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

por Chen, Gang, Kennedy, Scott D., Turner, Douglas H.
Publicado 2009

Novel Conformation of an RNA Structural Switch

por Kennedy, Scott D., Kierzek, Ryszard, Turner, Douglas H.
Publicado 2012

Structural Features of a 3′ Splice Site in Influenza A

por Chen, Jonathan L., Kennedy, Scott D., Turner, Douglas H.
Publicado 2015

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

por Hart, James M., Kennedy, Scott D., Mathews, David H., Turner, Douglas H.
Publicado 2008

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

por Hammond, Nicholas B., Tolbert, Blanton S., Kierzek, Ryszard, Turner, Douglas H., Kennedy, Scott D.
Publicado 2010

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

por Jiang, Tian, Kennedy, Scott D., Moss, Walter N., Kierzek, Elzbieta, Turner, Douglas H.
Publicado 2014

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

por Bottaro, Sandro, Bussi, Giovanni, Kennedy, Scott D., Turner, Douglas H., Lindorff-Larsen, Kresten
Publicado 2018

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

por Yildirim, Ilyas, Stern, Harry A., Kennedy, Scott D., Tubbs, Jason D., Turner, Douglas H.
Publicado 2010

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

por Yildirim, Ilyas, Stern, Harry A., Tubbs, Jason D., Kennedy, Scott D., Turner, Douglas H.
Publicado 2011

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

por Yildirim, Ilyas, Kennedy, Scott D., Stern, Harry A., Hart, James M., Kierzek, Ryszard, Turner, Douglas H.
Publicado 2011

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

por Condon, David E., Yildirim, Ilyas, Kennedy, Scott D., Mort, Brendan C., Kierzek, Ryszard, Turner, Douglas H.
Publicado 2013

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

por Condon, David E., Kennedy, Scott D., Mort, Brendan C., Kierzek, Ryszard, Yildirim, Ilyas, Turner, Douglas H.
Publicado 2015

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

por Kauffmann, Andrew D., Kennedy, Scott D., Moss, Walter N., Kierzek, Elzbieta, Kierzek, Ryszard, Turner, Douglas H.
Publicado 2022

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 Dynamic...

por Tubbs, Jason D., Condon, David E., Kennedy, Scott D., Hauser, Melanie, Bevilacqua, Philip C., Turner, Douglas H.
Publicado 2013

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

por Tubbs, Jason D., Condon, David E., Kennedy, Scott D., Hauser, Melanie, Bevilacqua, Philip C., Turner, Douglas H.
Publicado 2013

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

por Spasic, Aleksandar, Kennedy, Scott D., Needham, Laura, Manoharan, Muthiah, Kierzek, Ryszard, Turner, Douglas H., Mathews, David H.
Publicado 2018

Secondary structure prediction for RNA sequences including N(6)-methyladenosine

por Kierzek, Elzbieta, Zhang, Xiaoju, Watson, Richard M., Kennedy, Scott D., Szabat, Marta, Kierzek, Ryszard, Mathews, David H.
Publicado 2022

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

por Chen, Jonathan L., Dishler, Abigael L., Kennedy, Scott D., Yildirim, Ilyas, Liu, Biao, Turner, Douglas H., Serra, Martin J.
Publicado 2012

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

por Chen, Jonathan L., Bellaousov, Stanislav, Tubbs, Jason D., Kennedy, Scott D., Lopez, Michael J., Mathews, David H., Turner, Douglas H.
Publicado 2015

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

por Mutisya, Daniel, Hardcastle, Travis, Cheruiyot, Samwel K., Pallan, Pradeep S., Kennedy, Scott D., Egli, Martin, Kelley, Melissa L., Smith, Anja van Brabant, Rozners, Eriks
Publicado 2017