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List of works by Ronald Breaker

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

scientific article

A DNA enzyme that cleaves RNA

scientific article

A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity

scientific article

A Second Riboswitch Class for the Enzyme Cofactor NAD

scientific article published on 21 October 2020

A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer

scientific article published on 05 April 2019

A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation

scientific article published on 28 April 2020

A common speed limit for RNA-cleaving ribozymes and deoxyribozymes

scientific article published on August 2003

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

scientific article

A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate

scientific article

A glycine-dependent riboswitch that uses cooperative binding to control gene expression

scientific article

A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis ⬇️

scientific article

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs

scientific article published on 19 April 2009

A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine

scientific article published on 25 August 2020

A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria

scientific article

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

scientific article

A widespread self-cleaving ribozyme class is revealed by bioinformatics.

scientific article

Adenine riboswitches and gene activation by disruption of a transcription terminator

scientific article (publication date: 2004)

Allosteric nucleic acid catalysts

scientific article published on 01 June 2000

Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP.

scientific article published in November 1999

Altering molecular recognition of RNA aptamers by allosteric selection

scientific article published in May 2000

An allosteric self-splicing ribozyme triggered by a bacterial second messenger

scientific article

An amino acid as a cofactor for a catalytic polynucleotide

scientific article published on May 1998

An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism

scientific article

An expanded collection and refined consensus model of glmS ribozymes

scientific article published on 2 March 2011

An mRNA structure in bacteria that controls gene expression by binding lysine

scientific article

Ancient, giant riboswitches at atomic resolution

scientific article published on 11 November 2012

Antibacterial lysine analogs that target lysine riboswitches

scientific article published on 3 December 2006

Architectures and complex functions of tandem riboswitches

scientific article published in 2022

Are engineered proteins getting competition from RNA?

scientific article published on August 1996

Association of OLE RNA with bacterial membranes via an RNA-protein interaction

scientific article published on 16 November 2010

Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.

scientific article

Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria

scientific article published on 25 November 2020

Biochemical analysis of hatchet self-cleaving ribozymes.

scientific article

Biochemical analysis of pistol self-cleaving ribozymes.

scientific article

Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria

scientific article published on 11 June 2019

Capping DNA with DNA.

scientific article published in March 2000

Catalytic DNA: in training and seeking employment

scientific article published on 01 May 1999

Challenges of ligand identification for riboswitch candidates

scientific article

Challenges of ligand identification for the second wave of orphan riboswitch candidates

scientific article

Characteristics of ligand recognition by a glmS self-cleaving ribozyme

scientific article published in October 2006

Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.

scientific article published on 16 February 2006

Characterization of a DNA-cleaving deoxyribozyme

scientific article

Cleaving DNA with DNA.

scientific article published in March 1998

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes

scientific article (publication date: 2004)

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

scientific article

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes

scientific article

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

scientific article

Control of alternative RNA splicing and gene expression by eukaryotic riboswitches

scientific article

Control of bacterial exoelectrogenesis by c-AMP-GMP.

scientific article

Control of gene expression by a natural metabolite-responsive ribozyme

scientific article

DNA enzymes

scientific article

Deoxyribozymes: new activities and new applications

scientific article

Deoxyribozymes: new players in the ancient game of biocatalysis

scientific article

Design and antimicrobial action of purine analogues that bind Guanine riboswitches

scientific article

Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization

scientific article published on 01 July 1999

Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans

scientific article published on 22 September 2019

Emergence of a replicating species from an in vitro RNA evolution reaction

scientific article published on June 1994

Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen

scientific article published on 14 November 2019

Engineered allosteric ribozymes as biosensor components

scientific article

Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate.

scientific article

Engineering high-speed allosteric hammerhead ribozymes

scientific article

Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches

scientific article published on 09 July 2009

Engineering precision RNA molecular switches

scientific article

Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing

scientific article published on February 2013

Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins

scientific article

Evidence for widespread gene control function by the ydaO riboswitch candidate

scientific article

Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD

scientific article published on 29 August 2019

Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection

scientific article published on 18 September 2006

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.

scientific article

Finding non-coding RNAs through genome-scale clustering.

scientific article

Fluoride enhances the activity of fungicides that destabilize cell membranes

scientific article published on 8 March 2012

Former Orphan Riboswitches Reveal Unexplored Areas of Bacterial Metabolism, Signaling and Gene Control Processes

scientific article published on 12 March 2020

Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes

scientific article

Genetic control by a metabolite binding mRNA

scientific article (publication date: September 2002)

Genetic control by metabolite-binding riboswitches

scientific article published on October 2003

Gramicidin D enhances the antibacterial activity of fluoride

scientific article

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine

scientific article

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics

scientific article published on 13 October 2017

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

scientific article

Identification of hammerhead ribozymes in all domains of life reveals novel structural variations

scientific article

Identification of ligand analogues that control c-di-GMP riboswitches.

