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Scott D. Kennedy, Ph.D.

Scott D. Kennedy, Ph.D.

About Me

Faculty Appointments

Research Assistant Professor (Part-Time) - Department of Biochemistry and Biophysics (SMD)



PhD | Univ Rochester Sch Med/Dent. Biophysics. 1987

MS | Univ Minnesota-Twin City Cmp. Biophysics. 1984

BA | Univ Minnesota-Twin City Cmp. Physics. 1981


Journal Articles

Secondary structure prediction for RNA sequences including N-methyladenosine.

Kierzek E, Zhang X, Watson RM, Kennedy SD, Szabat M, Kierzek R, Mathews DH

Nature communications.. 2022 March 1113 (1):1271. Epub 03/11/2022.

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

Zhao J, Kennedy SD, Turner DH

Journal of chemical theory and computation.. 2022 January 6 Epub 01/06/2022.

Nuclear Magnetic Resonance reveals a two hairpin equilibrium near the 3'-splice site of Influenza A segment 7 mRNA that can be shifted by oligonucleotides.

Kauffmann AD, Kennedy SD, Moss WN, Kierzek E, Kierzek R, Turner DH

RNA.. 2022 January 4 Epub 01/04/2022.

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

Zhao J, Kennedy SD, Berger KD, Turner DH

Journal of chemical theory and computation.. 2020 January 6 Epub 01/06/2020.

Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids.

Kumpina I, Brodyagin N, MacKay JA, Kennedy SD, Katkevics M, Rozners E

The Journal of organic chemistry.. 2019 November 184 (21):13276-13298. Epub 10/02/2019.

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

Kennedy SD, Bauer WJ, Wang W, Kielkopf CL

Biochemical and biophysical research communications.. 2019 February 20 Epub 02/20/2019.

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

Kotikam V, Kennedy SD, MacKay JA, Rozners E

Chemistry : a European journal.. 2019 February 11 Epub 02/11/2019.

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

Berger KD, Kennedy SD, Turner DH

Biochemistry.. 2019 January 31 Epub 01/31/2019.

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

Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews D

RNA.. 2018 May 24 (5):656-672. Epub 02/06/2018.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K

Science advances.. 2018 May 4 (5):eaar8521. Epub 05/18/2018.

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

Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH

Biochemistry.. 2018 April 1057 (14):2121-2131. Epub 03/23/2018.

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

Hardcastle T, Novosjolova I, Kotikam V, Cheruiyot SK, Mutisya D, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E

ACS chemical biology.. 2018 March 1613 (3):533-536. Epub 01/10/2018.

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

Novosjolova I, Kennedy SD, Rozners E

Chembiochem : a European journal of chemical biology.. 2017 November 218 (21):2165-2170. Epub 09/26/2017.

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

Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E

Nucleic acids research.. 2017 August 2145 (14):8142-8155. Epub 1900 01 01.

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

Nganou C, Kennedy SD, McCamant DW

The journal of physical chemistry. B. 2016 February 25120 (7):1250-8. Epub 02/17/2016.

NMR Methods for Characterization of RNA Secondary Structure.

Kennedy SD

Methods in molecular biology.. 2016 1490 :253-64. Epub 1900 01 01.

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

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH

Biochemistry.. 2015 November 1754 (45):6769-82. Epub 11/03/2015.

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.

Condon DE, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH

Journal of chemical theory and computation.. 2015 June 911 (6):2729-2742. Epub 04/16/2015.

Structural features of a 3' splice site in influenza a.

Chen JL, Kennedy SD, Turner DH

Biochemistry.. 2015 June 254 (21):3269-85. Epub 05/21/2015.

Secondary structure of a conserved domain in an intron of influenza A M1 mRNA.

Jiang T, Kennedy SD, Moss WN, Kierzek E, Turner DH

Biochemistry.. 2014 August 1953 (32):5236-48. Epub 08/06/2014.

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

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

Nature methods.. 2014 April 11 (4):413-6. Epub 03/02/2014.

