Yildirium, I., Kennedy, S. D., Stern, H. A., Hart, J. M., Kierzek, R., Turner, D. H.
"Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions of Tetramer Duplexes with GC and iGiC Base Pairs,"
J. Chem. Theory, Comput.
2012,
8,
172-181.
Van Nostrand, K., Kennedy, S. D., Turner, D. H., Mathews, D. H.
"Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change,"
J. Chem. Theory, Comput.
2011,
7,
3779-3792.
Moss, W. N., Eickbush, D. G., Lopez, M. J., Eickbush, T. H., Turner, D. H.
"The R2 Retrotransposon RNA Families,"
RNA Biology
2011,
8,
714-718.
Yildirium, I., Stern, H. A., Tubbs, J. D., Kennedy, S. D., Turner, D. H.
"Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-stranded r(GACC) are Improved by Revised χ Torsions,"
J. Phys. Chem. B
2011,
115,
9261-9270.
Noble, E., Mathews, D. H., Chen, J. L., Turner, D. H., Takamoto, T., Kim, B.
"Biophysical analysis of influenza A virus RNA promoter at physiological temperatures,"
J. Biol. Chem.
2011,
286,
24872-24881.
Lerman, Y., Kennedy, S. D., Shankar, N., Parisien, M., Major, F., Turner, D. H.
"NMR Structure of a 4X4 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,
17,
1664-1677.
Moss, W. N., Priore, S. F., Turner, D. H.
"Identification of Potential Conserved RNA Secondary Structure throughout Influenza A Coding Regions,"
RNA
2011,
17,
991-1011.
Liu, B., Diamond, J. M., Mathews, D. H., Turner, D. H.
"Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters,"
Biochemistry
2011,
50,
640-653.
Liang, R., Kierzek, E., Kierzek, R., Turner, D. H.
"Comparisons between Chemical Mapping and Binding to Isoenergetic Oligonucleotide Microarrays Reveal Unexpected Patterns of Binding to the Bacillus subtilis RNase P RNA Specificity Domain,"
Biochemistry
2010,
49,
5817-5827.
Hammond, N. B., Tolbert, B. S., Kierzek, R., Turner, D. H., Kennedy, S. D.
"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,
49,
5817-5827.
Yildirium, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., Turner, D. H.
"Re-parameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine,"
J. Chem. Theory, Comput.
2010,
6,
1520-1531.
Reblova, K., Strelcova, Z., Kulhanek, P., Besseova, I., Mathews, D. H., Van Nostrand, K., Yildirium, I., Turner, D. H., Sponer, J.
"An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5’-UAA/5’-GAN Internal Loops Studied by Molecular Dynamics Methods,"
J. Chem. Theory, Comput.
2010,
6,
910-929.
Turner, D. H., Mathews, D. H.
"NNDB: The Nearest Neighbor Parameter Database for Predicting Stability of Nucleic Acid Secondary Structure,"
Nucleic Acids Res.
2010,
38,
D280-D282.
Liu, B., Shankar, N., Turner, D. H.
"Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots,"
Biochemistry
2010,
49,
623-634.
Liu, B., Mathews, D. H., Turner, D. H.
"RNA Pseudoknots: Folding and Finding,"
f1000 Biology Reports
2010,
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8.
Mathews, D. H., Moss, W. N., Turner, D. H.
"Folding and Finding the RNA Secondary Structure,"
The RNA Worlds,
2010,
293-307, ed. by Atkins, J. F., Gesteland, R. F., and T. R. Cech, Cold Spring Harbor Press.
Carlucci, M., Kierzek, E., Olejnik, A., Turner, D. H., Kierzek, R.
"The Chemical Synthesis of LNA-2-thiouridine and it’s Influence on Stability and Selectivity of Oligonucleotide Binding to RNA,"
Biochemistry
2009,
48,
10822-10893.
Shroeder, S. J., Turner, D. H.
"Optical Melting Measurements of Nucleic Acid Thermodynamics,"
Methods in Enzymology
2009,
371-387, ed. by D. Herschlag, Academic Press, Burlington.
Yildirim, I., Stern, H. A., Sponer, J., Spackova, N., Turner, D. H.
"Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC, or iCiG Base Pairs,"
J. Chem. Theory, Comput.
2009,
5,
2088-2100.
Kierzek, E., Christensen, S. M., Eickbush, T. H., Kierzek, R., Turner, D. H., Moss, W. N.
"Secondary Structures for 5' Regions of R2 Retrotransposon RNAs Reveal a Novel Conserved Pseudoknot and Regions that Evolve under Different Constraints,"
J. Mol. Biol.
2009,
390,
428-442.
Hart, J. M., Kennedy, S. D., Mathews, D. H., Turner, D. H.
"NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon,"
J. Am. Chem. Soc.
2008,
130,
10233-10239.
Chen, G., Kierzek, R., Yildirim, I., Krugh, T. R., Turner, D. H., Kennedy, S. D.
"Stacking Effects on Local Structure in RNA: The Structure of Tandem GA Pairs Changes When Flanking GC Pairs are Replaced by isoG-isoC Pairs,"
J. Phys. Chem. B
2007,
111,
6718-6727.
Shankar, N., Kennedy, S. D., Chen, G., Krugh, T. R., Turner, D. H.
"The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from its Structure in Crystals of 50S Ribosomal Subunits,"
Biochemistry
2006,
45,
11776-11789.
Chen, G., Turner, D. H.
"Consecutive GA Pairs Stabilize Medium-Size RNA Internal Loops,"
Biochemistry
2006,
45,
4025-4043.
Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., Turner, D. H.
"Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure,"
Proc. Natl. Acad. Sci. U.S.A.
2004,
101,
7287-7292.