1-11.
2008: Regulski Elizabeth E; Breaker Ronald R
In-line probing analysis of riboswitches.
Methods in molecular biology (Clifton, N.J.) 2008;419():53-67.
2007: Wachter Andreas; Tunc-Ozdemir Meral; Grove Beth C; Green Pamela J; Shintani David K; Breaker Ronald R
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs.
The Plant cell 2007;19(11):3437-50.
2007: Stern Eric; Wagner Robin; Sigworth Fred J; Breaker Ronald; Fahmy Tarek M; Reed Mark A
Importance of the Debye screening length on nanowire field effect transistor sensors.
Nano letters 2007;7(11):3405-9.
2007: Kim Jane N; Roth Adam; Breaker Ronald R
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(41):16092-7.
2007: Link Kristian H; Guo Lixia; Ames Tyler D; Yen Laising; Mulligan Richard C; Breaker Ronald R
Engineering high-speed allosteric hammerhead ribozymes.
Biological chemistry 2007;388(8):779-86.
2007: Yao Zizhen; Barrick Jeffrey; Weinberg Zasha; Neph Shane; Breaker Ronald; Tompa Martin; Ruzzo Walter L
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.
PLoS computational biology 2007;3(7):e126.
2007: Cheah Ming T; Wachter Andreas; Sudarsan Narasimhan; Breaker Ronald R
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches.
Nature 2007;447(7143):497-500.
2007: Roth Adam; Winkler Wade C; Regulski Elizabeth E; Lee Bobby W K; Lim Jinsoo; Jona Inbal; Barrick Jeffrey E; Ritwik Ankita; Kim Jane N; Welz Rüdiger; Iwata-Reuyl Dirk; Breaker Ronald R
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain.
Nature structural & molecular biology 2007;14(4):308-17.
2007: Welz Rüdiger; Breaker Ronald R
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis.
RNA (New York, N.Y.) 2007;13(4):573-82.
2007: Barrick Jeffrey E; Breaker Ronald R
The power of riboswitches.
Scientific American 2007;296(1):50-7.
2007: Blount Kenneth F; Wang Joy Xin; Lim Jinsoo; Sudarsan Narasimhan; Breaker Ronald R
Antibacterial lysine analogs that target lysine riboswitches.
Nature chemical biology 2007;3(1):44-9.
2007: Barrick Jeffrey E; Breaker Ronald R
The distributions, mechanisms, and structures of metabolite-binding riboswitches.
Genome biology 2007;8(11):R239.
2007: Boese Benjamin J; Breaker Ronald R
In vitro selection and characterization of cellulose-binding DNA aptamers.
Nucleic acids research 2007;35(19):6378-88.
2007: Weinberg Zasha; Barrick Jeffrey E; Yao Zizhen; Roth Adam; Kim Jane N; Gore Jeremy; Wang Joy Xin; Lee Elaine R; Block Kirsten F; Sudarsan Narasimhan; Neph Shane; Tompa Martin; Ruzzo Walter L; Breaker Ronald R
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
Nucleic acids research 2007;35(14):4809-19.
2006: Puerta-Fernandez Elena; Barrick Jeffrey E; Roth Adam; Breaker Ronald R
Identification of a large noncoding RNA in extremophilic eubacteria.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(51):19490-5.
2006: Blount Kenneth F; Breaker Ronald R
Riboswitches as antibacterial drug targets.
Nature biotechnology 2006;24(12):1558-64.
2006: Sudarsan Narasimhan; Hammond Ming C; Block Kirsten F; Welz Rüdiger; Barrick Jeffrey E; Roth Adam; Breaker Ronald R
Tandem riboswitch architectures exhibit complex gene control functions.
Science (New York, N.Y.) 2006;314(5797):300-4.
2006: Lim Jinsoo; Grove Beth C; Roth Adam; Breaker Ronald R
Characteristics of ligand recognition by a glmS self-cleaving ribozyme.
Angewandte Chemie (International ed. in English) 2006;45(40):6689-93.
