Kletzien OA, Wuttke DS, Batey RT (2024) 鈥淭he RNA-binding selectivity of the RGG/RG motifs of hnRNP U is abolished by elements within the C-terminal intrinsically disordered region.鈥&苍产蝉辫;J Mol Biol436: 168702.
Kletzien OA, Wuttke DS, Batey RT (2024) 鈥淭he RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs.鈥&苍产蝉辫;Biochemistry63: 460-474.
Lammer NC, Allen MA, Batey RT, Wuttke DS (2023) 鈥淨uantification of transcriptome changes to investigate the role of glucocorticoid receptor-RNA binding during dexamethasone treatment.鈥&苍产蝉辫;BMC Res Notes16: 181.
Lammer NC, Ashraf HM, Ugay DA, Spencer SL, Allen MA, Batey RT, Wuttke DS (2023) 鈥淩NA binding by the glucocorticoid receptor attenuates dexamethasone-induced gene activation.鈥&苍产蝉辫;Sci Rep13:9385.
Lennon SR, Wierzba AJ, Siwik SH, Gryko D, Palmer AE, Batey RT (2023) 鈥淭argeting riboswitches with beta-axial-substituted cobalamins.鈥&苍产蝉辫;ACS Chem Biol18:1136-1147.
Steiner HR, Lammer NC, Batey RT, Wuttke DS (2022) 鈥淎n extended DNA binding domain of the estrogen receptor alpha directly interacts with RNAs in vitro.鈥&苍产蝉辫;Biochemistry61: 2490 鈥 2494.
Hamilton DJ, Hein AE, Holmes ZE, Wuttke DS, Batey RT (2022) 鈥淭he DNA-binding high-mobility group box domain of Sox family proteins directly interact with RNA in vitro.鈥&苍产蝉辫;Biochemistry61: 943-951.
Drogalis LK, Batey RT. (2020) 鈥淩equirements for efficient ligand-gated co-transcriptional switching in designed variants of the B. subtilis pbuE adenine-responsive riboswitch in E. coli.鈥&苍产蝉辫;PLoS One. 15:e0243155.
Nakamoto MY, Lammer NC, Batey RT*, Wuttke DS*. (2020) 鈥渉nRNPK recognition of the B motif of Xist and other biological RNAs.鈥&苍产蝉辫;Nucleic Acids Res.48: 9320-9335.
Iwasaki RS, Batey RT. (2020) 鈥淪PRINT: a Cas13a-based platform for detection of small molecules.鈥&苍产蝉辫;Nucleic Acids Res.48: e101.
Matyjasik MM, Hall SD, Batey RT. (2020) 鈥淗igh affinity binding of N2-modified guanine derivatives significantly disrupts the ligand binding pocket of the guanine riboswitch.鈥&苍产蝉辫;Molecules25: 2295.
Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, Longaker MT, Khavari PA, Batey RT, Wuttke DS, Chang HY. (2020) 鈥淪pen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.鈥&苍产蝉辫;Elife 9: e54508.
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Pi膮tkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, 呕y艂a A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. (2020) 鈥淩NA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.鈥&苍产蝉辫;RNA26:982-995.
Iwasaki RS, Ozdilek BA, Garst AD, Choudhury A, Batey RT. (2020) 鈥淪mall molecule regulated sgRNAs enable control of genome editing in E. coli by Cas9鈥 Nature Comm.11: 1394.
Matyjasik MM, Batey RT. (2019) 鈥淪tructural basis for 2鈥-deoxyguanosine recognition by the 2鈥-dG-II class of riboswitches.鈥&苍产蝉辫;Nucleic Acids Res.47: 10931-10941.
Vicens Q, Mondrag贸n 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, Chromi艅ski 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, Ferr茅-D'Amar茅 AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, 艁ach 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-Vel谩zquez JG, Matyjasik MM, Batey RT (2015) "Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch" Chem Biol 22(7):829-37
Marcano-Vel谩zquez 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
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) 鈥淣ucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.鈥&苍产蝉辫;J Mol Biol 425: 1596-1610.
Fiegland LR, Garst AD, Batey RT, Nesbitt DJ (2012) 鈥淪ingle-molecule studies of the lysine riboswitch reveal effector dependent conformational dynamics of the aptamer domain.鈥&苍产蝉辫;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). 鈥淚nsights into the regulatory landscape of the lysine riboswitch.鈥&苍产蝉辫;J Mol Biol. 423: 17-33.
