Ronald Breaker
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American biochemist
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Biology
Ronald Breaker's Degrees
- PhD Biochemistry University of California, Berkeley
- Bachelors Biochemistry University of California, Berkeley
Why Is Ronald Breaker Influential?
(Suggest an Edit or Addition)According to Wikipedia, Ronald R. Breaker is an American biochemist who is a Sterling Professor of Molecular, Cellular, and Developmental Biology at Yale University. He is best known for the discovery of riboswitches. His current research is focused on understanding advanced functions of nucleic acids, including the discovery and analysis of riboswitches and ribozymes.
Ronald Breaker's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression (2002) (1123)
- A DNA enzyme that cleaves RNA. (1994) (1111)
- Control of gene expression by a natural metabolite-responsive ribozyme (2004) (847)
- Gene regulation by riboswitches (2004) (809)
- Regulation of bacterial gene expression by riboswitches. (2005) (719)
- Genetic control by a metabolite binding mRNA. (2002) (699)
- Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria (2003) (685)
- Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP (2008) (683)
- Importance of the Debye screening length on nanowire field effect transistor sensors. (2007) (624)
- An mRNA structure that controls gene expression by binding FMN (2002) (623)
- Riboswitches and the RNA world. (2012) (569)
- Riboswitches as versatile gene control elements. (2005) (534)
- Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. (2004) (523)
- The structural and functional diversity of metabolite-binding riboswitches. (2009) (504)
- Adenine riboswitches and gene activation by disruption of a transcription terminator (2004) (495)
- Relationship between internucleotide linkage geometry and the stability of RNA. (1999) (487)
- The distributions, mechanisms, and structures of metabolite-binding riboswitches (2007) (457)
- New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. (2004) (456)
- Prospects for riboswitch discovery and analysis. (2011) (455)
- Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group (1999) (453)
- A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression (2004) (447)
- The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. (2005) (445)
- An mRNA structure that controls gene expression by binding S-adenosylmethionine (2003) (428)
- Riboswitches as antibacterial drug targets (2006) (422)
- Metabolite-binding RNA domains are present in the genes of eukaryotes. (2003) (416)
- Control of alternative RNA splicing and gene expression by eukaryotic riboswitches (2007) (397)
- Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch (2006) (392)
- Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes (2010) (363)
- Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride (2012) (356)
- A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity. (1995) (355)
- An mRNA structure in bacteria that controls gene expression by binding lysine. (2003) (344)
- An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger (2010) (333)
- Rational design of allosteric ribozymes. (1997) (318)
- In-line probing analysis of riboswitches. (2008) (318)
- Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. (2004) (316)
- Natural and engineered nucleic acids as tools to explore biology (2004) (314)
- Engineering precision RNA molecular switches. (1999) (306)
- Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline (2007) (306)
- Riboswitch diversity and distribution. (2017) (297)
- Riboswitch Control of Gene Expression in Plants by Splicing and Alternative 3′ End Processing of mRNAs[W][OA] (2007) (294)
- The kinetics of ligand binding by an adenine-sensing riboswitch. (2005) (277)
- Genetic Control by Metabolite‐Binding Riboswitches (2003) (275)
- Structural basis of ligand binding by a c-di-GMP riboswitch (2009) (271)
- Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions (2006) (254)
- Riboswitches in eubacteria sense the second messenger c-di-AMP (2013) (243)
- Engineered allosteric ribozymes as biosensor components. (2002) (239)
- 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. (2005) (234)
- Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria (2005) (232)
- Cleaving DNA with DNA. (1998) (223)
- A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain (2007) (223)
- Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. (2005) (221)
- Antibacterial lysine analogs that target lysine riboswitches. (2007) (207)
- R2R - software to speed the depiction of aesthetic consensus RNA secondary structures (2011) (204)
- In Vitro Selection of Catalytic Polynucleotides. (1997) (202)
- A widespread self-cleaving ribozyme class is revealed by bioinformatics (2013) (196)
- In vitro selection of self-cleaving DNAs. (1996) (194)
- Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression (2009) (192)
