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Scott D. Kennedy, Ph.D.


Showing all 80 journal articles & 0 books available

Journal Articles

Kennedy SD, Bauer WJ, Wang W, Kielkopf CL. "Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites." Biochemical and biophysical research communications.. 2019 Feb 20; Epub 2019 Feb 20.

Kotikam V, Kennedy SD, MacKay JA, Rozners E. "Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids." Chemistry : a European journal.. 2019 Feb 11; Epub 2019 Feb 11.

"Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures." Biochemistry.. 2019 Jan 31; Epub 2019 Jan 31.

Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews D. "Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation." RNA.. 2018 May 0; 24(5):656-672. Epub 2018 Feb 06.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. "Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations." Science advances.. 2018 May 0; 4(5):eaar8521. Epub 2018 May 18.

Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH. "Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops." Biochemistry.. 2018 Apr 10; 57(14):2121-2131. Epub 2018 Mar 23.

Hardcastle T, Novosjolova I, Kotikam V, Cheruiyot SK, Mutisya D, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E. "A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs." ACS chemical biology.. 2018 Mar 16; 13(3):533-536. Epub 2018 Jan 10.

Novosjolova I, Kennedy SD, Rozners E. "2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies." Chembiochem : a European journal of chemical biology.. 2017 Nov 2; 18(21):2165-2170. Epub 2017 Sep 26.

Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E. "Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs." Nucleic acids research.. 2017 Aug 21; 45(14):8142-8155.

Kauffmann AD, Kennedy SD, Zhao J, Turner DH. "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." Biochemistry.. 2017 Jul 25; 56(29):3733-3744. Epub 2017 Jul 12.

Nganou C, Kennedy SD, McCamant DW. "Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields." The journal of physical chemistry. B. 2016 Feb 25; 120(7):1250-8. Epub 2016 Feb 17.

Kennedy SD. "NMR Methods for Characterization of RNA Secondary Structure." Methods in molecular biology.. 2016 1490:253-64.

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. "Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints." Biochemistry.. 2015 Nov 17; 54(45):6769-82. Epub 2015 Nov 03.

Condon DE, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH. "Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics." Journal of chemical theory and computation.. 2015 Jun 9; 11(6):2729-2742. Epub 2015 Apr 16.

Chen JL, Kennedy SD, Turner DH. "Structural features of a 3' splice site in influenza a." Biochemistry.. 2015 Jun 2; 54(21):3269-85. Epub 2015 May 21.

Jiang T, Kennedy SD, Moss WN, Kierzek E, Turner DH. "Secondary structure of a conserved domain in an intron of influenza A M1 mRNA." Biochemistry.. 2014 Aug 19; 53(32):5236-48. Epub 2014 Aug 06.

Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RK, Turner DH, Das R. "Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts." Nature methods.. 2014 Apr 0; 11(4):413-6. Epub 2014 Mar 02.

Tanui P, Kennedy SD, Lunstad BD, Haas A, Leake D, Rozners E. "Synthesis, biophysical studies and RNA interference activity of RNA having three consecutive amide linkages." Organic & biomolecular chemistry.. 2014 Feb 28; 12(8):1207-10.

Condon DE, Yildirim I, Kennedy SD, Mort BC, Kierzek R, Turner DH. "Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU)." The journal of physical chemistry. B. 2014 Feb 6; 118(5):1216-28. Epub 2014 Jan 24.

Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH. "Correction to NMR of CCCC RNA Reveals a Right-Handed Helix and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics." Biochemistry.. 2013 May 14; 52(19):3390-2. Epub 2013 Apr 29.

Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH. "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." Biochemistry.. 2013 Feb 12; 52(6):996-1010. Epub 2013 Jan 29.

Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL. "Structure of phosphorylated SF1 bound to U2AF?? in an essential splicing factor complex." Structure.. 2013 Feb 5; 21(2):197-208. Epub 2012 Dec 27.

Kennedy SD, Kierzek R, Turner DH. "Novel conformation of an RNA structural switch." Biochemistry.. 2012 Nov 20; 51(46):9257-9. Epub 2012 Nov 12.

