The Breaker laboratory is exploring the enormous diversity of structures and functions exhibited by RNA and DNA. New functions for nucleic acids can be created using evolution in a test tube, and ancient functions can be found by searching for nucleotide sequences in modern organisms that have been preserved amongst many species.

Of special interest are ribozymes and riboswitches - RNA molecules that catalyze chemical reactions or that serve as chemical sensors and gene control elements. We employ a wide range of bioinformatics, genetics, and biochemical techniques to discover and study these functional RNAs - some of which might be molecular relics from primitive life forms that have been extinct for billions of years.

A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. Poiata E, Meyer MM, Ames TD, Breaker RR. RNA. 2009 Nov;15(11):2046-56. Epub 2009 Sep 23.

Design and Antimicrobial Action of Purine Analogs that Bind Guanine Riboswitches. Kim JN, Blount KF, Lim J, Link KH, Breaker R. ACS Chem Biol. 2009 Sep 9. [Epub ahead of print]

Riboswitches: from ancient gene-control systems to modern drug targets. Breaker RR. Future Microbiol. 2009 Sep;4:771-3.

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique' Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. BMC Genomics. 2009 Jun 16;10(1):268. [Epub ahead of print]

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Hammond MC, Wachter A, Breaker RR. Nat Struct Mol Biol. 2009 May;16(5):541-9. Epub 2009 Apr 19.

Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. Lee ER, Blount KF, Breaker RR. RNA Biol. 2009 Apr 30;6(2).

Finding non-coding RNAs through genome-scale clustering. Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. J Bioinform Comput Biol. 2009 Apr;7(2):373-88.

The structural and functional diversity of metabolite-binding riboswitches. Roth A, Breaker RR. Annu Rev Biochem. 2009;78:305-34.

Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ. Environ Microbiol. 2009 Jan;11(1):230-8.

In vitro selection of glmS ribozymes. Link KH, Breaker RR. Methods Mol Biol. 2009;540:349-64.

In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification. Boese BJ, Corbino K, Breaker RR. Nucleosides Nucleotides Nucleic Acids. 2008 Aug;27(8):949-66.

Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. Science. 2008 Jul 18;321(5887):411-3.

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. Mol Microbiol. 2008 May;68(4):918-32. Epub 2008 Mar 19.

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. RNA. 2008 May;14(5):822-8. Epub 2008 Mar 27.

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Wang JX, Breaker RR. Biochem Cell Biol. 2008 Apr;86(2):157-68. Review.

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR. RNA. 2008 Apr;14(4):685-95. Epub 2008 Feb 27.

Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. Mol Cell. 2008 Mar 28;29(6):691-702.

Complex riboswitches. Breaker RR. Science. 2008 Mar 28;319(5871):1795-7.

Purine sensing by riboswitches. Kim JN, Breaker RR. Biol Cell. 2008 Jan;100(1):1-11.

In-line probing analysis of riboswitches. Regulski EE, Breaker RR. Methods Mol Biol. 2008;419:53-67.

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