Relevant Publications

  1. "Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models" G. Pinamonti, J. Zhao, D. E. Condon, F. Paul, F. Noe, D. H. Turner, and G. Bussi, J. Chem. Theory Comput 2017 Link

  2. "Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication" E. Lenartowicz, A. Nogales, E. Kierzek, R. Kierzek, L. Martinez-Sobrido, and D. H. Turner, Nucleic Acid Therapeutics 2016 Link

  3. "Crystal Structure of a Poly(rA) Staggered Zipper at Acidic pH: Evidence that Adenine N1 Protonation Mediates Parallel Double Helix Formation" M. L. Gleghorn, J. Zhao, D. H. Turner, and L. E. Maquat, Nucleic Acids Res 2016 Link

  4. "Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture" T. Jiang, A. Nogales, S. F. Baker, L. Martinez-Sobrido, and D. H. Turner, PLoS ONE 2016 Link

  5. "Self-folding of Naked Segment 8 Genomic RNA of Influenza A Virus" E. Lenartowicz, J. Kesy, A. Ruszkowska, M. Soszynska-Jozwiak, P. Michalak, W. N. Moss, D. H. Turner, R. Kierzek, and E. Kierzek, PLoS ONE 2016 Link

  6. "Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints" J. L. Chen, S. Bellaousov, J. D. Tubbs, S. D. Kennedy, M. J. Lopez, D. H. Mathews, and D. H. Turner, 54, 6769-6782, Biochemistry 2015 Link

  7. "The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot" S. F. Priore, A. D. Kauffmann, J. R. Baman, and D. H. Turner, 54, 3413-3415, Biochemistry 2015 Link

  8. "Structural Features of a 3' Splice Site in Influenza A" J. L. Chen, S. D. Kennedy, and D. H. Turner, 54, 3269-3285, Biochemistry 2015 Link

  9. "Microarrays for Identifying Binding Sites and Probing Structure of RNAs" R. Kierzek, D. H. Turner, and E. Kierzek Nucleic Acids Res. 2015 Link

  10. "Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics" David E. Condon, Scott D. Kennedy, Brendan C. Mort, Ryszard Kierzek, Ilyas Yildirim, and Douglas H. Turner J. Chem. Theory Comput. 2015 Link

  11. "Structure Determination of Noncanonical RNA Motifs Guided by NMR Chemical Shifts" Sripakdeevong, M. Cevec, A. T. Chang, M. C. Erat, M. Ziegler, Q. Zhao, G. E. Fox, X. Gao, S. D. Kennedy, R. Kierzek, E. P. Nikonowicz, H. Schwalbe, R. K. Sigel, D. H. Turner, and R. Das, Nature Methods 11, 413-416, 2014 Link

  12. "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, 53, (32), pp.5236-5248. Link

  13. "Fundamental Interactions in RNA: Questions Answered and Remaining" D. H. Turner, Biopolymers 99, 1097-1104, 2013 Link

  14. "Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU)," D. E. Condon, I. Yildirim, S. D. Kennedy, B. C. Mort, R. Kierzek, and D. H. Turner,J. Phys. Chem. B(2013) Link.

  15. "The Contribution of Pseudouridine to Stabilities and Structure of RNAs" E. Kierzek, M. Malgowska, J. Liswiec, D. H. Turner, Z. Gdaniec, R. Kierzek Nucleic Acids Res. (2013) Link.

  16. "The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Predictions from Molecular Dynamics," J. D. Tubbs, D. E. Condon, S. D. Kennedy, M. Hauser, P. C. Bevilacqua, and D. H. Turner,Biochemistry 52, 996-1010 (2013) Link.

  17. "Identification of Conserved RNA Secondary Structures at Influenza B and C Splice Sites Reveals Similarities and Differences between Influenza A, B, and C" L. I. Dela-Moss, W. N. Moss, and D. H. Turner, BMC Research Notes, 7:22. Doi:10.1186/1756-0500-7-22 (2014).Link.

