Turner DH - Search Results

1

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.

Pinamonti G, Zhao J, Condon DE, Paul F, Noè F, Turner DH, Bussi G. Pinamonti G, et al. Among authors: turner dh. J Chem Theory Comput. 2017 Feb 14;13(2):926-934. doi: 10.1021/acs.jctc.6b00982. Epub 2017 Jan 5. J Chem Theory Comput. 2017. PMID: 28001394 Free PMC article.

2

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. Zhao J, et al. Among authors: turner dh. J Chem Theory Comput. 2020 Mar 10;16(3):1968-1984. doi: 10.1021/acs.jctc.9b00912. Epub 2020 Feb 17. J Chem Theory Comput. 2020. PMID: 31904966

3

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

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Bottaro S, et al. Among authors: turner dh. Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May. Sci Adv. 2018. PMID: 29795785 Free PMC article.

4

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. Tubbs JD, et al. Among authors: turner dh. Biochemistry. 2013 Feb 12;52(6):996-1010. doi: 10.1021/bi3010347. Epub 2013 Jan 29. Biochemistry. 2013. PMID: 23286901 Free PMC article.

5

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. Condon DE, et al. Among authors: turner dh. J Phys Chem B. 2014 Feb 6;118(5):1216-28. doi: 10.1021/jp408909t. Epub 2014 Jan 24. J Phys Chem B. 2014. PMID: 24377321 Free PMC article.

6

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

Condon DE, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH. Condon DE, et al. Among authors: turner dh. J Chem Theory Comput. 2015 Jun 9;11(6):2729-2742. doi: 10.1021/ct501025q. Epub 2015 Apr 16. J Chem Theory Comput. 2015. PMID: 26082675 Free PMC article.

7

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. Zhao J, et al. Among authors: turner dh. J Chem Theory Comput. 2022 Feb 8;18(2):1241-1254. doi: 10.1021/acs.jctc.1c00643. Epub 2022 Jan 6. J Chem Theory Comput. 2022. PMID: 34990548

8

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.

Kauffmann AD, Kennedy SD, Zhao J, Turner DH. Kauffmann AD, et al. Among authors: turner dh. Biochemistry. 2017 Jul 25;56(29):3733-3744. doi: 10.1021/acs.biochem.7b00201. Epub 2017 Jul 12. Biochemistry. 2017. PMID: 28700212 Free PMC article.

9

Physics-based all-atom modeling of RNA energetics and structure.

Smith LG, Zhao J, Mathews DH, Turner DH. Smith LG, et al. Among authors: turner dh. Wiley Interdiscip Rev RNA. 2017 Sep;8(5):10.1002/wrna.1422. doi: 10.1002/wrna.1422. Wiley Interdiscip Rev RNA. 2017. PMID: 28815951 Free PMC article. Review.

10

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation.

Gleghorn ML, Zhao J, Turner DH, Maquat LE. Gleghorn ML, et al. Among authors: turner dh. Nucleic Acids Res. 2016 Sep 30;44(17):8417-24. doi: 10.1093/nar/gkw526. Epub 2016 Jun 10. Nucleic Acids Res. 2016. PMID: 27288442 Free PMC article.

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