Publications

Peer-reviewed research publications

Vicens Q, Mondragón E, Reyes FE, Coish P, Aristoff P, Berman J, Kaur H, Kells KW, Wickens P, Wilson J, Gadwood RC, Schostarez HJ, Suto RK, Blount KF, Batey RT (2018) "Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch" ACS Chem Biol 13(10):2908-2919
Braselmann E, Wierzba AJ, Polaski JT, Chromiński M, Holmes ZE, Hung ST, Batan D, Wheeler JR, Parker R, Jimenez R, Gryko D, Batey RT, Palmer AE (2018) "A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells" Nat Chem Biol 14(10):964-971
Polaski JT, Kletzien OA, Drogalis LK, Batey RT (2018) "A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity" Nucleic Acids Res 46(17):9094-9105
Ozdilek BA, Thompson VF, Ahmed NS, White CI, Batey RT, Schwartz JC (2017) "Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding" Nucleic Acids Res 45(13):7984-7996
Polaski JT, Webster SM, Johnson JE Jr, Batey RT (2017) "Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin" J Biol Chem 292(28):11650-11658
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E (2017) "RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme" RNA 23(5):655-672
Porter EB, Polaski JT, Morck MM, Batey RT (2017) "Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors" Nat Chem Biol 13(3):295-301
Polaski JT, Holmstrom ED, Nesbitt DJ, Batey RT (2016) "Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch" Cell Rep 15(5):1100-1110
Wostenberg C, Ceres P, Polaski JT, Batey RT (2015) "A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning" J Mol Biol 427(22):3473-3490
Trausch JJ, Marcano-Velázquez JG, Matyjasik MM, Batey RT (2015) "Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch" Chem Biol 22(7):829-37
Trausch JJ, Batey RT (2015) "Design of modular "plug-and-play" expression platforms derived from natural riboswitches for engineering novel genetically encodable RNA regulatory devices" Methods Enzymol 550:41-71
Marcano-Velázquez JG, Batey RT (2015) "Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context" J Biol Chem 290(7):4464-75
Holmstrom ED, Polaski JT, Batey RT, Nesbitt DJ (2014) "Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch" J Am Chem Soc 136(48):16832-43
Trausch JJ, Xu Z, Edwards AL, Reyes FE, Ross PE, Knight R, Batey RT (2014) "Structural basis for diversity in the SAM clan of riboswitches" Proc Natl Acad Sci U S A 111(18):6624-9
Porter EB, Marcano-Velázquez JG, Batey RT (2014) "The purine riboswitch as a model system for exploring RNA biology and chemistry" Biochim Biophys Acta 1839(10):919-930
Trausch JJ, Batey RT (2014) "A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch" Chem Biol 21(2):205-16
Ceres P, Trausch JJ, Batey RT (2013) "Engineering modular 'ON' RNA switches using biological components" Nucleic Acids Research 41(22):10449-61.
Ceres P, Garst AD, Marcano-Velazquez JG, Batey RT (2013) "Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices" ACS Synth Biol 2: 463-472.
Stoddard CD, Widmann J, Trausch JJ, Marcano-Velazquez JG, Knight R, and Batey RT (2013) “Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.” J Mol Biol 425: 1596-1610.
Fiegland LR, Garst AD, Batey RT, Nesbitt DJ (2012) “Single-molecule studies of the lysine riboswitch reveal effector dependent conformational dynamics of the aptamer domain.” Biochemistry 51: 9223-9233.
Johnson JE, Reyes FE, Polaski J, Batey RT (2012) "B12 cofactors directly stabilize an mRNA regulatory switch." Nature 492: 133-137.
Garst AD, Porter EB, Batey RT (2012). “Insights into the regulatory landscape of the lysine riboswitch.” J Mol Biol. 423: 17-33.
Trausch J, Reyes FE, Ceres P, Batey RT (2011). “The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.” Structure 19: 1413-1423.