Trausch J, Reyes FE, Ceres P, Batey RT (2011). 鈥淭he structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.鈥 Structure19: 1413-1423.
Vicens Q, Mondrag贸n E, Batey RT (2011). 鈥淢olecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection.鈥&苍产蝉辫;Nucleic Acids Research39: 8586-8598.
Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R (2011). 鈥淣ovel ligands for a purine riboswitch discovered by RNA-ligand docking.鈥Chemistry & Biology18: 324-335.
Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT (2010). 鈥淔ree state conformational sampling of the SAM-I riboswitch aptamer domain.鈥&苍产蝉辫; Structure 18: 787-797.
Edwards AL, Reyes FE, Heroux A, Batey RT (2010). 鈥淪tructural basis for recognition of S-adenosylhomocysteine by riboswitches.鈥&苍产蝉辫;RNA 16: 2144-2155.
Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT (2010). 鈥淒iscrimination between closely related cellular metabolites by the SAM-I riboswitch.鈥&苍产蝉辫; J Mol Biol 396: 761-772.
Gelinas, AD, Paschini M, Reyes, FE, Heroux, A, Batey RT Lundblad V, Wuttke DS (2009) 鈥淭elomere capping proteins are structurally related to RPA with an additional telomere-specific domain鈥 Proc Natl Acad Sci U S A106: 19298-19303.
Vicens, Q., Gooding, A. R., Duarte, L. F., and Batey, R. T. (2009) 鈥淧reparation of group I introns for biochemical studies and crystallization assays by native affinity purification鈥 PLoS One4:e6740.
Gilbert, S. D., Reyes, F. E., Edwards, A. L., and Batey, R. T. (2009) 鈥淎daptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs鈥 Structure17: 857-868.
Hardin, J. W., Reyes, F. E., and Batey, R. T. (2009) 鈥淎nalysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex鈥 J. Biol. Chem.284: 15317-15324.
Edwards, A. L. and Batey, R. T. (2008) 鈥淎 structural basis for the recognition of 2鈥-deoxyguanosine by the purine riboswitch鈥 J. Mol Biol.385: 938-948.
Garst, A.D., H茅roux, A., Rambo, R. P., and Batey, R. T. (2008) 鈥淐rystal structure of the lysine riboswitch regulatory mRNA element鈥 J. Biol. Chem.283: 22347-22351.
Stoddard, C. D., Gilbert, S. D., and Batey, R. T. (2008) 鈥淟igand-dependent folding of the purine riboswitch鈥 RNA14, 675-684.
20. Gilbert, S.D., Rambo, R. P., Van Tyne, D., and Batey, R. T. (2008) 鈥淪tructure of the SAM-II riboswitch bound to S-补诲别苍辞蝉测濒尘别迟丑颈辞苍颈苍别鈥&苍产蝉辫;Nature Structural and Molecular Biology15, 177-182.
Gilbert, S. D., Love, C. E., Edwards, A. L., and Batey, R. T. (2007) 鈥淢utational analysis of the purine riboswitch aptamer domain.鈥&苍产蝉辫;Biochemistry46, 13297-13309.
Keel, A. Y., Rambo, R. P., Batey, R. T., Kieft, J. S. (2007) 鈥淎 general strategy to solve the phase problem in RNA crystallography.鈥&苍产蝉辫;Structure15, 761-772.
Batey, R. T., Kieft, J.S. (2007) 鈥淚mproved native affinity purification of RNA.鈥RNA13, 1384-1389.
Gilbert, S. D., Mediatore, S. J. and Batey, R. T. (2006) 鈥淢odified pyrimidines specifically bind the purine riboswitch.鈥&苍产蝉辫;Journal of the American Chemical Society128, 14214-14215.
25. Hardin, J. W. and Batey R. T. (2006) 鈥淭he bipartite architecture of the sRNA in an Archaeal Box C/D complex is a primary determinant of specificity.鈥&苍产蝉辫;Nucleic Acids Research34, 5039-5051.
Montange, R. K. and Batey, R. T. (2006) 鈥淪tructure of the S-adenosylmethionine riboswitch regulatory element.鈥&苍产蝉辫;Nature441, 1172-1175.
Gilbert, S. D., Wise, S. J., Stoddard, C. and Batey, R. T. (2006) 鈥淭hermodynamic and kinetic investigation of ligand binding by the purine riboswitch.鈥&苍产蝉辫;Journal of Molecular Biology359, 754-768.
