 Connection
Robert Batey to Nucleic Acid Conformation
This is a "connection" page, showing publications Robert Batey has written about Nucleic Acid Conformation.
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Connection Strength |
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6.578 |
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Polaski JT, Kletzien OA, Drogalis LK, Batey RT. A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity. Nucleic Acids Res. 2018 09 28; 46(17):9094-9105.
Score: 0.498
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Batey RT. Structural biology: Lariat lessons. Nature. 2014 Oct 09; 514(7521):173-4.
Score: 0.377
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Johnson JE, Reyes FE, Polaski JT, Batey RT. B12 cofactors directly stabilize an mRNA regulatory switch. Nature. 2012 Dec 06; 492(7427):133-7.
Score: 0.329
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Batey RT. Structure and mechanism of purine-binding riboswitches. Q Rev Biophys. 2012 Aug; 45(3):345-81.
Score: 0.325
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Edwards AL, Reyes FE, H?roux A, Batey RT. Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA. 2010 Nov; 16(11):2144-55.
Score: 0.285
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Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure. 2010 Jul 14; 18(7):787-97.
Score: 0.282
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Edwards AL, Batey RT. A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol. 2009 Jan 23; 385(3):938-48.
Score: 0.251
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Montange RK, Batey RT. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature. 2006 Jun 29; 441(7097):1172-5.
Score: 0.213
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Batey RT, Gilbert SD, Montange RK. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature. 2004 Nov 18; 432(7015):411-5.
Score: 0.190
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Lennon SR, Wierzba AJ, Siwik SH, Gryko D, Palmer AE, Batey RT. Targeting Riboswitches with Beta-Axial-Substituted Cobalamins. ACS Chem Biol. 2023 05 19; 18(5):1136-1147.
Score: 0.171
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Hansen LN, Kletzien OA, Urquijo M, Schwanz LT, Batey RT. Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions. J Mol Biol. 2023 05 15; 435(10):168070.
Score: 0.170
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Batey RT, Sagar MB, Doudna JA. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol. 2001 Mar 16; 307(1):229-46.
Score: 0.148
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Drogalis LK, Batey RT. Requirements for efficient ligand-gated co-transcriptional switching in designed variants of the B. subtilis pbuE adenine-responsive riboswitch in E. coli. PLoS One. 2020; 15(12):e0243155.
Score: 0.145
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Iwasaki RS, Ozdilek BA, Garst AD, Choudhury A, Batey RT. Small molecule regulated sgRNAs enable control of genome editing in E. coli by Cas9. Nat Commun. 2020 Mar 13; 11(1):1394.
Score: 0.138
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Matyjasik MM, Batey RT. Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches. Nucleic Acids Res. 2019 11 18; 47(20):10931-10941.
Score: 0.135
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Batey RT, Doudna JA. The parallel universe of RNA folding. Nat Struct Biol. 1998 May; 5(5):337-40.
Score: 0.121
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Porter EB, Polaski JT, Morck MM, Batey RT. Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors. Nat Chem Biol. 2017 03; 13(3):295-301.
Score: 0.111
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Polaski JT, Holmstrom ED, Nesbitt DJ, Batey RT. Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch. Cell Rep. 2016 05 03; 15(5):1100-1110.
Score: 0.105
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Batey RT, Kieft JS. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol. 2016; 1320:219-32.
Score: 0.103
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Wostenberg C, Ceres P, Polaski JT, Batey RT. A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol. 2015 Nov 06; 427(22):3473-3490.
Score: 0.101
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Trausch JJ, Marcano-Vel?zquez JG, Matyjasik MM, Batey RT. Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch. Chem Biol. 2015 Jul 23; 22(7):829-37.
Score: 0.099
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Batey RT. Riboswitches: still a lot of undiscovered country. RNA. 2015 Apr; 21(4):560-3.
Score: 0.098
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Marcano-Vel?zquez JG, Batey RT. Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. J Biol Chem. 2015 Feb 13; 290(7):4464-75.
Score: 0.096
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Trausch JJ, Xu Z, Edwards AL, Reyes FE, Ross PE, Knight R, Batey RT. Structural basis for diversity in the SAM clan of riboswitches. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6624-9.
Score: 0.091
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Trausch JJ, Batey RT. A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch. Chem Biol. 2014 Feb 20; 21(2):205-16.
Score: 0.090
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Stoddard CD, Widmann J, Trausch JJ, Marcano-Vel?zquez JG, Knight R, Batey RT. Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch. J Mol Biol. 2013 May 27; 425(10):1596-611.
Score: 0.084
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Fiegland LR, Garst AD, Batey RT, Nesbitt DJ. Single-molecule studies of the lysine riboswitch reveal effector-dependent conformational dynamics of the aptamer domain. Biochemistry. 2012 Nov 13; 51(45):9223-33.
Score: 0.083
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Garst AD, Porter EB, Batey RT. Insights into the regulatory landscape of the lysine riboswitch. J Mol Biol. 2012 Oct 12; 423(1):17-33.
