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Publications

2017

Montemayor EJ, Didychuk AL, Liao H, Hu P, Brow DA, Butcher SE. (2017) Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.Acta Crystallogr D Struct Biol. PMID: 28045380 [PubMed]

2016

Rodgers ML, Didychuk AL, Butcher SE, Brow DA, Hoskins AA. (2016) A multi-step model for facilitated unwinding of the yeast U4/U6 RNA duplex. Nucleic Acids Res. PMCID: 27484481 [PubMed]

Butcher SE, Jan E. (2016) tRNA-mimicry in IRES-mediated translation and recoding. RNA Biol. PMID: 27654067. [PubMed]

Garcia-Miranda P, Becker JT, Benner BE, Blume A, Sherer NM, Butcher SE. (2016) Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity. J Virol. 90(15):6906-17. PMCID: PMC4944283 [PubMed]

Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. (2016) Integrative NMR for biomolecular research. J Biomol NMR. 64(4):307-32. PMCID: PMC4861749 [PubMed]

Hilimire TA, Bennett RP, Stewart RA, Garcia-Miranda P, Blume A, Becker J, Sherer N, Helms ED, Butcher SE, Smith HC, Miller BL. (2016) N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNAACS Chem Biol  1(1):88-94 [PubMed]

Vander Meulen KA, Horowitz S, Trievel RC, Butcher SE. (2016) Measuring the Kinetics of Molecular Association by Isothermal Titration Calorimetry. Methods Enzymol. 567:181-213. [PubMed]

Didychuk AL, Montemayor EJ, Brow DA, Butcher SE. (2016) Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly. Nucleic Acids Res. 44(3):1398-410. PMCID: PMC4756825 [PubMed]

Cornilescu G, Didychuk AL, Rodgers ML, Michael LA, Burke JE, Montemayor EJ, Hoskins AA, Butcher SE. (2016) Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA. J Mol Biol.
428(5 Pt A):777-789. PMCID: PMC4790120 [PubMed]

2015

Au HH, Cornilescu G, Mouzakis KD, Ren Q, Burke JE, Lee S, Butcher SE, Jan E. (2015) Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci USA 112 (47):E6446-55. [PubMed]

Hilimire TA, Bennett RP, Stewart RA, Garcia-Miranda P, Blume A, Becker J, Sherer N, Helms ED, Butcher SE, Smith HC, Miller BL. (2015) N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA. ACS Chem Biol  1(1):88-94 [PubMed]

Burke JE, Butcher SE, Brow DA. (2015) Spliceosome assembly in the absence of stable U4/U6 RNA pairing. RNA 21(5):923-34. [PubMed]

Manthei KA, Hill MC, Burke JE, Butcher SE, Keck JL. (2015) Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases. Proc Natl Acad Sci USA 112 (14):4292-7. [PubMed]

Mouzakis KD, Dethoff EA, Tonelli M, Al-Hashimi H, Butcher SE. (2015) Dynamic motions of the HIV-1 frameshift site RNA. Biophys J 108(3):644-54. [PubMed]

2014

Low JT, Garcia-Miranda P, Mouzakis KD, Gorelick RJ, Butcher SE, Weeks KM. (2014). Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry. 53(26):4282-91. [PubMed]

Montemayor, EJ, Curran EC, Liao HH, Andrews KL, Treba CN, Butcher SE, Brow DA. (2014). Core structure of the U6 small nuclear ribonucleoprotein at 1.7-A resolution. Nat Struct Mol Biol. 21(6):544-551. [PubMed]

2013

Mouzakis KD, Lang AL, Vander Meulen KA, Easterday PD, Butcher SE. (2013). HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome. Nucleic Acids Res. 41(3):1901-1913. [PubMed]

2012

Burke JE, Butcher SE. (2012). Nucleic acid structure characterization by small angle X-ray scattering (SAXS). Curr Protoc Nucleic Acid Chem. Chapter 7, Unit 7.18. [PubMed]

Lennon CW, Ross W, Martin-Tumasz S, Toulokhonov I, Vrentas CE, Rutherford ST, Lee JH, Butcher SE, Gourse RL. (2012). Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation. Genes Dev. 26(23):2634-2646. [PubMed]

Bahrami A, Clos LJ 2nd, Markley JL, Butcher SE, Eghbalnia HR. (2012). RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. J Biomol NMR. 52(4):289-302. [PubMed]

Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE. (2012). Structure of the yeast U2/U6 snRNA complex. RNA. 18(4):673-683. [PubMed]

Brakier-Gingras L, Charbonneau J, Butcher SE. (2012). Targeting frameshifting in the human immunodeficiency virus. Expert Opin Ther Targets.16(3):249-258. [PubMed]

Vander Meulen KA, Butcher SE. (2012). Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry. Nucleic Acids Res. 40(5):2140-2151. [PubMed]

2011

Butcher SE, Pyle AM. (2011). The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res. 44(12):1302-1311. [PubMed]

Martin-Tumasz S, Richie AC, Clos LJ 2nd, Brow DA, Butcher SE. (2011). A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop. Nucleic Acids Res. 39(17):7837-7847. [PubMed]

Marcheschi RJ, Tonelli M, Kumar A, Butche SE. (2011). Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication. ACS Chem Biol. 6(8):857-864. [PubMed]

Butcher SE. (2011). The spliceosome and its metal ions. Met Ions Life Sci. 9:253-251. [PubMed]