- An amino acid as a cofactor for a catalytic polynucleotide. (1998) (189)
- Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes (2005) (188)
- Immobilized RNA switches for the analysis of complex chemical and biological mixtures (2001) (185)
- Ribozyme speed limits. (2003) (183)
- Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP (1999) (176)
- DNA aptamers and DNA enzymes. (1997) (163)
- A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism (2008) (157)
- New classes of self-cleaving ribozymes revealed by comparative genomics analysis (2015) (155)
- Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. (2008) (154)
- Phosphorylating DNA with DNA. (1999) (153)
- Production of RNA by a polymerase protein encapsulated within phospholipid vesicles (1994) (146)
- Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine (2007) (138)
- DNA enzymes (1997) (133)
- Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations (2011) (131)
- Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. (2015) (125)
- Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. (2007) (123)
- Deoxyribozymes: new activities and new applications (2002) (123)
- Nucleic acid molecular switches. (1999) (120)
- Deoxyribozymes: new players in the ancient game of biocatalysis. (1999) (119)
- Riboswitches and Translation Control. (2018) (119)
- The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. (2008) (116)
- Design and antimicrobial action of purine analogues that bind Guanine riboswitches. (2009) (115)
- A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. (2009) (113)
- Altering molecular recognition of RNA aptamers by allosteric selection. (2000) (113)
- Capping DNA with DNA. (2000) (112)
- Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. (2008) (112)
- Small, highly active DNAs that hydrolyze DNA. (2013) (111)
- Allosteric nucleic acid catalysts. (2000) (111)
- New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. (2011) (109)
- Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. (2017) (109)
- Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. (2006) (108)
- Structural diversity of self-cleaving ribozymes. (2000) (104)
- A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. (2003) (103)
- Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. (2008) (101)
- Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins (2013) (100)
- Making Catalytic DNAs (2000) (98)
- Purine sensing by riboswitches (2008) (98)
- Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions (2017) (97)
- Inventing and improving ribozyme function: rational design versus iterative selection methods. (1994) (97)
- Characterization of a DNA-cleaving deoxyribozyme. (2001) (95)
- Bacterial aptamers that selectively bind glutamine (2011) (95)
- Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. (2009) (95)
- An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. (2015) (93)
- A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes (2007) (92)
- A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. (2010) (91)
- Cooperative binding of effectors by an allosteric ribozyme. (2001) (91)
- Emergence of a replicating species from an in vitro RNA evolution reaction. (1994) (90)
- Ligating DNA with DNA. (2004) (88)
- Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing (2013) (87)
- Control of bacterial exoelectrogenesis by c-AMP-GMP (2015) (85)
- Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. (1999) (82)
- The expanding view of RNA and DNA function. (2014) (82)
- The lost language of the RNA World (2017) (80)
- Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. (2017) (76)
- Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. (2001) (76)
- Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. (1998) (76)
- Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches (2009) (76)
- Molecular recognition of cAMP by an RNA aptamer. (2000) (68)
- Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. (2014) (67)
- Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity (2017) (67)
- A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis (2012) (66)
- Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems (2018) (66)
- Development and Application of a High-Throughput Assay for glmS Riboswitch Activators (2006) (65)
- Challenges of ligand identification for riboswitch candidates (2011) (64)
- Evidence for Widespread Gene Control Function by the ydaO Riboswitch Candidate (2010) (63)
- Mechanism for gene control by a natural allosteric group I ribozyme. (2011) (62)
- Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique' (2009) (62)
- Complex Riboswitches (2008) (60)
- Extraordinary Structured Noncoding RNAs Revealed by Bacterial Metagenome Analysis (2009) (59)
- Riboswitches: from ancient gene-control systems to modern drug targets. (2009) (58)
- Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria. (2017) (57)
- Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. (1997) (57)
- Novel Riboswitch-Binding Flavin Analog That Protects Mice against Clostridium difficile Infection without Inhibiting Cecal Flora (2015) (56)
- Characteristics of ligand recognition by a glmS self-cleaving ribozyme. (2006) (54)
- Engineered allosteric ribozymes that respond to specific divalent metal ions (2005) (54)
- An expanded collection and refined consensus model of glmS ribozymes. (2011) (53)
- Engineering high-speed allosteric hammerhead ribozymes (2007) (52)
- Biochemical analysis of pistol self-cleaving ribozymes (2015) (51)
- Molecular-recognition characteristics of SAM-binding riboswitches. (2006) (50)
- Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria (2018) (49)
- In vitro selection and characterization of cellulose-binding DNA aptamers (2007) (49)
- The power of riboswitches. (2007) (48)
- Catalytic DNA: in training and seeking employment (1999) (47)
- A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria (2018) (47)
- A Plant 5S Ribosomal RNA Mimic Regulates Alternative Splicing of Transcription Factor IIIA Pre-mRNAs (2009) (46)
- Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate. (2012) (45)
- New Insight on the Response of Bacteria to Fluoride (2012) (45)
- Continuous in vitro evolution of bacteriophage RNA polymerase promoters. (1994) (40)
- Rapid synthesis of oligoribonucleotides using 2′-O-(o-nitrobenzyloxymethyl)-protected monomers (1992) (40)
- Identification of ligand analogues that control c-di-GMP riboswitches. (2012) (40)
- Large Noncoding RNAs in Bacteria. (2018) (38)
- Biochemical analysis of hatchet self-cleaving ribozymes (2015) (38)
- Identification of a large noncoding RNA in extremophilic eubacteria (2006) (36)
- SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches (2018) (35)
- Genome-wide discovery of structured noncoding RNAs in bacteria (2019) (33)
- Finding Non-coding RNAs Through Genome-Scale Clustering (2007) (33)
- The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds (2016) (32)
- Fluoride enhances the activity of fungicides that destabilize cell membranes. (2012) (29)
- Challenges of ligand identification for the second wave of orphan riboswitch candidates (2018) (29)
- Self-Incorporation of coenzymes by ribozymes (2004) (28)
- Association of OLE RNA with bacterial membranes via an RNA–protein interaction (2011) (27)
- A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer (2019) (27)
- RNA switches out in the cold. (2010) (26)
- The Biology of Free Guanidine As Revealed by Riboswitches. (2017) (26)
- Bacterial Riboswitch Discovery and Analysis (2010) (25)
- Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products. (2013) (25)
- Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes (2020) (25)
- Are engineered proteins getting competition from RNA? (1996) (24)
- A universal adapter for chemical synthesis of DNA or RNA on any single type of solid support (1995) (24)
- Mechanistic Debris Generated by Twister Ribozymes. (2017) (23)
- Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria (2020) (23)
- Selection in vitro of allosteric ribozymes. (2004) (22)
- Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates. (2018) (22)
- Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD+ (2019) (22)
- Allosteric ribozymes sensitive to the second messengers cAMP and cGMP. (1999) (21)
- Small molecule fluoride toxicity agonists. (2015) (20)
- In Vitro Selection and Characterization of Cellulose-Binding RNA Aptamers Using isothermal Amplification (2008) (20)
- Integron attI1 Sites, Not Riboswitches, Associate with Antibiotic Resistance Genes (2013) (20)
- Synthesis and properties of adenosine oligonucleotide analogues containing methylene groups in place of phosphodiester 5'-oxygens. (1993) (20)
- 4 Riboswitches and the RNA World (2006) (20)
- Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection (2006) (19)
- Mechanism and distribution of glmS ribozymes. (2012) (18)
- In vitro selection of kinase and ligase deoxyribozymes. (2001) (18)
- Singlet glycine riboswitches bind ligand as well as tandem riboswitches (2016) (17)
- Imaginary Ribozymes. (2020) (17)
- The Biochemical Landscape of Riboswitch Ligands (2022) (17)
- Substrate specificity and reaction kinetics of an X-motif ribozyme. (2003) (17)
- Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics (2017) (17)
- OLE RNA protects extremophilic bacteria from alcohol toxicity (2012) (16)
- Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity (2018) (15)
- In vitro selection of nucleic acid enzymes. (1999) (15)
- A second riboswitch class for the enzyme cofactor NAD+ (2020) (14)
- A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation (2020) (13)
- Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria (2019) (13)
- Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers (2017) (12)
- Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-throughput Screen. (2019) (11)