Score: 0.081
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Trausch JJ, Ceres P, Reyes FE, Batey RT. The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure. 2011 Oct 12; 19(10):1413-23.
Score: 0.076
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Vicens Q, Mondrag?n E, Batey RT. Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection. Nucleic Acids Res. 2011 Oct; 39(19):8586-98.
Score: 0.075
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Garst AD, Edwards AL, Batey RT. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol. 2011 Jun 01; 3(6).
Score: 0.075
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Batey RT. Recognition of S-adenosylmethionine by riboswitches. Wiley Interdiscip Rev RNA. 2011 Mar-Apr; 2(2):299-311.
Score: 0.073
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Montange RK, Mondrag?n E, van Tyne D, Garst AD, Ceres P, Batey RT. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol. 2010 Feb 26; 396(3):761-72.
Score: 0.068
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Reyes FE, Garst AD, Batey RT. Strategies in RNA crystallography. Methods Enzymol. 2009; 469:119-39.
Score: 0.067
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Vicens Q, Gooding AR, Duarte LF, Batey RT. Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification. PLoS One. 2009 Aug 27; 4(8):e6740.
Score: 0.066
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Garst AD, Batey RT. A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta. 2009 Sep-Oct; 1789(9-10):584-91.
Score: 0.066
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Gilbert SD, Reyes FE, Edwards AL, Batey RT. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure. 2009 Jun 10; 17(6):857-68.
Score: 0.065
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Edwards AL, Garst AD, Batey RT. Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol. 2009; 535:135-63.
Score: 0.063
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Gilbert SD, Batey RT. Monitoring RNA-ligand interactions using isothermal titration calorimetry. Methods Mol Biol. 2009; 540:97-114.
Score: 0.063
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Garst AD, H?roux A, Rambo RP, Batey RT. Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem. 2008 Aug 15; 283(33):22347-51.
Score: 0.061
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Stoddard CD, Gilbert SD, Batey RT. Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA. 2008 Apr; 14(4):675-84.
Score: 0.060
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Gilbert SD, Love CE, Edwards AL, Batey RT. Mutational analysis of the purine riboswitch aptamer domain. Biochemistry. 2007 Nov 20; 46(46):13297-309.
Score: 0.058
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Keel AY, Rambo RP, Batey RT, Kieft JS. A general strategy to solve the phase problem in RNA crystallography. Structure. 2007 Jul; 15(7):761-72.
Score: 0.057
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Batey RT, Kieft JS. Improved native affinity purification of RNA. RNA. 2007 Aug; 13(8):1384-9.
Score: 0.057
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Gilbert SD, Mediatore SJ, Batey RT. Modified pyrimidines specifically bind the purine riboswitch. J Am Chem Soc. 2006 Nov 08; 128(44):14214-5.
Score: 0.055
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Gilbert SD, Batey RT. Riboswitches: fold and function. Chem Biol. 2006 Aug; 13(8):805-7.
Score: 0.054
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Gilbert SD, Stoddard CD, Wise SJ, Batey RT. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol. 2006 Jun 09; 359(3):754-68.
Score: 0.053
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Gilbert SD, Montange RK, Stoddard CD, Batey RT. Structural studies of the purine and SAM binding riboswitches. Cold Spring Harb Symp Quant Biol. 2006; 71:259-68.
Score: 0.051
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Gilbert SD, Batey RT. Riboswitches: natural SELEXion. Cell Mol Life Sci. 2005 Nov; 62(21):2401-4.
Score: 0.051
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Kieft JS, Batey RT. A general method for rapid and nondenaturing purification of RNAs. RNA. 2004 Jun; 10(6):988-95.
Score: 0.046
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Doherty EA, Batey RT, Masquida B, Doudna JA. A universal mode of helix packing in RNA. Nat Struct Biol. 2001 Apr; 8(4):339-43.
Score: 0.037
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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, Piatkowski 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, Zyla A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA. 2020 08; 26(8):982-995.
Score: 0.035
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Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 2000 Feb 18; 287(5456):1232-9.
Score: 0.034
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Parsonnet NV, Lammer NC, Holmes ZE, Batey RT, Wuttke DS. The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity. Nucleic Acids Res. 2019 09 05; 47(15):8180-8192.
Score: 0.033
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Batey RT, Williamson JR. Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. RNA. 1998 Aug; 4(8):984-97.
Score: 0.031
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Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferr?-D'Amar? AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 05; 23(5):655-672.
Score: 0.028
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Batey RT, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site. J Mol Biol. 1996 Aug 30; 261(4):536-49.
Score: 0.027
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Batey RT, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition. J Mol Biol. 1996 Aug 30; 261(4):550-67.
Score: 0.027
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Batey RT, Inada M, Kujawinski E, Puglisi JD, Williamson JR. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Res. 1992 Sep 11; 20(17):4515-23.
Score: 0.020
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Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R. Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Chem Biol. 2011 Mar 25; 18(3):324-35.
Score: 0.018
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Cochrane JC, Batey RT, Strobel SA. Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping. RNA. 2003 Oct; 9(10):1282-9.
Score: 0.011
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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