Scott D. Kennedy, Ph.D.

Scott D. Kennedy, Ph.D.

Contact Information

University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, NY 14642

Office: (585) 275-7585
Fax: (585) 275-6007

Journal Articles

Showing all 67 journal articles available.

2016 Feb 2
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 2; Epub 2016 Feb 02.
2015 Jun 9
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.
2014 Aug 19
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.
2014 Apr
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; 11(4):413-6. Epub 2014 Mar 02.
2014 Feb 28
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.
2014 Feb 6
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.
2013 May 14
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.
2013 Feb 12
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.
2013 Feb 5
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.
2012 Nov 20
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.
2012 Apr 24
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.
2012 Jan 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.
2011 Nov 8
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.
2011 Sep
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; 17(9):1664-77. Epub 2011 Jul 21.
2011 Jul 28
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.
2011 Jun 1
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.
2011 Feb 25
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.
2010 Jul 13
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.
2010 May 18
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.
2010 May 11
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.
2009 Jun 23
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.
2009 Jan
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; 20(1):19-25. Epub 2008 Sep 19.
2008 Aug 6
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.
2007 Nov 6
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.
2007 Jun 21
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.
2007 Apr
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; 185(2):247-58. Epub 2007 Jan 10.
2007 Feb 13
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.
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 20(5-6):255-64. Epub 2007 Dec 05.
2006 Oct 3
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.
2006 Aug
Zheng B, Chen Z, Kennedy SD, Zhong J. "iDQC MRI weighted by longitudinal relaxation in the rotating frame." Magnetic resonance in medicine. 2006 Aug; 56(2):327-33.
2006 Jun 6
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.
2005 Mar 1
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.
2004 Oct 26
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.
2004 Jul
Kennedy SD, Zhong J. "Diffusion measurements free of motion artifacts using intermolecular dipole-dipole interactions." Magnetic resonance in medicine. 2004 Jul; 52(1):1-6.
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 43(50):15822-37.
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 42(48):14184-96.
2002 Oct 18
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 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 16(6):733-40.
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. Link
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. Link
Chen Z, Kennedy SD, Zhong J. "Quantitation of intermolecular dipolar effects in NMR spectroscopy and high order MSE MR imaging." Magma. 2000 11(3):122-8.
1999 Oct
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; 277(4 Pt 1):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. Link
1996 Sep
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; 17(7):495-506.
1996 Feb
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; 70(2):715-22.
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 35(48):15228-35.
1995 Aug
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; 69(2):399-408.
1994 Mar
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; 31(3):292-301.
1994 Feb
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; 71(2):230-5.
1993 Aug 1
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. Link
1991 Jun
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; 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.
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. Link
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 SD, Bryant RG. "Structural effects of hydration: studies of lysozyme by 13C solids NMR." Biopolymers. 1990 29(14):1801-6.
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. Link
Bryant, R.G. ; Ganapathy, S.; Kennedy, S.D.;. "High Resolution Calcium-43 NMR in Solids". Journal of Magnetic Resonance. 1987; 72(3): 376-378. Link
1986 Oct
Kennedy SD, Bryant RG. "Manganese-deoxyribonucleic acid binding modes. Nuclear magnetic relaxation dispersion results." Biophysical journal. 1986 Oct; 50(4):669-76.
1986 Jul
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; 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. Link
1985 Feb
Kennedy SD, Bryant RG. "Proton magnetic relaxation in aqueous glycerol solutions containing manganese(II) ion." Magnetic resonance in medicine. 1985 Feb; 2(1):14-9.
1984 Oct
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; 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. Link