S. Kennedy

发表

Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns.

Brent M. Znosko, D. Turner, S. Kennedy, 2004, Biochemistry.

The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits.

D. Turner, S. Kennedy, T. Krugh, 2006, Biochemistry.

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

D. Turner, R. Kierzek, H. Schwalbe, 2014, Nature Methods.

NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.

D. Turner, F. Major, S. Kennedy, 2011, RNA.

Novel Conformation of an RNA Structural Switch

D. Turner, R. Kierzek, S. Kennedy, 2012, Biochemistry.

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Jonathan L Chen, D. Turner, Ilyas Yildirim, 2012, Biochemistry.

Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

Walter N. Moss, D. Turner, S. Kennedy, 2014, Biochemistry.

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints

Jonathan L Chen, D. Turner, D. Mathews, 2015, Biochemistry.

Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity

S. Kennedy, T. Boggon, M. Hodsdon, 2010, Proceedings of the National Academy of Sciences.

A CA+ Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops†

D. Turner, S. Kennedy, Gang Chen, 2009, Biochemistry.

Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields.

S. Kennedy, C. Nganou, D. McCamant, 2016, The journal of physical chemistry. B.

Flow through clots determines the rate and pattern of fibrinolysis.

C. Francis, S. Kennedy, R. Bryant, 1994, Thrombosis and haemostasis.

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Brent M. Znosko, D. Turner, D. Mathews, 2018, Biochemistry.

High‐resolution MRS in the presence of field inhomogeneity via intermolecular double‐quantum coherences on a 3‐T whole‐body scanner

S. Kennedy, Zhong Chen, J. Zhong, 2010, Magnetic resonance in medicine.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation

D. Turner, D. Mathews, R. Kierzek, 2018, RNA.

Structural Features of a 3′ Splice Site in Influenza A

Jonathan L Chen, D. Turner, S. Kennedy, 2015, Biochemistry.

Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.

D. Turner, S. Kennedy, Jianbo Zhao, 2017, Biochemistry.

Cellular energetics of frozen wood frogs (Rana sylvatica) revealed via NMR spectroscopy

S. Kennedy, J. R. Layne, 2002 .

Synthesis and RNA binding properties of extended nucleobases for triplex-forming peptide nucleic acids.

S. Kennedy, E. Rozners, M. Katkevics, 2019, The Journal of organic chemistry.

Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids.

S. Kennedy, E. Rozners, Venubabu Kotikam, 2019, Chemistry.

NMR Reveals that GU Base Pairs Flanking Internal Loops can Adopt Diverse Structures

D. Turner, S. Kennedy, K. D. Berger, 2019 .

Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

D. Turner, Sandro Bottaro, K. Lindorff-Larsen, 2017, bioRxiv.

A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs.

S. Kennedy, M. Egli, A. Smith, 2018, ACS chemical biology.

Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange.

S. Kennedy, S. Koide, Shude Yan, 2002, Journal of molecular biology.

Nuclear Magnetic Resonance

S. Kennedy, P. Knauf, D. Liu, 2005 .

Identification of a human heavy chain antibody fragment directed against human platelet alloantigen 1a by phage display library.

H. Inoko, S. Kennedy, J. Casella, 2008, Tissue antigens.

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

Harry A. Stern, Scott D. Kennedy, Douglas H. Turner, 2010, Journal of chemical theory and computation.

The magnetic field dependence of water proton T1 in aqueous solutions: implications for magnetic imaging contrast media.

S. Kennedy, R. Bryant, C. Polnaszek, 1984, Medical physics.

Synthesis, biophysical studies and RNA interference activity of RNA having three consecutive amide linkages.

D. Leake, S. Kennedy, E. Rozners, 2014, Organic & biomolecular chemistry.

Theoretical studies of the effect of the dipolar field in multiple spin-echo sequences with refocusing pulses of finite duration.

S. Kennedy, E. Kwok, J. Zhong, 2007, Journal of magnetic resonance.

Manganese-deoxyribonucleic acid binding modes. Nuclear magnetic relaxation dispersion results.