Vicens Q, Mondragón E, Batey RT (2011). “Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection.” Nucleic Acids Research 39: 8586-8598.
Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R (2011). “Novel ligands for a purine riboswitch discovered by RNA-ligand docking.”Chemistry & Biology 18: 324-335.
Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT (2010). “Free state conformational sampling of the SAM-I riboswitch aptamer domain.” Structure 18: 787-797.
Edwards AL, Reyes FE, Heroux A, Batey RT (2010). “Structural basis for recognition of S-adenosylhomocysteine by riboswitches.” RNA 16: 2144-2155.
Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT (2010). “Discrimination between closely related cellular metabolites by the SAM-I riboswitch.” J Mol Biol 396: 761-772.
Gelinas, AD, Paschini M, Reyes, FE, Heroux, A, Batey RT Lundblad V, Wuttke DS (2009) “Telomere capping proteins are structurally related to RPA with an additional telomere-specific domain” Proc Natl Acad Sci U S A 106: 19298-19303.
Vicens, Q., Gooding, A. R., Duarte, L. F., and Batey, R. T. (2009) “Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification” PLoS One 4:e6740.
Gilbert, S. D., Reyes, F. E., Edwards, A. L., and Batey, R. T. (2009) “Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs” Structure 17: 857-868.
Hardin, J. W., Reyes, F. E., and Batey, R. T. (2009) “Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex” J. Biol. Chem.284: 15317-15324.
Edwards, A. L. and Batey, R. T. (2008) “A structural basis for the recognition of 2’-deoxyguanosine by the purine riboswitch” J. Mol Biol. 385: 938-948.
Garst, A.D., Héroux, A., Rambo, R. P., and Batey, R. T. (2008) “Crystal structure of the lysine riboswitch regulatory mRNA element” J. Biol. Chem. 283: 22347-22351.
Stoddard, C. D., Gilbert, S. D., and Batey, R. T. (2008) “Ligand-dependent folding of the purine riboswitch” RNA 14, 675-684.
20. Gilbert, S.D., Rambo, R. P., Van Tyne, D., and Batey, R. T. (2008) “Structure of the SAM-II riboswitch bound to S-adenosylmethionine” Nature Structural and Molecular Biology 15, 177-182.
Gilbert, S. D., Love, C. E., Edwards, A. L., and Batey, R. T. (2007) “Mutational analysis of the purine riboswitch aptamer domain.” Biochemistry 46, 13297-13309.
Keel, A. Y., Rambo, R. P., Batey, R. T., Kieft, J. S. (2007) “A general strategy to solve the phase problem in RNA crystallography.” Structure 15, 761-772.
Batey, R. T., Kieft, J.S. (2007) “Improved native affinity purification of RNA.”RNA 13, 1384-1389.
Gilbert, S. D., Mediatore, S. J. and Batey, R. T. (2006) “Modified pyrimidines specifically bind the purine riboswitch.” Journal of the American Chemical Society 128, 14214-14215.
25. Hardin, J. W. and Batey R. T. (2006) “The bipartite architecture of the sRNA in an Archaeal Box C/D complex is a primary determinant of specificity.” Nucleic Acids Research 34, 5039-5051.
Montange, R. K. and Batey, R. T. (2006) “Structure of the S-adenosylmethionine riboswitch regulatory element.” Nature 441, 1172-1175.
Gilbert, S. D., Wise, S. J., Stoddard, C. and Batey, R. T. (2006) “Thermodynamic and kinetic investigation of ligand binding by the purine riboswitch.” Journal of Molecular Biology 359, 754-768.
Pleshe, E., Truesdell, J. and Batey R. T. (2005) “Crystal structure of a class II TrmH tRNA modifying enzyme from Aquifex aeolicus.” Acta Crystallographica F 61, 722-728.
Batey, R. T., Gilbert, S. D., and Montange, R. K. (2004) “Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.” Nature432, 411-416.
Kieft, J. S. and Batey, R. T. (2004). “A general method for rapid and nondenaturing purification of RNAs.” RNA 10, 988-995.
Cochrane, J. C., Batey, R. T., and Strobel, S. A. (2003). “Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping.” RNA 9, 1282-1289.