scientific article

Immobilized RNA switches for the analysis of complex chemical and biological mixtures

scientific article published in April 2001

Importance of the Debye screening length on nanowire field effect transistor sensors

scientific article

Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125

scientific article published on March 2011

In vitro selection and characterization of cellulose-binding DNA aptamers

scientific article published on 18 September 2007

In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification

scientific article

In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP.

scientific article published on January 2014

In vitro selection of glmS ribozymes

scientific article published on January 2009

In vitro selection of kinase and ligase deoxyribozymes

scientific article

In-line probing analysis of riboswitches

scientific article

Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes

scientific article published on June 2013

Inventing and improving ribozyme function: rational design versus iterative selection methods

scientific article published on July 1994

Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis

scientific article

Ligating DNA with DNA.

scientific article published in March 2004

Mechanism and distribution of glmS ribozymes

scientific article published on January 2012

Mechanism for allosteric inhibition of an ATP-sensitive ribozyme

scientific article published on September 1998

Mechanism for gene control by a natural allosteric group I ribozyme

scientific article

Mechanistic Debris Generated by Twister Ribozymes

scientific article published on 13 February 2017

Metabolite-binding RNA domains are present in the genes of eukaryotes

scientific article

Molecular recognition of cAMP by an RNA aptamer

scientific article published in August 2000

Molecular-recognition characteristics of SAM-binding riboswitches

scientific article published in January 2006

Natural and engineered nucleic acids as tools to explore biology

scientific article

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

scientific article

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

scientific article (publication date: August 2015)

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

scientific article

New insight on the response of bacteria to fluoride

scientific article published on 10 February 2012

Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora

scientific article

Nucleic acid molecular switches

scientific article

OLE RNA protects extremophilic bacteria from alcohol toxicity

scientific article

Phosphorylating DNA with DNA.

scientific article

Polynucleotide phosphorylase forms polymers from an ADP analog in which the 5' oxygen is replaced by a methylene group

scientific article published in May 1990

Production of RNA by a polymerase protein encapsulated within phospholipid vesicles

article

Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products

scientific article

Prospects for riboswitch discovery and analysis

scientific article

Purine sensing by riboswitches

scientific article published on January 2008

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures

scientific article

RNA science and its applications-a look toward the future: Albany, NY USA, November 3-4, 2011.

scientific article published on August 2012

RNA switches out in the cold

scientific article

Regulation of bacterial gene expression by riboswitches

scientific article (publication date: 2005)

Relationship between internucleotide linkage geometry and the stability of RNA.

scientific article

Riboswitch diversity and distribution

scientific article published on 10 April 2017

Riboswitches and the RNA world

scientific article (publication date: February 2012)

Riboswitches as antibacterial drug targets

scientific article

Riboswitches as versatile gene control elements

scientific article

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

scientific article (publication date: 30 May 2003)

Riboswitches in eubacteria sense the second messenger c-di-AMP

scientific article

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine

scientific article published on April 2008

Riboswitches: from ancient gene-control systems to modern drug targets

scientific article published on September 2009

Ribozyme speed limits

scientific article

SAM-VI RNAs Selectively Bind S-adenosylmethionine and Exhibit Similarities to SAM-III Riboswitches.

scientific article

Self-Incorporation of coenzymes by ribozymes

scientific article published on 01 June 1995

Singlet glycine riboswitches bind ligand as well as tandem riboswitches.

scientific article

Small molecule fluoride toxicity agonists

scientific article

Small, highly active DNAs that hydrolyze DNA.

scientific article published on 6 June 2013

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

scientific article

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

scientific article (publication date: 29 June 2006)

Structural basis of ligand binding by a c-di-GMP riboswitch

scientific article

Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes.

scientific article

Substrate specificity and reaction kinetics of an X-motif ribozyme

scientific article published in June 2003

Tandem riboswitch architectures exhibit complex gene control functions

scientific article

Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria.

scientific article published on 5 March 2018

Tech.Sight. Molecular biology. Making catalytic DNAs

scientific article

The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch

scientific article published on 01 April 2005

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

scientific article

The distributions, mechanisms, and structures of metabolite-binding riboswitches

scientific article

The expanding view of RNA and DNA function

scientific article

The kinetics of ligand binding by an adenine-sensing riboswitch

scientific article

The lost language of the RNA World.

scientific article

The structural and functional diversity of metabolite-binding riboswitches

scientific article

The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

scientific article

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression

scientific article (publication date: 31 October 2002)

Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine

scientific article published in December 2005

Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates

article

Widespread genetic switches and toxicity resistance proteins for fluoride

scientific article

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