Pleshe, E., Truesdell, J. and Batey R. T. (2005) 鈥淐rystal structure of a class II TrmH tRNA modifying enzyme from Aquifex aeolicus.鈥&苍产蝉辫; Acta Crystallographica F61, 722-728.
Batey, R. T., Gilbert, S. D., and Montange, R. K. (2004) 鈥淪tructure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.鈥&苍产蝉辫; Nature432, 411-416.
Kieft, J. S. and Batey, R. T. (2004). 鈥淎 general method for rapid and nondenaturing purification of RNAs.鈥&苍产蝉辫; RNA10, 988-995.
Cochrane, J. C., Batey, R. T., and Strobel, S. A. (2003). 鈥淨uantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping.鈥&苍产蝉辫;RNA9, 1282-1289.
Olenginski LT, Spradlin SF, Batey RT (2024) 鈥淔lipping the script: Understanding riboswitches from an alternative perspective.鈥&苍产蝉辫;J Biol Chem300: 105730.
Hamilton DJ, Hein AE, Wuttke DS, Batey RT (2023) 鈥淭he DNA binding high mobility group box protein family functionally binds RNA.鈥&苍产蝉辫;Wiley Interdiscip Rev RNA. e1778.
Lennon SR, Batey RT (2023) 鈥淩egulation of gene expression through effector-dependent conformational switching by cobalamin riboswitches.鈥&苍产蝉辫;J Mol Biol434:167585.
Childs-Disney JL, Yan X, Gibaut QMR, Tong Y, Batey RT, Disney MD. (2022) 鈥淭argeting RNA structures with small molecules.鈥&苍产蝉辫;Nat Rev Drug Discov.21: 736-762.
Batey RT, Kieft JS (2016) "Soaking hexamine cations into RNA crystals to obtain derivatives for phasing diffraction data." Methods in Molecular Biology1320: 219-32.
Batey RT (2015) "Riboswitches: still a lot of undiscovered country" RNA21: 560-3.
Trausch JJ, Batey RT (2015) 鈥淒esign of modular 鈥減lug-and-play鈥 expression platforms derived from natural riboswitches for engineering novel genetically encodable RNA regulatory devices鈥 Methods Enzymol550:41-71.
Porter EB, Marcano-Vel谩zquez JG, Batey RT (2014) "The purine riboswitch as a model system for exploring RNA biology and chemistry" Biochem Biophys Acta1839: 919-930.
Batey RT (2014). "Advances in methods for native expression and purification of RNA for structural studies." Curr Op Struct Biol26: 1-8.
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). 鈥淪tructure and mechanism of purine binding riboswitches.鈥&苍产蝉辫;Q. Rev. Biophys.45: 345-381.
Batey RT (2011). 鈥淩ecognition of S-adenosylmethionine by riboswitches.鈥&苍产蝉辫;Wires: RNA2: 299-311.
Garst AD, Edwards AL, Batey RT (2010). 鈥淩iboswitches: Structures and mechanisms.鈥&苍产蝉辫; Cold Spring Harbor Perspect. Biol. (Epub Oct 13, 2010).
Edwards AL, Batey RT (2010). 鈥淩iboswitches: A common RNA regulatory element.鈥&苍产蝉辫; Nature Education 3: 9.
Reyes, F. E., and Batey, R. T. (2009) 鈥淪trategies in RNA Crystallography鈥 Meth. Enz.469: 119-139.
Garst, A. D., and Batey, R. T. (2009) 鈥淎 switch in time: Detailing the life of a riboswitch鈥 Biochim Biophys Acta1789: 584-591.
Stoddard, C. D. and Batey, R. T. (2009) 鈥淏eyond Crystallography: Investigating the conformational dynamics of the purine riboswitch鈥 Non-Protein Coding RNAs, Springer Series in Biophysics13: 215-228.
Gilbert, S. D. and Batey, R. T. (2009) 鈥淢onitoring RNA-ligand interactions using Isothermal Titration Calorimetry鈥 Methods in Molecular Biology540: 97-114.
Edwards, A. L., Garst, A. D., and Batey, R. T. (2009) 鈥淒etermining structures of RNA aptamers and riboswitches by X-ray crystallography鈥 Methods in Molecular Biology535: 135-163.