- RNA Second Messengers and Riboswitches: Relics from the RNA World?: Some riboswitches and their ligands may be relics of signaling networks used when organisms relied on RNA instead of DNA and proteins (2010) (9)
- Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C‐125 (2011) (9)
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes (2021) (8)
- The case of the missing allosteric ribozymes (2021) (7)
- In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP. (2014) (7)
- Gramicidin D enhances the antibacterial activity of fluoride. (2014) (7)
- A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex (2018) (7)
- Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database. (2017) (7)
- Polynucleotide phosphorylase forms polymers from an ADP analog in which the 5' oxygen is replaced by a methylene group. (1990) (6)
- Witnessing the structural evolution of an RNA enzyme (2021) (5)
- Riboswitches That Sense Cyclic Di-GMP (2010) (5)
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2′-deoxyguanosine (2022) (5)
- Gene expression control: Harnessing RNA switches (2005) (5)
- Ancient, giant riboswitches at atomic resolution (2012) (4)
- Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes (2022) (4)
- Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans (2019) (4)
- Na+ riboswitches regulate genes for diverse physiological processes in bacteria (2022) (4)
- Minimonsters: Evolutionary Byproducts of In Vitro RNA Amplification (1994) (3)
- In vitro selection of deoxyribozymes with DNA capping activity. (1999) (3)
- A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine (2020) (3)
- Architectures and complex functions of tandem riboswitches (2022) (3)
- DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria (2021) (3)
- Bacillus halodurans OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE (2020) (2)
- In vitro selection of glmS ribozymes. (2009) (2)
- Tech.Sight. Molecular biology. Making catalytic DNAs. (2000) (2)
- Genome-wide discovery of structured noncoding RNAs in bacteria (2019) (1)
- RNA Science and its Applications—a look toward the future (2012) (1)
- Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal form II) (1)
- Author response: A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer (2019) (1)
- Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (native, crystal form I) (1)
- Crystal structure of Bacillus halodurans OapB (native) at 1.2 A (2021) (1)
- Selection for Catalytic Function with Nucleic Acids (2000) (1)
- Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex (2021) (1)
- Exploiting natural riboswitches for aptamer engineering and validation (2023) (1)
- PROSPECTS FOR RIBOZYME DISCOVERY AND ANALYSIS (2018) (0)
- Chemical Exposure Study Leads : (2021) (0)
- Riboswitches as Genetic Control Elements (2006) (0)
- Acides nucleiques en tant que catalyseurs (1998) (0)
- Genetic Control by Metabolite-Binding Riboswitches (2003) (0)
- The large, noncoding OLE RNA is associated with membrane biochemistry (2010) (0)
- Reviewer List for 2002 (2002) (0)
- Connecticut Academy of Science and Engineering Elects 50 New Members in 2014 (2014) (0)
- NASA / CR .-207595 L X . : ,6-. '-A DNA enzyme with MgZ +-dependent RNA phosphoesterase activity (0)
- Self-Incorporation of Coenzymes by Ribozymes jou..A, ofMOLECULAR IEVOLUTION (1995) (0)
- Riboswitches: Natural Metabolite‐binding RNAs Controlling Gene Expression (2006) (0)
- Additional file 8: of Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics (2017) (0)
- Author response: Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria (2018) (0)
- Faculty Opinions recommendation of An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. (2002) (0)
- Deoxyribozymes and Medical Innovation (2004) (0)
- The chemical and enzymatic synthesis of RNA oligomers for the analysis of ribozyme structure and action (1992) (0)
- Aptamers in Bioanalysis.Edited byMarco Mascini. Hoboken (New Jersey): Wiley. $125.00. xvii + 313 p. + 12 pl.; ill.; index. 978‐0‐470‐14830‐3. 2009. (2009) (0)
- The expression of PBAN-like peptides in two ontogenetic stages of the commercial white shrimp Litopenaeus setiferus from the gulf of Mexico (2005) (0)
- Riboswitches: Regulators of modern and ancient metabolism (2006) (0)
- Chapter 8:The Structure and Action of glmS Ribozymes (2007) (0)
- Nucleozymes a activite d'endonuclease (2001) (0)
- Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics (2017) (0)
- Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal form I) (2021) (0)
- Crystal structure of Bacillus halodurans OapB (iodine-derivative) at 1.0 A (2021) (0)
- Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. (2023) (0)
- Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function (2022) (0)
- RNA World theory (2018) (0)
- In vitro Selection of Catalytic Polynucleotides (1997) (0)
- Active enzyme dna molecules (1995) (0)
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