2010

Wang YX, Zuo X, Wang J, Yu P, Butcher SE. (2010). Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods. 52(2):180-191. [PubMed]

Martin-Tumasz S, Reiter NJ, Brow DA, Butcher SE. (2010). Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24. RNA. 16(4):792-804. [PubMed]

2009

Martin-Tumasz S, Butcher SE. (2009). (1)H, (13)C and (15)N resonance assignments of a ribonucleoprotein complex consisting of Prp24-RRM2 bound to a fragment of U6 RNA. Biomol NMR Assign. 3(2):227-30. [PubMed]

Marcheschi RJ, Mouzakis KD, Butcher SE. (2009). Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA. ACS Chem Biol. 4(10):844-54 [PubMed]

Butcher SE. (2009). The spliceosome as ribozyme hypothesis takes a second step. Proc Natl Acad Sci USA. 106(30):12211-2. [PubMed]

Venditti V, Clos L 2nd, Niccolai N, Butcher SE. (2009). Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping. J Mol Biol. 391(5):894-905. [PubMed]

Shereda RD, Reiter NJ, Butcher SE, Keck JL. (2009). Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus. J Mol Biol. 386(3):612-25. [PubMed]

2008

Vander Meulen KA, Davis JH, Foster TR, Record MT Jr, Butcher SE. (2008). Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing. J Mol Biol. 384(3):702-17. [PubMed]

Zuo X, Wang J, Foster TR, Schwieters CD, Tiede DM, Butcher SE, Wang YX. (2008). Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc. 130(11):3292-3. [PubMed]

Reiter NJ, Maher LJ 3rd, Butcher SE. (2008). DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer. Nucleic Acids Res. 36(4):1227-36. [PubMed]

Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE. (2008). Guanidinoneomycin B recognition of an HIV-1 RNA helix. Chembiochem. 9(1):93-102. [PubMed]

Venditti V, Niccolai N, Butcher SE. (2008). Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucleic Acids Res. 36(4):e20. [PubMed]

2007

McManus CJ, Schwartz ML, Butcher SE, Brow DA. (2007). A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA. 13(12):2252-65. [PubMed]

Marcheschi RJ, Staple DW, Butcher SE.(2007). Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop. J Mol Biol. 373(3):652-63. [PubMed]

Bae E, Reiter NJ, Bingman CA, Kwan SS, Lee D, Phillips GN Jr, Butcher SE, Brow DA. (2007). Structure and interactions of the first three RNA recognition motifs of splicing factor prp24. J Mol Biol. 367(5):1447-58. [PubMed]

Sashital DG, Venditti V, Angers CG, Cornilescu G, Butcher SE.(2007). Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA. 13(3):328-38. [PubMed]

Davis JH, Foster TR, Tonelli M, Butcher SE. (2007). Role of metal ions in the tetraloop-receptor complex as analyzed by NMR. RNA. 13(1):76-86. [PubMed]

2006

Sashital DG, Butcher SE. (2006). Flipping off the riboswitch: RNA structures that control gene expression. ACS Chem Biol. 1(6):341-5. Review. [PubMed]

Reiter NJ, Lee D, Wang YX, Tonelli M, Bahrami A, Cornilescu CC, Butcher SE. (2006). Resonance assignments for the two N-terminal RNA recognition motifs (RRM) of the S. cerevisiae pre-mRNA processing protein Prp24. J Biomol NMR. 36 Suppl 1:58. [PubMed]

2005

Blad H, Reiter NJ, Abildgaard F, Markley JL, Butcher SE. (2005). Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR. J Mol Biol. 353(3):540-55. [PubMed]

Davis JH, Tonelli M, Scott LG, Jaeger L, Williamson JR, Butcher SE. (2005). RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol. 2005 351(2):371-82. Erratum in: J Mol Biol. (2006) 360(3):742. [PubMed]

Staple DW, Butcher SE. (2005). Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3(6):e213. [PubMed]

Staple DW, Butcher SE. (2005). Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J Mol Biol. 2349(5):1011-23. [PubMed]

Butcher SE, Brow DA. (2005). Towards understanding the catalytic core structure of the spliceosome. Biochem Soc Trans. 33(Pt 3):447-9. Review. [PubMed]

2004

Sashital DG, Cornilescu G, McManus CJ, Brow DA, Butcher SE. (2004). U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat Struct Mol Biol. 11(12):1237-42. Erratum in: Nat Struct Mol Biol. (2005) 12(1):99. [PubMed]

Reiter NJ, Blad H, Abildgaard F, Butcher SE. (2004). Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change. Biochemistry. 43(43):13739-47. [PubMed]

Borbat PP, Davis JH, Butcher SE, Freed JH. (2004). Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes. J Am Chem Soc. 126(25):7746-7. [PubMed]

Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. (2004). Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nat Struct Mol Biol. 11(2):187-92. [PubMed]

Butcher SE, Wickens M. (2004). STAR-studded circuitry. Nat Struct Mol Biol. 11(1):2-3. [PubMed]

2003

Staple DW, Butcher SE. (2003). Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Nucleic Acids Res. 31(15):4326-31. [PubMed]

Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE. (2003). Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification. RNA. 9(5):533-42. [PubMed]

Sashital DG, Allmann AM, Van Doren SR, Butcher SE. (2003). Structural basis for a lethal mutation in U6 RNA. Biochemistry. 42(6):1470-7. [PubMed]

2002

Huppler A, Nikstad LJ, Allmann AM, Brow DA, Butcher SE. (2002). Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure. Nat Struct Biol. 9(6):431-5. [PubMed]