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- 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.鈥澨�J Mol Biol听436:听168702.
- Kletzien OA, Wuttke DS, Batey RT (2024) 鈥淭he RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs.鈥澨�Biochemistry听63:听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.鈥澨�BMC Res Notes听16:听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.鈥澨�Sci Rep听13:9385.
- Lennon SR, Wierzba AJ, Siwik SH, Gryko D, Palmer AE, Batey RT (2023) 鈥淭argeting riboswitches with beta-axial-substituted cobalamins.鈥澨�ACS Chem Biol听18:1136-1147.
- Hanson LN, Kletzien OA, Urquijo M, Schwanz LT, Batey RT (2023) 鈥淐ontext-dependence of T-loop mediated long-range RNA tertiary interactions.鈥澨�J Mol Biol听425:168070
- 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.鈥澨�Biochemistry听61: 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.鈥澨�Biochemistry听61: 943-951.
- Drogalis LK, Batey RT. (2020) 鈥淩equirements for efficient ligand-gated co-transcriptional switching in designed variants of the听B. subtilis pbuE听adenine-responsive riboswitch in听E. coli.鈥澨�PLoS One.听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.鈥澨�Nucleic Acids Res.听48:听9320-9335.
- Iwasaki RS, Batey RT. (2020) 鈥淪PRINT: a Cas13a-based platform for detection of small molecules.鈥澨�Nucleic Acids Res.听48:听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.鈥澨�Molecules听25:听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.鈥澨�Elife听9:听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,听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.鈥澨�RNA听26:982-995.
- Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS,听Batey RT (2020) 鈥淭he Sox2 transcription factor binds RNA鈥澨�Nature Comm.听11:听1805.
- Iwasaki RS, Ozdilek BA, Garst AD, Choudhury A,听Batey RT. (2020) 鈥淪mall molecule regulated sgRNAs enable control of genome editing in听E. coli听by Cas9鈥澨�Nature Comm.听11:听1394.
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- Parsonnet NV, Lammer NC, Holmes ZE,听Batey RT*, Wuttke DS*. (2019) 鈥淭he glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity.鈥澨�Nucleic Acids Res.听47:听8180-8192. (*co-corresponding authors)
- 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"听ACS Synth Biol听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.鈥澨�J Mol Biol听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.鈥澨�Biochemistry听51: 9223-9233.
- Johnson JE, Reyes FE, Polaski J, Batey RT (2012) "B12 cofactors directly stabilize an mRNA regulatory switch."听Nature听492: 133-137.
- Garst AD, Porter EB, Batey RT (2012).听 鈥淚nsights into the regulatory landscape of the lysine riboswitch.鈥澨�J Mol Biol.听423: 17-33.
- Trausch J, Reyes FE, Ceres P, Batey RT (2011). 听鈥淭he structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.鈥�听Structure听19:听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.鈥澨�Nucleic Acids Research听39:听8586-8598.
- Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R (2011).听 鈥淣ovel ligands for a purine riboswitch discovered by RNA-ligand docking.鈥�Chemistry & Biology听18:听324-335.
- Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT (2010).听 鈥淔ree state conformational sampling of the SAM-I riboswitch aptamer domain.鈥澨�Structure听18: 787-797.
- Edwards AL, Reyes FE, Heroux A, Batey RT (2010).听 鈥淪tructural basis for recognition of S-adenosylhomocysteine by riboswitches.鈥澨�RNA听16: 2144-2155.
- Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT (2010).听 鈥淒iscrimination between closely related cellular metabolites by the SAM-I riboswitch.鈥澨�J Mol Biol听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鈥澨�Proc Natl Acad Sci U S A听106:听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鈥澨�PLoS One听4: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鈥澨�Structure听17:听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鈥澨�J. Biol. Chem.284:听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鈥澨�J. Mol Biol.听385:听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鈥澨�J. Biol. Chem.听283: 22347-22351.
- Stoddard, C. D., Gilbert, S. D., and Batey, R. T. (2008) 鈥淟igand-dependent folding of the purine riboswitch鈥澨�RNA听14, 675-684.
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- Gilbert, S. D., Love, C. E., Edwards, A. L., and Batey, R. T. (2007) 鈥淢utational analysis of the purine riboswitch aptamer domain.鈥澨�Biochemistry听46, 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.鈥澨�Structure听15, 761-772.
- Batey, R. T., Kieft, J.S. (2007) 鈥淚mproved native affinity purification of RNA.鈥�RNA听13, 1384-1389.
- Gilbert, S. D., Mediatore, S. J. and Batey, R. T. (2006) 鈥淢odified pyrimidines specifically bind the purine riboswitch.鈥澨�Journal of the American Chemical Society听128, 14214-14215.
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- Montange, R. K. and Batey, R. T. (2006) 鈥淪tructure of the S-adenosylmethionine riboswitch regulatory element.鈥澨�Nature听441, 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.鈥澨�Journal of Molecular Biology听359, 754-768.
- Pleshe, E., Truesdell, J. and Batey R. T. (2005) 鈥淐rystal structure of a class II TrmH tRNA modifying enzyme from听Aquifex aeolicus.鈥澨�Acta Crystallographica F听61, 722-728.
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- Olenginski LT, Spradlin SF, Batey RT (2024) 鈥淔lipping the script: Understanding riboswitches from an alternative perspective.鈥澨�J Biol Chem听300:听105730.
- Hamilton DJ, Hein AE, Wuttke DS, Batey RT (2023) 鈥淭he DNA binding high mobility group box protein family functionally binds RNA.鈥澨�Wiley Interdiscip Rev RNA.听e1778.
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