Chen JL, Dishler AL, Kennedy SD, Yildirim I, Liu B, Turner DH, Serra MJ. "Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters." Biochemistry.. 2012 Apr 24; 51(16):3508-22. Epub 2012 Apr 10.

Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH. "Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs." Journal of chemical theory and computation.. 2012 Jan 10; 8(1):172-181. Epub 2011 Dec 01.

Van Nostrand KP, Kennedy SD, Turner DH, Mathews DH. "Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change." Journal of chemical theory and computation.. 2011 Nov 8; 7(11):3779-3792.

Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH. "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." RNA.. 2011 Sep 0; 17(9):1664-77. Epub 2011 Jul 21.

Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH. "Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised ? torsions." The journal of physical chemistry. B. 2011 Jul 28; 115(29):9261-70. Epub 2011 Jul 01.

Mutisya D, Selvam C, Kennedy SD, Rozners E. "Synthesis and properties of triazole-linked RNA." Bioorganic & medicinal chemistry letters.. 2011 Jun 1; 21(11):3420-2. Epub 2011 Apr 05.

Selvam C, Thomas S, Abbott J, Kennedy SD, Rozners E. "Amides as excellent mimics of phosphate linkages in RNA." Angewandte Chemie.. 2011 Feb 25; 50(9):2068-70. Epub 2011 Jan 21.

Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD. "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." Biochemistry.. 2010 Jul 13; 49(27):5817-27.

Petri ET, Celic A, Kennedy SD, Ehrlich BE, Boggon TJ, Hodsdon ME. "Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity." Proceedings of the National Academy of Sciences of the United States of America.. 2010 May 18; 107(20):9176-81. Epub 2010 May 03.

Yildirim I, Stern HA, Kennedy SD, Tubbs JD, Turner DH. "Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine." Journal of chemical theory and computation.. 2010 May 11; 6(5):1520-1531. Epub 2010 Apr 16.

Chen G, Kennedy SD, Turner DH. "A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops." Biochemistry.. 2009 Jun 23; 48(24):5738-52.

McNanley AR, Johnson AM, Flynn MK, Wood RW, Kennedy SD, Reeder JE. "Inherited pelvic organ prolapse in the mouse: preliminary evaluation of a new murine model." International urogynecology journal and pelvic floor dysfunction.. 2009 Jan 0; 20(1):19-25. Epub 2008 Sep 19.

Hart JM, Kennedy SD, Mathews DH, Turner DH. "NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon." Journal of the American Chemical Society.. 2008 Aug 6; 130(31):10233-9. Epub 2008 Jul 10.

Gu T, Kennedy SD, Chen Z, Schneider KA, Zhong J. "Functional MRI at 3T using intermolecular double-quantum coherence (iDQC) with spin-echo (SE) acquisitions." Magma.. 2007 Dec 0; 20(5-6):255-64. Epub 2007 Dec 05.

Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH. "NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA." Biochemistry.. 2007 Nov 6; 46(44):12665-78. Epub 2007 Oct 11.

Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD. "Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs." The journal of physical chemistry. B. 2007 Jun 21; 111(24):6718-27. Epub 2007 Apr 06.

Wong CK, Kennedy SD, Kwok E, Zhong J. "Theoretical studies of the effect of the dipolar field in multiple spin-echo sequences with refocusing pulses of finite duration." Journal of magnetic resonance.. 2007 Apr 0; 185(2):247-58. Epub 2007 Jan 10.

Tolbert BS, Kennedy SD, Schroeder SJ, Krugh TR, Turner DH. "NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs." Biochemistry.. 2007 Feb 13; 46(6):1511-22. Epub 2007 Jan 20.

Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. "The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits." Biochemistry.. 2006 Oct 3; 45(39):11776-89.

Zheng B, Chen Z, Kennedy SD, Zhong J. "iDQC MRI weighted by longitudinal relaxation in the rotating frame." Magnetic resonance in medicine.. 2006 Aug 0; 56(2):327-33.

Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH. "An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA." Biochemistry.. 2006 Jun 6; 45(22):6889-903.

Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH. "Solution structure of an RNA internal loop with three consecutive sheared GA pairs." Biochemistry.. 2005 Mar 1; 44(8):2845-56.

