S. Butcher

发表

Open access, freely available online Primer Pseudoknots: RNA Structures with Diverse Functions

D. W. Staple, S. Butcher, 2022 .

Spliceosome assembly in the absence of stable U4/U6 RNA pairing

S. Butcher, J. Burke, D. Brow, 2015, RNA.

The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks.

S. Butcher, A. Pyle, 2011, Accounts of chemical research.

U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

Dipali G. Sashital, Dipali G Sashital, Gabriel Cornilescu, 2004, Nature Structural &Molecular Biology.

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.

S. Butcher, D. Brow, E. Montemayor, 2017, Acta crystallographica. Section D, Structural biology.

Structure of the yeast U2/U6 snRNA complex.

Dipali G. Sashital, Yun-Xing Wang, S. Butcher, 2012, RNA.

Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.

Lawrence J. Clos, S. Butcher, V. Venditti, 2009, Journal of molecular biology.

The spliceosome as ribozyme hypothesis takes a second step

S. Butcher, 2009, Proceedings of the National Academy of Sciences.

Corrigendum: U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

Dipali G. Sashital, Gabriel Cornilescu, S. Butcher, 2005, Nature Structural &Molecular Biology.

Structural basis for a lethal mutation in U6 RNA.

Dipali G. Sashital, S. Butcher, S. V. Van Doren, 2003, Biochemistry.

N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA

S. Butcher, N. Sherer, B. Miller, 2015, ACS chemical biology.

Reconstitution of Hairpin Ribozyme Activity following Separation of Functional Domains (*)

S. Butcher, J. Heckman, John M. Burke, 1995, The Journal of Biological Chemistry.

Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop.

D. W. Staple, S. Butcher, Ryan J. Marcheschi, 2007, Journal of molecular biology.

Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA.

S. Butcher, Ryan J. Marcheschi, K. Mouzakis, 2009, ACS chemical biology.

Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes

S. Butcher, D. Brow, E. Montemayor, 2020, bioRxiv.

Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA

S. Butcher, D. Brow, E. Montemayor, 2018, Nature Communications.

Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities

S. Butcher, W. M. Westler, D. Brow, 2017, Nature Communications.

Pathogenic TFG Mutations Underlying Hereditary Spastic Paraplegia Impair Secretory Protein Trafficking and Axon Fasciculation

S. Butcher, S. Stagg, A. Audhya, 2018, Cell reports.

Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation.

S. Butcher, R. Gourse, W. Ross, 2012, Genes & development.

Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes.

J. Freed, S. Butcher, P. Borbat, 2004, Journal of the American Chemical Society.

Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

Gabriel Cornilescu, S. Butcher, J. Burke, 2015, Proceedings of the National Academy of Sciences.

Solution structure of a GAAA tetraloop receptor RNA

J. Feigon, S. Butcher, T. Dieckmann, 1997, The EMBO journal.

Solution structure of the HIV-1 frameshift inducing stem-loop RNA.

D. W. Staple, S. Butcher, 2003, Nucleic acids research.

Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors.

S. Butcher, M. Tonelli, J. Vergara, 2020, Biochemistry.

Targeting frameshifting in the human immunodeficiency virus

S. Butcher, L. Brakier-Gingras, J. Charbonneau, 2012, Expert opinion on therapeutic targets.

Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication.

S. Butcher, Ryan J. Marcheschi, M. Tonelli, 2011, ACS chemical biology.

Measuring the Kinetics of Molecular Association by Isothermal Titration Calorimetry.

S. Butcher, K. Vander Meulen, R. Trievel, 2016, Methods in enzymology.

Faculty Opinions recommendation of Control of gene expression by a natural metabolite-responsive ribozyme.

S. Butcher, 2004 .

The life of U6 small nuclear RNA, from cradle to grave

S. Butcher, D. Brow, A. Didychuk, 2018, RNA.

Optimization of triple-resonance HCN experiments for application to larger RNA oligonucleotides.

J. Feigon, S. Butcher, V. Sklenar, 1998, Journal of magnetic resonance.

Structure and function of the small ribozymes.