Montange R. K. and Batey R. T. (2008) 鈥淩iboswitches: Emerging Themes in RNA Structure and Function.鈥&苍产蝉辫;Annual Reviews of Biophysics37, 117-133.
Vincens, Q., Allen, M. A., Gilbert, S. D., Reznik, B. Gooding, A. R., and Batey, R.T. (2008). 鈥淭he Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom鈥 RNA14, 397-403.
Stoddard, C.D., Batey R. T. (2006) 鈥淢ix-and-match riboswitches.鈥&苍产蝉辫;ACS Chemical Biology1, 751-754.
Gilbert, S. D., Montange, R. K., Stoddard, C. D., and Batey, R. T. (2006). 鈥淪tructural studies of the purine and SAM binding riboswitches鈥 Cold Spring Harbor Symposium on Quantitative Biology71: 259-268.
Gilbert, S. D. and Batey, R. T. (2006) 鈥淩iboswitches: Fold and Function.鈥Chemistry and Biology13, 805-807.
Batey, R. T. (2006). 鈥淪tructures of regulatory elements in mRNAs.鈥&苍产蝉辫; Current Opinion in Structural Biology16, 299-306.
Gilbert, S. D. and Batey, R. T. (2005). 鈥淩iboswitches: natural SELEXion.鈥&苍产蝉辫;Cellular and Molecular Life Sciences62, 2401-2404.
Hardin, J. W. and Batey, R. T. (2004). 鈥淐urse of the Hairpin Loop.鈥&苍产蝉辫;Structure12, 731-732.
Doudna, J. A. and Batey, R. T. (2004). 鈥淪tructural Insights into the Signal Recognition Particle.鈥&苍产蝉辫;Annual Reviews of Biochemistry73, 539-57.
Batey, R. T., and Doudna, J. A. (2002). 鈥淪tructural and energetic analysis of metal ions essential to SRP signal recognition domain assembly.鈥&苍产蝉辫;Biochemistry41: 11703-11710.
Doherty, E. A., Batey, R. T., Masquida, B. and Doudna, J. A. (2001). 鈥淎 universal mode of helix packing in RNA.鈥&苍产蝉辫;Nature Structural Biology8: 339-343.
Batey, R. T., Sagar, M. B., and Doudna. J. A. (2001). 鈥淪tructural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.鈥&苍产蝉辫;Journal of Molecular Biology307: 229-246.
Lucast, L. J., Batey, R. T., and Doudna, J. A. (2001). 鈥淟arge-scale purification of a stable form of recombinant tobacco etch virus protease.鈥&苍产蝉辫;Biotechniques30: 544-550.
Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. (2000). 鈥淐rystal structure of the ribonucleoprotein core of the signal recognition particle.鈥Science287:1232-1239.
Batey, R. T., Rambo, R. P., and Doudna, J. A. (1999). 鈥淭ertiary motifs in RNA structure and folding.鈥&苍产蝉辫;Angewandte Chemie International Edition38:2326-2343.
Batey, R. T., and Doudna, J. A. (1998). 鈥淭he parallel universe of RNA folding.鈥Nature Structural Biology5:337-340.
Batey, R. T., and Williamson, J. R. (1998). 鈥淓ffects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15.鈥&苍产蝉辫;RNA4:984-997.
Batey, R. T., Cloutier, N., Mao, H., and Williamson, J. R. (1996). 鈥淚mproved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides.鈥&苍产蝉辫;Nucleic Acids Research24:4836-4837.
Batey, R. T., and Williamson, J. R. (1996). 鈥淚nteraction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition.鈥&苍产蝉辫;Journal of Molecular Biology261:550-567.
Batey, R. T., and Williamson, J. R. (1996). 鈥淚nteraction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site.鈥&苍产蝉辫;Journal of Molecular Biology261:536-549.
Batey, R. T., Battiste, J. L., and Williamson, J. R. (1995). 鈥淧reparation of isotopically enriched RNAs for heteronuclear NMR.鈥&苍产蝉辫;Methods in Enzymology261:300-322.
Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., and Williamson, J. R. (1992). 鈥淧reparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA.鈥&苍产蝉辫;Nucleic Acids Research20:4515-4523.
Senear, D. F., and Batey, R. (1991). "Comparison of operator specific and nonspecific DNA binding of lamda cI repressor: [KCl] and pH effects.鈥&苍产蝉辫;Biochemistry30:6677-6688.