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

Tanui P, Kennedy SD, Lunstad BD, Haas A, Leake D, Rozners E

Organic & biomolecular chemistry.. 2014 February 2812 (8):1207-10. Epub 1900 01 01.

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).

Condon DE, Yildirim I, Kennedy SD, Mort BC, Kierzek R, Turner DH

The journal of physical chemistry. B. 2014 February 6118 (5):1216-28. Epub 01/24/2014.

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.

Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH

Biochemistry.. 2013 May 1452 (19):3390-2. Epub 04/29/2013.

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.

Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH

Biochemistry.. 2013 February 1252 (6):996-1010. Epub 01/29/2013.

Structure of phosphorylated SF1 bound to U2AF?? in an essential splicing factor complex.

Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL

Structure.. 2013 February 521 (2):197-208. Epub 12/27/2012.

Novel conformation of an RNA structural switch.

Kennedy SD, Kierzek R, Turner DH

Biochemistry.. 2012 November 2051 (46):9257-9. Epub 11/12/2012.

Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.

Chen JL, Dishler AL, Kennedy SD, Yildirim I, Liu B, Turner DH, Serra MJ

Biochemistry.. 2012 April 2451 (16):3508-22. Epub 04/10/2012.

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

Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH

Journal of chemical theory and computation.. 2012 January 108 (1):172-181. Epub 12/01/2011.

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

Van Nostrand KP, Kennedy SD, Turner DH, Mathews DH

Journal of chemical theory and computation.. 2011 November 87 (11):3779-3792. Epub 1900 01 01.

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised ? torsions.

Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH

The journal of physical chemistry. B. 2011 July 28115 (29):9261-70. Epub 07/01/2011.

Synthesis and properties of triazole-linked RNA.

Mutisya D, Selvam C, Kennedy SD, Rozners E

Bioorganic & medicinal chemistry letters.. 2011 June 121 (11):3420-2. Epub 04/05/2011.

Amides as excellent mimics of phosphate linkages in RNA.

Selvam C, Thomas S, Abbott J, Kennedy SD, Rozners E

Angewandte Chemie.. 2011 February 2550 (9):2068-70. Epub 01/21/2011.

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.

Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD

Biochemistry.. 2010 July 1349 (27):5817-27. Epub 1900 01 01.

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

Petri ET, Celic A, Kennedy SD, Ehrlich BE, Boggon TJ, Hodsdon ME

Proceedings of the National Academy of Sciences of the United States of America.. 2010 May 18107 (20):9176-81. Epub 05/03/2010.

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

Yildirim I, Stern HA, Kennedy SD, Tubbs JD, Turner DH

Journal of chemical theory and computation.. 2010 May 116 (5):1520-1531. Epub 04/16/2010.

A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.

Chen G, Kennedy SD, Turner DH

Biochemistry.. 2009 June 2348 (24):5738-52. Epub 1900 01 01.

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

McNanley AR, Johnson AM, Flynn MK, Wood RW, Kennedy SD, Reeder JE

International urogynecology journal and pelvic floor dysfunction.. 2009 January 20 (1):19-25. Epub 09/19/2008.

NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.

Hart JM, Kennedy SD, Mathews DH, Turner DH

Journal of the American Chemical Society.. 2008 August 6130 (31):10233-9. Epub 07/10/2008.

Functional MRI at 3T using intermolecular double-quantum coherence (iDQC) with spin-echo (SE) acquisitions.

Gu T, Kennedy SD, Chen Z, Schneider KA, Zhong J

Magma.. 2007 December 20 (5-6):255-64. Epub 12/05/2007.

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

Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH

Biochemistry.. 2007 November 646 (44):12665-78. Epub 10/11/2007.

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.

Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD

The journal of physical chemistry. B. 2007 June 21111 (24):6718-27. Epub 04/06/2007.

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

Wong CK, Kennedy SD, Kwok E, Zhong J

Journal of magnetic resonance.. 2007 April 185 (2):247-58. Epub 01/10/2007.