S. Butcher, 2001, Current opinion in structural biology.

Solution structure of the loop B domain from the hairpin ribozyme

Frédéric H.-T. Allain, F. Allain, J. Feigon, 1999, Nature Structural Biology.

Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex.

S. Butcher, John M. Burke, 1994, Journal of molecular biology.

A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme.

S. Butcher, John M. Burke, 1994, Biochemistry.

Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme.

S. Butcher, John M. Burke, A. Berzal-Herranz, 1993, The EMBO journal.

Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates.

S. Butcher, John M. Burke, A. Berzal-Herranz, 1993, Genes & development.

Structural Analysis and Modifications of the Hairpin Ribozyme

S. Butcher, J. Burke, B. Sargueil, 1996 .

Deoxyoligonucleotides bearing neutral analogs of phosphodiester linkages recognize duplex DNA via triple-helix formation

S. Butcher, K. Lin, M. Matteucci, 1991 .

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

S. Butcher, J. Burke, K. Manthei, 2015, Proceedings of the National Academy of Sciences.

RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex.

L. Scott, S. Butcher, L. Jaeger, 2005, Journal of molecular biology.

A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III

J. Feigon, S. Butcher, G. Chanfreau, 2001, The EMBO journal.

Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA

S. Butcher, D. Brow, E. Montemayor, 2018, Nature Communications.

Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy

S. Butcher, H. Kaur, E. Montemayor, 2022, bioRxiv.

Dynamic motions of the HIV-1 frameshift site RNA.

S. Butcher, H. Al‐Hashimi, Elizabeth A. Dethoff, 2015, Biophysical journal.

A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation.

S. Butcher, D. Brow, C. J. McManus, 2007, RNA.

Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element.

D. W. Staple, S. Butcher, Samuel E Butcher, 2005, Journal of molecular biology.

An Atypical RNA Quadruplex Marks RNAs as Vectors for Gene Silencing

M. Wickens, Scott Kennedy, S. Butcher, 2021, bioRxiv.

Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.

S. Butcher, J. Keck, N. J. Reiter, 2009, Journal of molecular biology.

DNA mimicry by a high-affinity anti-NF-κB RNA aptamer

S. Butcher, N. J. Reiter, L. Maher, 2007, Nucleic acids research.

A multi-step model for facilitated unwinding of the yeast U4/U6 RNA duplex

S. Butcher, D. Brow, A. Hoskins, 2016, Nucleic acids research.

Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution

S. Butcher, D. Brow, E. Montemayor, 2014, Nature Structural & Molecular Biology.

Core structure of the U6 snRNP at 1.7 Å resolution

S. Butcher, D. Brow, E. Montemayor, 2014, Nature Structural &Molecular Biology.

Structure and interactions of the first three RNA recognition motifs of splicing factor prp24.

G. Phillips, E. Bae, S. Butcher, 2007, Journal of molecular biology.

Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human.

Dipali G. Sashital, Gabriel Cornilescu, S. Butcher, 2007, RNA.

Solution structure of the conserved 16 S-like ribosomal RNA UGAA tetraloop.

J. Feigon, S. Butcher, T. Dieckmann, 1997, Journal of molecular biology.

Investigating RNAs Involved in Translational Control by NMR and SAXS

S. Butcher, J. Burke, K. Mouzakis, 2012 .

Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR.

S. Butcher, J. Markley, F. Abildgaard, 2005, Journal of molecular biology.

Solution nuclear magnetic resonance probing of cation binding sites on nucleic acids.

J. Feigon, S. Butcher, L. Finger, 2001, Methods in enzymology.

Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24.

S. Butcher, D. Brow, N. J. Reiter, 2010, RNA.

Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24.

S. Butcher, D. Brow, N. J. Reiter, 2010, RNA.

HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

S. Butcher, K. Vander Meulen, K. Mouzakis, 2012, Nucleic acids research.

Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

S. Butcher, N. Sherer, P. García-Miranda, 2016, Journal of Virology.

Structure and Dynamics of the HIV-1 Frameshift Element RNA

K. Weeks, S. Butcher, R. Gorelick, 2014, Biochemistry.

Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1

S. Butcher, Q. Cui, E. Montemayor, 2018, Nucleic acids research.

Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly

S. Butcher, D. Brow, E. Montemayor, 2015, Nucleic acids research.

Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding.

