Publications by authors named "Scott D Kennedy"

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NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.
Olayinka Akinyemi, Scott D Kennedy, James P McSally, David H Mathews

Biophys J· November 2025

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Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.
Carly R Reed, Scott D Kennedy, Rachel H Horowitz, Anees Mohammed Keedakkatt Puthenpeedikakkal, Harry A Stern

J Phys Chem B· November 2024

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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.
Andrew D Kauffmann, Scott D Kennedy, Walter N Moss, Elzbieta Kierzek, Ryszard Kierzek

RNA· April 2022

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Secondary structure prediction for RNA sequences including N-methyladenosine.
Elzbieta Kierzek, Xiaoju Zhang, Richard M Watson, Scott D Kennedy, Marta Szabat

Nat Commun· March 2022

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Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA.
Jianbo Zhao, Scott D Kennedy, Douglas H Turner

J Chem Theory Comput· February 2022

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Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations.
Jianbo Zhao, Scott D Kennedy, Kyle D Berger, Douglas H Turner

J Chem Theory Comput· March 2020

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Distributed processing of movement signaling.
Scott D Kennedy, Andrew B Schwartz

Proc Natl Acad Sci U S A· December 2019

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Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids.
Ilze Kumpina, Nikita Brodyagin, James A MacKay, Scott D Kennedy, Martins Katkevics

J Org Chem· November 2019

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Stiffness as a control factor for object manipulation.
Scott D Kennedy, Andrew B Schwartz

J Neurophysiol· August 2019

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Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites.
Scott D Kennedy, William J Bauer, Wenhua Wang, Clara L Kielkopf

Biochem Biophys Res Commun· April 2019

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Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids.
Venubabu Kotikam, Scott D Kennedy, James A MacKay, Eriks Rozners

Chemistry· March 2019

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Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.
Kyle D Berger, Scott D Kennedy, Douglas H Turner

Biochemistry· February 2019

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Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.
Aleksandar Spasic, Scott D Kennedy, Laura Needham, Muthiah Manoharan, Ryszard Kierzek

RNA· May 2018

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Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.
Sandro Bottaro, Giovanni Bussi, Scott D Kennedy, Douglas H Turner, Kresten Lindorff-Larsen

Sci Adv· May 2018

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Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.
Kyle D Berger, Scott D Kennedy, Susan J Schroeder, Brent M Znosko, Hongying Sun

Biochemistry· April 2018

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A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs.
Travis Hardcastle, Irina Novosjolova, Venubabu Kotikam, Samwel K Cheruiyot, Daniel Mutisya, Scott D Kennedy

ACS Chem Biol· March 2018

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NMR Methods for Characterization of RNA Secondary Structure.
Scott D Kennedy

Methods Mol Biol· January 2018

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2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies.
Irina Novosjolova, Scott D Kennedy, Eriks Rozners

Chembiochem· November 2017

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Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.
Daniel Mutisya, Travis Hardcastle, Samwel K Cheruiyot, Pradeep S Pallan, Scott D Kennedy

Nucleic Acids Res· August 2017

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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.
Andrew D Kauffmann, Scott D Kennedy, Jianbo Zhao, Douglas H Turner

Biochemistry· July 2017

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Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields.
Collins Nganou, Scott D Kennedy, David W McCamant

J Phys Chem B· February 2016

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Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.
Jonathan L Chen, Stanislav Bellaousov, Jason D Tubbs, Scott D Kennedy, Michael J Lopez

Biochemistry· November 2015

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Structural features of a 3' splice site in influenza a.
Jonathan L Chen, Scott D Kennedy, Douglas H Turner

Biochemistry· June 2015

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Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.
David E Condon, Scott D Kennedy, Brendan C Mort, Ryszard Kierzek, Ilyas Yildirim

J Chem Theory Comput· June 2015

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Secondary structure of a conserved domain in an intron of influenza A M1 mRNA.
Tian Jiang, Scott D Kennedy, Walter N Moss, Elzbieta Kierzek, Douglas H Turner

Biochemistry· August 2014

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