Publications

2009

 

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.

 

2008

 

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.

 

2007

 

Importance of the Debye screening length on nanowire field effect transistor sensors. Stern E, Wagner R, Sigworth FJ, Breaker R, Fahmy TM, Reed MA. Nano Lett. 2007 Nov;7(11):3405-9. Epub 2007 Oct 3.

 

Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Plant Cell. 2007 Nov;19(11):3437-50. Epub 2007 Nov 9.

 

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Kim JN, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16092-7. Epub 2007 Oct 2.

 

Engineering high-speed allosteric hammerhead ribozymes. Link KH, Guo L, Ames TD, Yen L, Mulligan RC, Breaker RR. Biol Chem. 2007 Aug;388(8):779-86.

 

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. PLoS Comput Biol. 2007 Jul;3(7):e126.

 

Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Cheah MT, Wachter A, Sudarsan N, Breaker RR. Nature. 2007 May 24;447(7143):497-500. Epub 2007 Apr 29.

 

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. Nat Struct Mol Biol. 2007 Apr;14(4):308-17. Epub 2007 Mar 25.

 

Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. Welz R, Breaker RR. RNA. 2007 Apr;13(4):573-82. Epub 2007 Feb 16.

 

The distributions, mechanisms, and structures of metabolite-binding riboswitches. Barrick JE, Breaker RR. Genome Biol. 2007;8(11):R239.

 

Antibacterial lysine analogs that target lysine riboswitches Blount, K. F.; Wang, J. X.; Lim, J.; Sudarsan, N.; Breaker, R. R. , Nature Chemical Biology, Volume 3, Number 1, p.44-49, (2007)

 

In vitro selection and characterization of cellulose-binding DNA aptamers. Boese BJ, Breaker RR. Nucleic Acids Res. 2007;35(19):6378-88. Epub 2007 Sep 18.

 

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Nucleic Acids Res. 2007;35(14):4809-19. Epub 2007 Jul 9.

 

The power of riboswitches. Barrick JE, Breaker RR. Sci Am. 2007 Jan;296(1):50-7.

<Present - 2007> <2006 - 2002> <2001 - 1994>