2006: Serganov Alexander; Polonskaia Anna; Phan Anh Tuân; Breaker Ronald R; Patel Dinshaw J
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
Nature 2006;441(7097):1167-71.
2006: Blount Kenneth; Puskarz Izabela; Penchovsky Robert; Breaker Ronald
Development and application of a high-throughput assay for glmS riboswitch activators.
RNA biology 2006;3(2):77-81.
2006: Roth Adam; Nahvi Ali; Lee Mark; Jona Inbal; Breaker Ronald R
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
RNA (New York, N.Y.) 2006;12(4):607-19.
2006: Lim Jinsoo; Winkler Wade C; Nakamura Shingo; Scott Valerie; Breaker Ronald R
Molecular-recognition characteristics of SAM-binding riboswitches.
Angewandte Chemie (International ed. in English) 2006;45(6):964-8.
2006: Link Kristian H; Guo Lixia; Breaker Ronald R
Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection.
Nucleic acids research 2006;34(17):4968-75.
2005: Sudarsan Narasimhan; Cohen-Chalamish Smadar; Nakamura Shingo; Emilsson Gail Mitchell; Breaker Ronald R
Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine.
Chemistry & biology 2005;12(12):1325-35.
2005: Penchovsky Robert; Breaker Ronald R
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.
Nature biotechnology 2005;23(11):1424-33.
2005: Wickiser J Kenneth; Cheah Ming T; Breaker Ronald R; Crothers Donald M
The kinetics of ligand binding by an adenine-sensing riboswitch.
Biochemistry 2005;44(40):13404-14.
2005: Tucker Brian J; Breaker Ronald R
Riboswitches as versatile gene control elements.
Current opinion in structural biology 2005;15(3):342-8.
2005: Barrick Jeffrey E; Sudarsan Narasimhan; Weinberg Zasha; Ruzzo Walter L; Breaker Ronald R
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
RNA (New York, N.Y.) 2005;11(5):774-84.
2005: Wickiser J Kenneth; Winkler Wade C; Breaker Ronald R; Crothers Donald M
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.
Molecular cell 2005;18(1):49-60.
2005: Winkler Wade C; Breaker Ronald R
Regulation of bacterial gene expression by riboswitches.
Annual review of microbiology 2005;59():487-517.
2005: Corbino Keith A; Barrick Jeffrey E; Lim Jinsoo; Welz Rüdiger; Tucker Brian J; Puskarz Izabela; Mandal Maumita; Rudnick Noam D; Breaker Ronald R
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
Genome biology 2005;6(8):R70.
2005: Zivarts Maris; Liu Yong; Breaker Ronald R
Engineered allosteric ribozymes that respond to specific divalent metal ions.
Nucleic acids research 2005;33(2):622-31.
2004: Serganov Alexander; Yuan Yu-Ren; Pikovskaya Olga; Polonskaia Anna; Malinina Lucy; Phan Anh Tuân; Hobartner Claudia; Micura Ronald; Breaker Ronald R; Patel Dinshaw J
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs.
Chemistry & biology 2004;11(12):1729-41.
2004: Breaker Ronald R
Natural and engineered nucleic acids as tools to explore biology.
Nature 2004;432(7019):838-45.
2004: Mandal Maumita; Lee Mark; Barrick Jeffrey E; Weinberg Zasha; Emilsson Gail Mitchell; Ruzzo Walter L; Breaker Ronald R
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Science (New York, N.Y.) 2004;306(5694):275-9.
2004: Mandal Maumita; Breaker Ronald R
Gene regulation by riboswitches.
Nature reviews. Molecular cell biology 2004;5(6):451-63.
2004: Barrick Jeffrey E; Corbino Keith A; Winkler Wade C; Nahvi Ali; Mandal Maumita; Collins Jennifer; Lee Mark; Roth Adam; Sudarsan Narasimhan; Jona Inbal; Wickiser J Kenneth; Breaker Ronald R
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 2004;101(17):6421-6.
2004: Winkler Wade C; Nahvi Ali; Roth Adam; Collins Jennifer A; Breaker Ronald R
Control of gene expression by a natural metabolite-responsive ribozyme.