S. Kennedy, R. Bryant, 1986, Biophysical journal.

Proton magnetic relaxation in aqueous glycerol solutions containing manganese(II) Ion

S. Kennedy, R. Bryant, 1985, Magnetic resonance in medicine.

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

D. Turner, Ilyas Yildirim, S. Kennedy, 2011, The journal of physical chemistry. B.

Conformational analysis of chirally deuterated tunicamycin as an active site probe of UDP-N-acetylhexosamine:polyprenol-P N-acetylhexosamine-1-P translocases.

F. Momany, S. Kennedy, M. Appell, 2004, Biochemistry.

Theoretical formalism and experimental confirmation of intermolecular dipolar effects under time-averaged magnetic field gradients

S. Kennedy, Zhong Chen, J. Zhong, 1999 .

Selenium-77 NMR and crystallographic studies of selenazofurin and its 5-amino derivative

S. Kennedy, W. Hennen, B. Goldstein, 1990 .

Infrared laser induced heterogeneous reactions: 2-propanol with cupric oxide

S. Kennedy, D. Hogenkamp, William D. Farneth, 1983 .

Carbon-13 spin-echo spectroscopy as a measure of slow motions in solid polymers

P. M. Henrichs, S. Kennedy, R. Bryant, 1986 .

High-resolution calcium-43 NMR in solids

S. Kennedy, R. Bryant, S. Ganapathy, 1987 .

Applications of multinuclear NMR in the solid state to structural and dynamical problems in macromolecular chemistry.

S. Kennedy, A. Blaurock, W. R. Croasmun, 1990, Basic life sciences.

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

Harry A. Stern, Scott D. Kennedy, Douglas H. Turner, 2011, Journal of chemical theory and computation.

Nuclear Magnetic Resonance of Single Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations.

D. Turner, S. Kennedy, Jianbo Zhao, 2020, Journal of chemical theory and computation.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

Kresten Lindorff-Larsen, Giovanni Bussi, Sandro Bottaro, 2018, Science Advances.

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

D. Turner, R. Kierzek, Ilyas Yildirim, 2015, Journal of chemical theory and computation.

Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU)

D. Turner, R. Kierzek, Ilyas Yildirim, 2013, The journal of physical chemistry. B.

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

D. Turner, S. Kennedy, P. Bevilacqua, 2013, Biochemistry.

Amides as excellent mimics of phosphate linkages in RNA.

S. Kennedy, C. Selvam, E. Rozners, 2011, Angewandte Chemie.

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

S. Kennedy, M. Egli, A. Smith, 2017, Nucleic acids research.

Inherited pelvic organ prolapse in the mouse: preliminary evaluation of a new murine model

Aimee M. Johnson, S. Kennedy, J. Reeder, 2008, International Urogynecology Journal.

2‐Methoxypyridine as a Thymidine Mimic in Watson–Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies

S. Kennedy, E. Rozners, Irina Novosjolova, 2017, Chembiochem : a European journal of chemical biology.

Use of carbon-13 stimulated echoes for measurement of nitrogen-14 spin relaxation in polycrystalline amino acids

S. Kennedy, R. Bryant, 1989 .

NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.

D. Turner, S. Schroeder, S. Kennedy, 2007, Biochemistry.

Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites.

S. Kennedy, C. Kielkopf, Wenhua Wang, 2019, Biochemical and biophysical research communications.

The role of HLA antibodies in neonatal thrombocytopenia: a prospective study.

S. Kennedy, K. Blakemore, P. Bray, 1996, Tissue antigens.

Studies using immobilized platelet glycoproteins for detection of platelet alloantibodies.

S. Kennedy, T. Kickler, T. Kickler, 1995, American journal of clinical pathology.

Structural effects of hydration: Studies of lysozyme by 13C solids nmr

S. Kennedy, R. Bryant, R G Bryant, 1990, Biopolymers.

Secondary structure prediction for RNA sequences including N6-methyladenosine

D. Mathews, R. Kierzek, S. Kennedy, 2021, Nature Communications.

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′GAGU/3′UGAG Loop Can Be Dramatically Different from Others, Including 5′AAGU/3′UGAA†

D. Turner, R. Kierzek, S. Kennedy, 2010, Biochemistry.

Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.