Znosko BM, Kennedy SD, Wille PC, Krugh TR, Turner DH. "Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns." Biochemistry.. 2004 Dec 21; 43(50):15822-37.

Xu L, Appell M, Kennedy S, Momany FA, Price NP. "Conformational analysis of chirally deuterated tunicamycin as an active site probe of UDP-N-acetylhexosamine:polyprenol-P N-acetylhexosamine-1-P translocases." Biochemistry.. 2004 Oct 26; 43(42):13248-55.

Kennedy SD, Zhong J. "Diffusion measurements free of motion artifacts using intermolecular dipole-dipole interactions." Magnetic resonance in medicine.. 2004 Jul 0; 52(1):1-6.

Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH. "Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron." Biochemistry.. 2003 Dec 9; 42(48):14184-96.

Zhong J, Chen Z, Kwok WE, Kennedy S, You Z. "Optimization of blood oxygenation level-dependent sensitivity in magnetic resonance imaging using intermolecular double-quantum coherence." Journal of magnetic resonance imaging : JMRI.. 2002 Dec 0; 16(6):733-40.

Yan S, Kennedy SD, Koide S. "Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange." Journal of molecular biology.. 2002 Oct 18; 323(2):363-75.

Layne Jr., J.R.; Kennedy, S.D.;. "Cellular energetics of frozen wood frogs (Rana sylvatica) revealed via NMR spectroscopy". J. Thermal Biology. 2002; 27(3): 167-173.

Zhong, J. ; Chen, Z.; Kwok, W.E.; Kennedy, S.D. ;. "Enhanced sensitivity to molecular diffusion with intermolecular double-quantum coherences: implications and potential applications". Magn. Reson. Imag. 2001; 19(3): 33-39.

Zhong, J.; Chen, Z.; Zheng, S.K.; Kennedy, S.D.;. "Theoretical and experimental characterization of NMR transverse relaxation process related to intermolecular dipolar interactions". Chem. Phys. Lett. 2001; 350(3): 260-268.

Chen Z, Kennedy SD, Zhong J. "Quantitation of intermolecular dipolar effects in NMR spectroscopy and high order MSE MR imaging." Magma.. 2000 Dec 0; 11(3):122-8.

Bahar S, Gunter CT, Wu C, Kennedy SD, Knauf PA. "Persistence of external chloride and DIDS binding after chemical modification of Glu-681 in human band 3." The American journal of physiology.. 1999 Oct 0; 277(4):C791-9.

Chen, Z.; Kennedy, S.D.; Zhong, J.;. "Theoretical formalism and experimental confirmation of intermolecular dipolar effects under time-averaged magnetic field gradients". Chem. Phys. Lett. 1999; 313(3): 217-224.

Liu D, Kennedy SD, Knauf PA. "Source of transport site asymmetry in the band 3 anion exchange protein determined by NMR measurements of external Cl- affinity." Biochemistry.. 1996 Dec 3; 35(48):15228-35.

Malek A, Miller RK, Mattison DR, Kennedy S, Panigel M, di Sant'Agnese PA, Jessee L. "Energy charge monitoring via magnetic resonance spectroscopy 31P in the perfused human placenta: effects of cadmium, dinitrophenol and iodoacetate." Placenta.. 1996 Sep 0; 17(7):495-506.

Liu D, Knauf PA, Kennedy SD. "Detection of Cl- binding to band 3 by double-quantum-filtered 35Cl nuclear magnetic resonance." Biophysical journal.. 1996 Feb 0; 70(2):715-22.

Liu D, Kennedy SD, Knauf PA. "35Cl nuclear magnetic resonance line broadening shows that eosin-5-maleimide does not block the external anion access channel of band 3." Biophysical journal.. 1995 Aug 0; 69(2):399-408.

Kennedy SD, Szczepaniak LS, Gibson SL, Hilf R, Foster TH, Bryant RG. "Quantitative MRI of Gd-DTPA uptake in tumors: response to photodynamic therapy." Magnetic resonance in medicine.. 1994 Mar 0; 31(3):292-301.

Blinc A, Kennedy SD, Bryant RG, Marder VJ, Francis CW. "Flow through clots determines the rate and pattern of fibrinolysis." Thrombosis and haemostasis.. 1994 Feb 0; 71(2):230-5.

