Nelson, JW, Sudarsan, N, Phillips, GE, Stav, S, Lünse, CE, McCown, PJ, Breaker, RR (2015 Apr) Control of bacterial exoelectrogenesis by c-AMP-GMP. Proc Natl Acad Sci U S A 112: 5389-94 [Article link]

Nelson, JW, Plummer, MS, Blount, KF, Ames, TD, Breaker, RR (2015 Apr) Small molecule fluoride toxicity agonists. Chem Biol 22: 527-34 [Article link]

Furukawa, K, Ramesh, A, Zhou, Z, Weinberg, Z, Vallery, T, Winkler, WC, Breaker, RR (2015 Mar) Bacterial riboswitches cooperatively bind ni(2+) or co(2+) ions and control expression of heavy metal transporters. Mol Cell 57: 1088-98 [Article link]

Kim, PB, Nelson, JW, Breaker, RR (2015 Jan) An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Mol Cell 57: 317-28 [Article link]


Breaker, RR, Joyce, GF (2014 Sep) The Expanding View of RNA and DNA Function. Chem Biol 21: [Article link]

Nelson, JW, Zhou, Z, Breaker, RR (2014 Jul) Gramicidin D enhances the antibacterial activity of fluoride. Bioorg Med Chem Lett 24: 2969-71 [Article link]

McCown, PJ, Liang, JJ, Weinberg, Z, Breaker, RR (2014 Jul) Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes. Chem Biol 21: 880-9 [Article link]

Furukawa K, Gu H, Breaker RR (2014 Feb) In Vitro Selection of Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMP Methods in Molecular Biology Volume 1111: 209-220 [Article link]


Li S., Smith K.D., Davis J.H., Gordon P.B., Breaker R.R., and Strobel S.A. (2013 Nov) Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins PNAS [Article link]

Roth A, Weinberg Z, Chen A, Kim B, Ames T & Breaker R (2013 Nov) A widespread self-cleaving ribozyme class is revealed by bioinformatics Nature Chemical Biology 10: 56-60 [Article link]

Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX & Breaker RR (2013 Oct) Riboswitches in eubacteria sense the second messenger c-di-AMP Nature Chemical Biology [Article link]

Gu H and Breaker RR (2013 Jun) Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products BioTechniques 54 (6): 337–343 [Article link]

Gu H, Furukawa K, Weinberg Z, Berenson D, and Breaker RR (2013 May) Small, highly-active DNAs that hydrolyze DNA Journal of the American Chemical Society [Article link]

Li S and Breaker RR (2013 Feb) Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing Nucleic Acids Research 41(3): [Article link]


Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker RR (2012 Jun) Identification of Ligand Analogs that Control c-di-GMP Riboswitches ACS Chem. Biol. [Article link]

Pedrolli DB, Matern A, Wang J, Ester M, Siedler K, Breaker RR and Mack M (2012 Jun) A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis Nucleic Acids Research [Article link]

Wallace JG, Zhou Z and Breaker RR (2012 May) OLE RNA protects extremophilic bacteria from alcohol toxicity Nucleic Acids Research [Article link]

Li S, Breaker RR (2012 Apr) Fluoride enhances the activity of fungicides that destabilize cell membranes Bioorganic & Medicinal Chemistry Letters [Article link]

Gu H, Furukawa K, and Breaker RR (2012 Apr) Engineered Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMP Analytical Chemistry [Article link]

Breaker RR (2012 Feb) New Insight on the Response of Bacteria to Fluoride Caries Research 46: 78-81 [Article link]

Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR (2012 Jan) Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335(6065): 233-5 [Article link]


Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker RR, Pedersen JS (2011 Oct) New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes Genome Research 21(11): 1929-43 [Article link]

Breaker RR (2011 Sep) Prospects for Riboswitch Discovery and Analysis Molecular Cell 43(6): 867-879 [Article link]

Chen AG, Sudarsan N, Breaker RR (2011 Sep) Mechanism for gene control by a natural allosteric group I ribozyme. RNA 17(11): 1967-72 [Article link]

Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR (2011 May) Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations PLoS Computation Biology 7(5): [Article link]

Wallace JG and Breaker RR (2011 Apr) Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125 Lett Appl Microbiol. 52(4): 430-2 [Article link]

McCown PJ, Roth A, Breaker RR. (2011 Apr) An expanded collection and refined consensus model of glmS ribozymes. RNA 17(4): 728-36 [Article link]

Ames TD and Breaker RR (2011 Jan) Bacterial aptamers that selectively bind glutamine RNA Biology 8, 1: [Article link]

Meyer MM, Hammond MC, Salinas Y, Roth A, Sudarsan N and Breaker RR (2011 Jan) Challenges of ligand identification for riboswitch candidates RNA Biology 8, 1: [Article link]

Weinberg Z, Breaker RR (2011 Jan) R2R - software to speed the depiction of aesthetic consensus RNA secondary structures BMC Bioinformatics 12: [Article link]

Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR. (2011 Jan) Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol. 79(1): 21-34 [Article link]


Breaker RR (2010 Nov) Riboswitches and the RNA World Cold Spring Harb Perspect Biol. [Article link]

Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR (2010 Aug) An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger Science 329(5993): 845 - 848 [Article link]

Ames TD, Breaker RR (2010 Aug) Bacterial Riboswitch Discovery and Analysis The Chemical Biology of Nucleic Acids [Article link]

Ames TD, Rodionov DA, Weinberg Z, Breaker RR (2010 Jul) A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol. 17(7): 681-5 [Article link]

Block KF, Hammond MC, Breaker RR (2010 May) Evidence for Widespread Gene Control Function by the ydaO Riboswitch Candidate J. Bacteriol. [Article link]

Block KF, Wallace J, Puerta-Fernandez E and Breaker RR (2010 Apr) The large, noncoding OLE RNA is associated with membrane biochemistry FASEB Journal [Article link]

Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (2010 Mar) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Genome Biol. 11(3): R31 [Article link]

Breaker RR (2010 Mar) RNA second messengers and riboswitches: Relics from the RNA world? Microbe 5(1): 13-20 [Article link]

Breaker RR (2010 Jan) RNA switches out in the cold Mol Cell. 37(1): 1-2 [Article link]