Nature 2004;428(6980):281-6.
2004: Sreedhara Alavattam; Li Yingfu; Breaker Ronald R
Ligating DNA with DNA.
Journal of the American Chemical Society 2004;126(11):3454-60.
2004: Mandal Maumita; Breaker Ronald R
Adenine riboswitches and gene activation by disruption of a transcription terminator.
Nature structural & molecular biology 2004;11(1):29-35.
2004: Roth Adam; Breaker Ronald R
Selection in vitro of allosteric ribozymes.
Methods in molecular biology (Clifton, N.J.) 2004;252():145-64.
2004: Nahvi Ali; Barrick Jeffrey E; Breaker Ronald R
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.
Nucleic acids research 2004;32(1):143-50.
2003: Sudarsan Narasimhan; Wickiser J Kenneth; Nakamura Shingo; Ebert Margaret S; Breaker Ronald R
An mRNA structure in bacteria that controls gene expression by binding lysine.
Genes & development 2003;17(21):2688-97.
2003: Winkler Wade C; Breaker Ronald R
Genetic control by metabolite-binding riboswitches.
Chembiochem : a European journal of chemical biology 2003;4(10):1024-32.
2003: Winkler Wade C; Nahvi Ali; Sudarsan Narasimhan; Barrick Jeffrey E; Breaker Ronald R
An mRNA structure that controls gene expression by binding S-adenosylmethionine.
Nature structural biology 2003;10(9):701-7.
2003: Breaker Ronald R; Emilsson Gail Mitchell; Lazarev Denis; Nakamura Shingo; Puskarz Izabela J; Roth Adam; Sudarsan Narasimhan
A common speed limit for RNA-cleaving ribozymes and deoxyribozymes.
RNA (New York, N.Y.) 2003;9(8):949-57.
2003: Emilsson Gail Mitchell; Nakamura Shingo; Roth Adam; Breaker Ronald R
Ribozyme speed limits.
RNA (New York, N.Y.) 2003;9(8):907-18.
2003: Lazarev Denis; Puskarz Izabela; Breaker Ronald R
Substrate specificity and reaction kinetics of an X-motif ribozyme.
RNA (New York, N.Y.) 2003;9(6):688-97.
2003: Sudarsan Narasimhan; Barrick Jeffrey E; Breaker Ronald R
Metabolite-binding RNA domains are present in the genes of eukaryotes.
RNA (New York, N.Y.) 2003;9(6):644-7.
2003: Mandal Maumita; Boese Benjamin; Barrick Jeffrey E; Winkler Wade C; Breaker Ronald R
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.
Cell 2003;113(5):577-86.
2002: Winkler Wade C; Cohen-Chalamish Smadar; Breaker Ronald R
An mRNA structure that controls gene expression by binding FMN.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):15908-13.
2002: Winkler Wade; Nahvi Ali; Breaker Ronald R
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
Nature 2002;419(6910):952-6.
2002: Nahvi Ali; Sudarsan Narasimhan; Ebert Margaret S; Zou Xiang; Brown Kenneth L; Breaker Ronald R
Genetic control by a metabolite binding mRNA.
Chemistry & biology 2002;9(9):1043.
2002: Emilsson G M; Breaker R R
Deoxyribozymes: new activities and new applications.
Cellular and molecular life sciences : CMLS 2002;59(4):596-607.
2002: Breaker Ronald R
Engineered allosteric ribozymes as biosensor components.
Current opinion in biotechnology 2002;13(1):31-9.
2001: Carmi N; Breaker R R
Characterization of a DNA-cleaving deoxyribozyme.
Bioorganic & medicinal chemistry 2001;9(10):2589-600.
2001: Breaker R R
Selection for catalytic function with nucleic acids.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2001;Chapter 9():Unit 9.4.
2001: Soukup G A; DeRose E C; Koizumi M; Breaker R R
Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes.
RNA (New York, N.Y.) 2001;7(4):524-36.