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

Tolbert BS, Kennedy SD, Schroeder SJ, Krugh TR, Turner DH

Biochemistry.. 2007 February 1346 (6):1511-22. Epub 01/20/2007.

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

Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH

Biochemistry.. 2006 October 345 (39):11776-89. Epub 1900 01 01.

iDQC MRI weighted by longitudinal relaxation in the rotating frame.

Zheng B, Chen Z, Kennedy SD, Zhong J

Magnetic resonance in medicine.. 2006 August 56 (2):327-33. Epub 1900 01 01.

An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.

Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH

Biochemistry.. 2006 June 645 (22):6889-903. Epub 1900 01 01.

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

Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH

Biochemistry.. 2005 March 144 (8):2845-56. Epub 1900 01 01.

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

Znosko BM, Kennedy SD, Wille PC, Krugh TR, Turner DH

Biochemistry.. 2004 December 2143 (50):15822-37. Epub 1900 01 01.

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

Xu L, Appell M, Kennedy S, Momany FA, Price NP

Biochemistry.. 2004 October 2643 (42):13248-55. Epub 1900 01 01.

Diffusion measurements free of motion artifacts using intermolecular dipole-dipole interactions.

Kennedy SD, Zhong J

Magnetic resonance in medicine.. 2004 July 52 (1):1-6. Epub 1900 01 01.

Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron.

Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH

Biochemistry.. 2003 December 942 (48):14184-96. Epub 1900 01 01.

Optimization of blood oxygenation level-dependent sensitivity in magnetic resonance imaging using intermolecular double-quantum coherence.

Zhong J, Chen Z, Kwok WE, Kennedy S, You Z

Journal of magnetic resonance imaging : JMRI.. 2002 December 16 (6):733-40. Epub 1900 01 01.

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

Yan S, Kennedy SD, Koide S

Journal of molecular biology.. 2002 October 18323 (2):363-75. Epub 1900 01 01.

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

Layne Jr., J.R.; Kennedy, S.D.;.

J. Thermal Biology. 2002; 27(3): 167-173.

Enhanced sensitivity to molecular diffusion with intermolecular double-quantum coherences: implications and potential applications

Zhong, J. ; Chen, Z.; Kwok, W.E.; Kennedy, S.D. ;.

Magn. Reson. Imag. 2001; 19(3): 33-39.

Theoretical and experimental characterization of NMR transverse relaxation process related to intermolecular dipolar interactions

Zhong, J.; Chen, Z.; Zheng, S.K.; Kennedy, S.D.;.

Chem. Phys. Lett. 2001; 350(3): 260-268.

Quantitation of intermolecular dipolar effects in NMR spectroscopy and high order MSE MR imaging.

Chen Z, Kennedy SD, Zhong J

Magma.. 2000 December 11 (3):122-8. Epub 1900 01 01.

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

Bahar S, Gunter CT, Wu C, Kennedy SD, Knauf PA

The American journal of physiology.. 1999 October 277 (4):C791-9. Epub 1900 01 01.

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

Chen, Z.; Kennedy, S.D.; Zhong, J.;.

Chem. Phys. Lett. 1999; 313(3): 217-224.

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

Liu D, Kennedy SD, Knauf PA

Biochemistry.. 1996 December 335 (48):15228-35. Epub 1900 01 01.

Energy charge monitoring via magnetic resonance spectroscopy 31P in the perfused human placenta: effects of cadmium, dinitrophenol and iodoacetate.

Malek A, Miller RK, Mattison DR, Kennedy S, Panigel M, di Sant'Agnese PA, Jessee L

Placenta.. 1996 September 17 (7):495-506. Epub 1900 01 01.

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

Liu D, Knauf PA, Kennedy SD

Biophysical journal.. 1996 February 70 (2):715-22. Epub 1900 01 01.

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

Liu D, Kennedy SD, Knauf PA

Biophysical journal.. 1995 August 69 (2):399-408. Epub 1900 01 01.

Quantitative MRI of Gd-DTPA uptake in tumors: response to photodynamic therapy.