Scott D Kennedy, David H Mathews, Douglas H Turner, 2011, Journal of chemical theory and computation.

Measurement of in vitro P-selectin expression by flow cytometry.

S. Kennedy, T. Kickler, Y. Igarashi, 1997, American journal of clinical pathology.

35Cl nuclear magnetic resonance line broadening shows that eosin-5-maleimide does not block the external anion access channel of band 3.

S. Kennedy, P. Knauf, D. Liu, 1995, Biophysical journal.

Solvent suppression in high-resolution proton nuclear magnetic resonance based on control of transverse relaxation rate.

S. Kennedy, R. Bryant, T. M. Eads, 1986, Analytical chemistry.

Source of transport site asymmetry in the band 3 anion exchange protein determined by NMR measurements of external Cl- affinity.

S. Kennedy, P. Knauf, D. Liu, 1996, Biochemistry.

Persistence of external chloride and DIDS binding after chemical modification of Glu-681 in human band 3.

S. Kennedy, P. Knauf, C. Wu, 1999, American Journal of Physiology.

Detection of Cl- binding to band 3 by double-quantum-filtered 35Cl nuclear magnetic resonance.

S. Kennedy, P. Knauf, D. Liu, 1996, Biophysical journal.

Quantitative MRI of Gd‐DTPA uptake in tumors: Response to photo dynamic therapy

T. Foster, S. Kennedy, R. Bryant, 1994, Magnetic resonance in medicine.

Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex.

Michael R. Green, J. Wedekind, S. Kennedy, 2013, Structure.

NMR Methods for Characterization of RNA Secondary Structure.

Scott D Kennedy, S. Kennedy, 2016, Methods in molecular biology.

iDQC MRI weighted by longitudinal relaxation in the rotating frame

S. Kennedy, Zhong Chen, J. Zhong, 2006, Magnetic resonance in medicine.

Comparison of agarose and cross-linked protein gels as magnetic resonance imaging phantoms.

S. Kennedy, R. Bryant, C. Lester, 1991, Magnetic resonance imaging.

Synthesis and properties of triazole-linked RNA.

S. Kennedy, C. Selvam, E. Rozners, 2011, Bioorganic & medicinal chemistry letters.

Hetergeneous tumour response to photodynamic therapy assessed by in vivo localised 31P NMR spectroscopy.

S. Kennedy, R. Bryant, S. Gibson, 1991, British Journal of Cancer.

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

D. Turner, D. Mathews, T. Xia, 2007, Biochemistry.

Spin-spin relaxation time (T2) dependence in MR saturation- and inversion- recovery images.

F. Earnest, R. Ehman, S. Kennedy, 1984, AJR. American journal of roentgenology.

Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.

D. Turner, S. Kennedy, K. D. Berger, 2019, Biochemistry.

A Sample-Shuttle Nuclear-Magnetic-Relaxation-Dispersion Spectrometer

S. Kennedy, S. Swanson, 1993 .

Cytokine induction of platelet activation.

S. Kennedy, Dietmar Kuhl, J. Lumadue, 1996, American journal of clinical pathology.

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA.

S. Kennedy, Jianbo Zhao, Douglas H Turner, 2022, Journal of chemical theory and computation.

NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon

David H. Mathews, Scott D. Kennedy, Douglas H. Turner, 2008, Journal of the American Chemical Society.

Solution structure of an RNA internal loop with three consecutive sheared GA pairs.

Brent M. Znosko, Brent M Znosko, Scott D Kennedy, 2005, Biochemistry.

Hydration effects on dynamics of polyglycine and sodium poly(L‐glutamate)

S. Kennedy, R. Bryant, 1990, Biopolymers.

Secondary structure prediction for RNA sequences including N6-methyladenosine

D. Mathews, R. Kierzek, S. Kennedy, 2022, Nature Communications.