J. Szostak, J. Feigon, S. Butcher, 1997, Journal of molecular biology.

Through-bond correlation of imino and aromatic resonances in 13C-,15N-labeled RNA via heteronuclear TOCSY

J. Feigon, S. Butcher, V. Sklenar, 1996, Journal of biomolecular NMR.

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

S. Butcher, E. Montemayor, Samuel M. Hayes, 2019, Nucleic acids research.

Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.

S. Butcher, N. J. Reiter, A. Allmann, 2003, RNA.

Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities

S. Butcher, W. M. Westler, D. Brow, 2017, Nature Communications.

Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering.

Jinbu Wang, Xiaobing Zuo, Yun-Xing Wang, 2010, Methods.

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry

S. Butcher, K. Vander Meulen, Kirk A. Vander Meulen, 2011, Nucleic acids research.

Role of metal ions in the tetraloop-receptor complex as analyzed by NMR.

S. Butcher, M. Tonelli, T. Foster, 2006, RNA.

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking

S. Butcher, S. Zimmerman, E. Montemayor, 2019, Acta crystallographica. Section F, Structural biology communications.

Conformational flexibility in the enterovirus RNA replication platform

Gabriel Cornilescu, S. Butcher, J. Burke, 2018, RNA.

Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study.

J. Feigon, S. Butcher, P. Qin, 2001, Biochemistry.

tRNA-mimicry in IRES-mediated translation and recoding

S. Butcher, E. Jan, 2016, RNA biology.

Perturbing HIV-1 Ribosomal Frameshifting Frequency Reveals a cis Preference for Gag-Pol Incorporation into Assembling Virions

S. Butcher, P. Ahlquist, N. Sherer, 2021, Journal of virology.

Guanidinoneomycin B Recognition of an HIV‐1 RNA Helix

D. W. Staple, S. Butcher, V. Venditti, 2007, Chembiochem : a European journal of chemical biology.

Towards understanding the catalytic core structure of the spliceosome.

S. Butcher, D. Brow, S E Butcher, 2005, Biochemical Society transactions.

Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure

S. Butcher, D. Brow, A. Allmann, 2002, Nature Structural Biology.

Nucleic Acid Structure Characterization by Small Angle X‐Ray Scattering (SAXS)

S. Butcher, J. Burke, 2012, Current protocols in nucleic acid chemistry.

Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change.

S. Butcher, F. Abildgaard, N. J. Reiter, 2004, Biochemistry.

Integrative NMR for biomolecular research

Gabriel Cornilescu, S. Butcher, W. M. Westler, 2016, Journal of biomolecular NMR.

Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

Aaron A Hoskins, Lauren A Michael, Gabriel Cornilescu, 2016, Journal of molecular biology.

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Lawrence J. Clos, S. Butcher, J. Markley, 2012, Journal of biomolecular NMR.

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Dipali G. Sashital, S. Butcher, A. Palmer, 2004, Nature Structural &Molecular Biology.

Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL

S. Butcher, V. Venditti, N. Niccolai, 2007, Nucleic acids research.

Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data.

C. Schwieters, Yun-Xing Wang, S. Butcher, 2008, Journal of the American Chemical Society.

Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.

F. Allain, J. Feigon, S. Butcher, 2000, Biochemistry.

Adenine protonation in domain B of the hairpin ribozyme.

J. Feigon, S. Butcher, S. Ravindranathan, 2000, Biochemistry.

A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop

Lawrence J. Clos, S. Butcher, D. Brow, 2011, Nucleic acids research.

Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.

S. Butcher, M. Record, K. Vander Meulen, 2008, Journal of molecular biology.

Core structure of the U 6 snRNP at 1 . 7 Å resolution

S. Butcher, D. Brow, E. Montemayor, 2016 .

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Lawrence J. Clos, S. Butcher, J. Markley, 2012, Journal of Biomolecular NMR.

Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

Gabriel Cornilescu, S. Butcher, J. Burke, 2016, Journal of molecular biology.