Li H, Kennedy SD, Goldstein BM. "Solid-state and solution conformations of isotiazofurin: crystallographic, computational and 1H NMR studies." Acta crystallographica. Section B, Structural science. 1993 Aug 1; 49 ( Pt 4):729-38.

Swanson, S.D. ; Kennedy, S.D.;. "A Sample Shuttle Nuclear-Magnetic-Relaxation-Dispersion Spectrometer." J. Magn. Reson. 1993; 102(33): 375-377.

Ceckler TL, Gibson SL, Kennedy SD, Hill R, Bryant RG. "Hetergeneous tumour response to photodynamic therapy assessed by in vivo localised 31P NMR spectroscopy." British journal of cancer.. 1991 Jun 0; 63(6):916-22.

Mendelson DA, Heinsbergen JF, Kennedy SD, Szczepaniak LS, Lester CC, Bryant RG. "Comparison of agarose and cross-linked protein gels as magnetic resonance imaging phantoms." Magnetic resonance imaging.. 1991 9(6):975-8.

Kennedy SD, Bryant RG. "Structural effects of hydration: studies of lysozyme by 13C solids NMR." Biopolymers.. 1990 Dec 0; 29(14):1801-6.

77Se NMR and Crystallographic Studies of Selenazofurin and Its 5-amino Derivative;. "Goldstein, B. M.; Kennedy, S. D.;Hennen, W. J." J. Amer. Chem. Soc. 1990; 112(3): 8265-8268.

Kennedy SD, Bryant RG. "Hydration effects on dynamics of polyglycine and sodium poly(L-glutamate)." Biopolymers.. 1990 30(7-8):691-701.

Bryant RG, Kennedy SD, Jackson CL, Eads TM, Croasmun WR, Blaurock AE. "Applications of multinuclear NMR in the solid state to structural and dynamical problems in macromolecular chemistry." Basic life sciences.. 1990 56:255-71.

Kennedy, S.D. ; Bryant, R.G.;. "Use of Carbon-13 Stimulated Echoes for Measurement of Nitrogen-14 Spin Relaxation in Polycrystalline Amino Acids". Journal of Magnetic Resonance. 1989; 83(3): 565-575.

Bryant, R.G. ; Ganapathy, S.; Kennedy, S.D.;. "High Resolution Calcium-43 NMR in Solids". Journal of Magnetic Resonance. 1987; 72(3): 376-378.

Kennedy SD, Bryant RG. "Manganese-deoxyribonucleic acid binding modes. Nuclear magnetic relaxation dispersion results." Biophysical journal.. 1986 Oct 0; 50(4):669-76.

Eads TM, Kennedy SD, Bryant RG. "Solvent suppression in high-resolution proton nuclear magnetic resonance based on control of transverse relaxation rate." Analytical chemistry.. 1986 Jul 0; 58(8):1752-6.

Carbon-13 Spin-echo Spectroscopy as a Measure of Slow Motions in Solid Polymers;. "Swanson, S.; Ganapathy,S.; Kennedy, S.; Henrichs, P.M.; Bryant, R.G." Journal of Magnetic Resonance. 1986; 69(33): 531-534.

Kennedy SD, Bryant RG. "Proton magnetic relaxation in aqueous glycerol solutions containing manganese(II) ion." Magnetic resonance in medicine.. 1985 Feb 0; 2(1):14-9.

Ehman RL, Gray JE, Bryant RG, Kennedy SD, Earnest F. "Spin-spin relaxation time (T2) dependence in MR saturation- and inversion- recovery images." AJR. American journal of roentgenology.. 1984 Oct 0; 143(4):903-6.

Bryant RG, Polnaszek C, Kennedy S, Hetzler J, Hickerson D. "The magnetic field dependence of water proton T1 in aqueous solutions: implications for magnetic imaging contrast media." Medical physics.. 1984 11(5):712-3.

Farneth, W.D.; Zimmerman, P.G.; Hogenkamp, D.J.; Kennedy, S.D.;. "Infrared Laser Induced Heterogeneous Reactions: 2-propanol with Cupric Oxide". Journal of the American Chemical Society. 1983; 105(35): 1126-1129.