2001: Seetharaman S; Zivarts M; Sudarsan N; Breaker R R
Immobilized RNA switches for the analysis of complex chemical and biological mixtures.
Nature biotechnology 2001;19(4):336-41.
2001: Jose A M; Soukup G A; Breaker R R
Cooperative binding of effectors by an allosteric ribozyme.
Nucleic acids research 2001;29(7):1631-7.
2001: Li Y; Breaker R R
In vitro selection of kinase and ligase deoxyribozymes.
Methods (San Diego, Calif.) 2001;23(2):179-90.
2000: Breaker R R
Tech.Sight. Molecular biology. Making catalytic DNAs.
Science (New York, N.Y.) 2000;290(5499):2095-6.
2000: Koizumi M; Breaker R R
Molecular recognition of cAMP by an RNA aptamer.
Biochemistry 2000;39(30):8983-92.
2000: Soukup G A; Breaker R R
Allosteric nucleic acid catalysts.
Current opinion in structural biology 2000;10(3):318-25.
2000: Tang J; Breaker R R
Structural diversity of self-cleaving ribozymes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(11):5784-9.
2000: Soukup G A; Emilsson G A; Breaker R R
Altering molecular recognition of RNA aptamers by allosteric selection.
Journal of molecular biology 2000;298(4):623-32.
2000: Li Y; Liu Y; Breaker R R
Capping DNA with DNA.
Biochemistry 2000;39(11):3106-14.
1999: Soukup G A; Breaker R R
Nucleic acid molecular switches.
Trends in biotechnology 1999;17(12):469-76.
1999: Koizumi M; Soukup G A; Kerr J N; Breaker R R
Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP.
Nature structural biology 1999;6(11):1062-71.
1999: Soukup G A; Breaker R R
Relationship between internucleotide linkage geometry and the stability of RNA.
RNA (New York, N.Y.) 1999;5(10):1308-25.
1999: Soukup G A; Breaker R R
Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization.
Structure (London, England : 1993) 1999;7(7):783-91.
1999: Li Y; Breaker R R
Deoxyribozymes: new players in the ancient game of biocatalysis.
Current opinion in structural biology 1999;9(3):315-23.
1999: Soukup G A; Breaker R R
Engineering precision RNA molecular switches.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(7):3584-9.
1999: Li Y; Breaker R R
Phosphorylating DNA with DNA.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(6):2746-51.
1999: Koizumi M; Kerr J N; Soukup G A; Breaker R R
Allosteric ribozymes sensitive to the second messengers cAMP and cGMP.
Nucleic acids symposium series 1999;(42):275-6.
1999: Li Y; Liu Y; Breaker R R
In vitro selection of deoxyribozymes with DNA capping activity.
Nucleic acids symposium series 1999;(42):237-8.
1999: Kurz M; Breaker R R
In vitro selection of nucleic acid enzymes.
Current topics in microbiology and immunology 1999;243():137-58.
1998: Tang J; Breaker R R
Mechanism for allosteric inhibition of an ATP-sensitive ribozyme.
Nucleic acids research 1998;26(18):4214-21.
1998: Roth A; Breaker R R
An amino acid as a cofactor for a catalytic polynucleotide.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):6027-31.
1998: Carmi N; Balkhi S R; Breaker R R
Cleaving DNA with DNA.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(5):2233-7.
1997: Tang J; Breaker R R
Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.
RNA (New York, N.Y.) 1997;3(8):914-25.
1997: Breaker R R
DNA aptamers and DNA enzymes.
Current opinion in chemical biology 1997;1(1):26-31.
1997: Tang J; Breaker R R
Rational design of allosteric ribozymes.
Chemistry & biology 1997;4(6):453-9.
1997: Breaker R R
DNA enzymes.
Nature biotechnology 1997;15(5):427-31.
1996: Carmi N; Shultz L A; Breaker R R
In vitro selection of self-cleaving DNAs.
Chemistry & biology 1996;3(12):1039-46.
1996: Breaker R R
Are engineered proteins getting competition from RNA?
Current opinion in biotechnology 1996;7(4):442-8.

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Ronald Breaker

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