Kennedy SD, Szczepaniak LS, Gibson SL, Hilf R, Foster TH, Bryant RG

Magnetic resonance in medicine.. 1994 March 31 (3):292-301. Epub 1900 01 01.

Flow through clots determines the rate and pattern of fibrinolysis.

Blinc A, Kennedy SD, Bryant RG, Marder VJ, Francis CW

Thrombosis and haemostasis.. 1994 February 71 (2):230-5. Epub 1900 01 01.

Solid-state and solution conformations of isotiazofurin: crystallographic, computational and 1H NMR studies.

Li H, Kennedy SD, Goldstein BM

Acta crystallographica. Section B, Structural science. 1993 August 149 ( Pt 4) :729-38. Epub 1900 01 01.

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

Swanson, S.D. ; Kennedy, S.D.;.

J. Magn. Reson. 1993; 102(33): 375-377.

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

Ceckler TL, Gibson SL, Kennedy SD, Hill R, Bryant RG

British journal of cancer.. 1991 June 63 (6):916-22. Epub 1900 01 01.

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

Mendelson DA, Heinsbergen JF, Kennedy SD, Szczepaniak LS, Lester CC, Bryant RG

Magnetic resonance imaging.. 1991 9 (6):975-8. Epub 1900 01 01.

Structural effects of hydration: studies of lysozyme by 13C solids NMR.

Kennedy SD, Bryant RG

Biopolymers.. 1990 December 29 (14):1801-6. Epub 1900 01 01.

Goldstein, B. M.; Kennedy, S. D.;Hennen, W. J.

77Se NMR and Crystallographic Studies of Selenazofurin and Its 5-amino Derivative;.

J. Amer. Chem. Soc. 1990; 112(3): 8265-8268.

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

Kennedy SD, Bryant RG

Biopolymers.. 1990 30 (7-8):691-701. Epub 1900 01 01.

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

Bryant RG, Kennedy SD, Jackson CL, Eads TM, Croasmun WR, Blaurock AE

Basic life sciences.. 1990 56 :255-71. Epub 1900 01 01.

Use of Carbon-13 Stimulated Echoes for Measurement of Nitrogen-14 Spin Relaxation in Polycrystalline Amino Acids

Kennedy, S.D. ; Bryant, R.G.;.

Journal of Magnetic Resonance. 1989; 83(3): 565-575.

High Resolution Calcium-43 NMR in Solids

Bryant, R.G. ; Ganapathy, S.; Kennedy, S.D.;.

Journal of Magnetic Resonance. 1987; 72(3): 376-378.

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

Kennedy SD, Bryant RG

Biophysical journal.. 1986 October 50 (4):669-76. Epub 1900 01 01.

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

Eads TM, Kennedy SD, Bryant RG

Analytical chemistry.. 1986 July 58 (8):1752-6. Epub 1900 01 01.

Swanson, S.; Ganapathy,S.; Kennedy, S.; Henrichs, P.M.; Bryant, R.G.

Carbon-13 Spin-echo Spectroscopy as a Measure of Slow Motions in Solid Polymers;.

Journal of Magnetic Resonance. 1986; 69(33): 531-534.

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

Kennedy SD, Bryant RG

Magnetic resonance in medicine.. 1985 February 2 (1):14-9. Epub 1900 01 01.

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

Ehman RL, Gray JE, Bryant RG, Kennedy SD, Earnest F

AJR. American journal of roentgenology.. 1984 October 143 (4):903-6. Epub 1900 01 01.

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

Bryant RG, Polnaszek C, Kennedy S, Hetzler J, Hickerson D

Medical physics.. 1984 11 (5):712-3. Epub 1900 01 01.

Infrared Laser Induced Heterogeneous Reactions: 2-propanol with Cupric Oxide

Farneth, W.D.; Zimmerman, P.G.; Hogenkamp, D.J.; Kennedy, S.D.;.

Journal of the American Chemical Society. 1983; 105(35): 1126-1129.