Other publications (reviews or not peer reviewed)

Batey RT, Kieft JS (2013). "Soaking hexamine cations into RNA crystals to obtain derivatives for phasing diffraction data." Methods in Molecular Biology (in press).
Batey RT (2012). “Structure and mechanism of purine binding riboswitches.” Q. Rev. Biophys. 45: 345-381.
Batey RT (2011). “Recognition of S-adenosylmethionine by riboswitches.” Wires: RNA 2: 299-311.
Garst AD, Edwards AL, Batey RT (2010). “Riboswitches: Structures and mechanisms.” Cold Spring Harbor Perspect. Biol. (Epub Oct 13, 2010).
Edwards AL, Batey RT (2010). “Riboswitches: A common RNA regulatory element.” Nature Education 3: 9.
Reyes, F. E., and Batey, R. T. (2009) “Strategies in RNA Crystallography” Meth. Enz. 469: 119-139.
Garst, A. D., and Batey, R. T. (2009) “A switch in time: Detailing the life of a riboswitch” Biochim Biophys Acta 1789: 584-591.
Stoddard, C. D. and Batey, R. T. (2009) “Beyond Crystallography: Investigating the conformational dynamics of the purine riboswitch” Non-Protein Coding RNAs, Springer Series in Biophysics 13: 215-228.
Gilbert, S. D. and Batey, R. T. (2009) “Monitoring RNA-ligand interactions using Isothermal Titration Calorimetry” Methods in Molecular Biology 540: 97-114.
Edwards, A. L., Garst, A. D., and Batey, R. T. (2009) “Determining structures of RNA aptamers and riboswitches by X-ray crystallography” Methods in Molecular Biology 535: 135-163.
Montange R. K. and Batey R. T. (2008) “Riboswitches: Emerging Themes in RNA Structure and Function.” Annual Reviews of Biophysics 37, 117-133.
Vincens, Q., Allen, M. A., Gilbert, S. D., Reznik, B. Gooding, A. R., and Batey, R.T. (2008). “The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom” RNA 14, 397-403.
Stoddard, C.D., Batey R. T. (2006) “Mix-and-match riboswitches.” ACS Chemical Biology 1, 751-754.
Gilbert, S. D., Montange, R. K., Stoddard, C. D., and Batey, R. T. (2006). “Structural studies of the purine and SAM binding riboswitches” Cold Spring Harbor Symposium on Quantitative Biology 71: 259-268.
Gilbert, S. D. and Batey, R. T. (2006) “Riboswitches: Fold and Function.”Chemistry and Biology 13, 805-807.
Batey, R. T. (2006). “Structures of regulatory elements in mRNAs.” Current Opinion in Structural Biology 16, 299-306.
Gilbert, S. D. and Batey, R. T. (2005). “Riboswitches: natural SELEXion.” Cellular and Molecular Life Sciences 62, 2401-2404.
Hardin, J. W. and Batey, R. T. (2004). “Curse of the Hairpin Loop.” Structure 12, 731-732.
Doudna, J. A. and Batey, R. T. (2004). “Structural Insights into the Signal Recognition Particle.” Annual Reviews of Biochemistry 73, 539-57.

Publications from work prior to becoming an independent investigator

Batey, R. T., and Doudna, J. A. (2002). “Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly.” Biochemistry 41: 11703-11710.
Doherty, E. A., Batey, R. T., Masquida, B. and Doudna, J. A. (2001). “A universal mode of helix packing in RNA.” Nature Structural Biology 8: 339-343.
Batey, R. T., Sagar, M. B., and Doudna. J. A. (2001). “Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.” Journal of Molecular Biology 307: 229-246.
Lucast, L. J., Batey, R. T., and Doudna, J. A. (2001). “Large-scale purification of a stable form of recombinant tobacco etch virus protease.” Biotechniques 30: 544-550.
Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. (2000). “Crystal structure of the ribonucleoprotein core of the signal recognition particle.”Science 287:1232-1239.
Batey, R. T., Rambo, R. P., and Doudna, J. A. (1999). “Tertiary motifs in RNA structure and folding.” Angewandte Chemie International Edition 38:2326-2343.
Batey, R. T., and Doudna, J. A. (1998). “The parallel universe of RNA folding.”Nature Structural Biology 5:337-340.
Batey, R. T., and Williamson, J. R. (1998). “Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15.” RNA4:984-997.
Batey, R. T., Cloutier, N., Mao, H., and Williamson, J. R. (1996). “Improved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides.” Nucleic Acids Research 24:4836-4837.
Batey, R. T., and Williamson, J. R. (1996). “Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition.” Journal of Molecular Biology 261:550-567.
Batey, R. T., and Williamson, J. R. (1996). “Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site.” Journal of Molecular Biology 261:536-549.
Batey, R. T., Battiste, J. L., and Williamson, J. R. (1995). “Preparation of isotopically enriched RNAs for heteronuclear NMR.” Methods in Enzymology 261:300-322.
Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., and Williamson, J. R. (1992). “Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA.” Nucleic Acids Research 20:4515-4523.
Senear, D. F., and Batey, R. (1991). "Comparison of operator specific and nonspecific DNA binding of lamda cI repressor: [KCl] and pH effects.” Biochemistry30:6677-6688.

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