  18. "Influenza B Virus has Global Ordered RNA Structure in (+) and (-) Strands but Relatively Less Stable Predicted RNA Folding Free Energy than Allowed by the Encoded Protein Sequence," S. F. Priore, W. N. Moss, and D. H. Turner, BMC Research Notes 6:330. Doi: 10.1186/1756-0500-6-330. (2013). Link.

  19. "Understanding the Role of Base Stacking in Nucleic Acids. MD and QM Analysis of Tandem GA Pairs in RNA Duplexes," C. A. Morgado, D. Svozil, D. H. Turner, and J. Sponer, Phys. Chem. Chem. Phys., 14, 12580-12591. Doi: 10.1039/c2cp40556c. Link.

  20. "Novel Conformation of an RNA Structural Switch," S. D. Kennedy, R. Kierzek, and D. H. Turner,"Biochemistry 51, p. 9257-9259 (2012) Link.

  21. "The 3' Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin," W. N. Moss, L. I. Dela-Moss, E. Kierzek, R. Kierzek, S. F. Priore, and D. H. Turner, PLoS ONE, 7(6):e38323. Doi:10.137/journal.pone.0038323 (2012).

  22. "Influenza A Virus Coding Regions Exhibit Host-specific Global Ordered RNA Structure," S. F. Priore, W. N. Moss, and D. H. Turner, PLoS ONE, 7(4): e35989, doi:10.1371/ journal.pone.0035989 (2012).

  23. "Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters," J. L. Chen, A. L. Dishler, S. D. Kennedy, I. Yildirim, B. Liu, D. H. Turner, and M. J. Serra, Biochemistry 51, 3508-3522 (2012).

  24. "Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions of Tetramer Duplexes with GC and iGiC Base Pairs," I. Yildirim, S. D. Kennedy, H. A. Stern, J. M. Hart, R. Kierzek, and D. H. Turner, J. Chem. Theory and Computation, 8, 172-181 (2012).

  25. "Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change," K. Van Nostrand, S. D. Kennedy, D. H. Turner, and D. H. Mathews, J. Chem. Theory and Computation, 7, 3779-3792 (2011)

  26. "The R2 Retrotransposon RNA Families," W.N. Moss, D.G. Eickbush, M.J. Lopez, T.H. Eickbush, and D.H. Turner, RNA Biology, Volume 8, Issue 5, September/October 2011

  27. "Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) are Improved by Revised Chi Torsions," I. Yildirim, H.A. Stern, J.D. Tubbs, S.D. Kennedy, and D.H. Turner. J. Phys. Chem. B, Vol. 115, Number 29, pp 9261-9270.

  28. "Biophysical Analysis of Influenza A virus RNA Promoter at physiological temperatures," E. Noble, D.H. Mathews, J.L. Chen, D.H. Turner, T. Takamoto, and B. Kim. J. Biol. Chem., 2011, 286: 24872-24881. doi:10.1074/jbc.M110.212183.

  29. "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," Y. Lerman, S.D. Kennedy, N. Shankar, M. Parisien, F. Major, and D.H. Turner, RNA, 17, pp 1664-1677. doi:10.1261/rna.2641911

  30. "Identification of Potential Conserved RNA Secondary Structure throughout Influenza A Coding Regions," W.N. Moss, S.F. Priore, and D.H. Turner, RNA, 17 pp 991-1011 (2011).

  31. "Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters," B. Liu, J.M. Diamond, D.H. Mathews, and D.H. Turner, Biochemistry, 50, 640-653 (2011).

  32. "Comparisons between Chemical Mapping and Binding to Isoenergetic Oligonucleotide Microarrays Reveal Unexpected Patterns of Binding to the Bacillus subtilis RNase P RNA Specificity Domain," R. Liang, E. Kierzek, R. Kierzek, and D.H. Turner, Biochemistry, 49, pp 8155-8168 (2010).

  33. "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"," N.B. Hammond, B. S. Tolbert, R. Kierzek, D. H. Turner, and S. D. Kennedy. Biochemistry, 49, pp 5817-5827 (2010).

  34. "Re-parameterization of RNA CHI Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine," I. Yildirim, H.A. Stern, S.D. Kennedy, J.D. Tubbs, and D.H. Turner, J. Chem. Theory and Comput. 6, 1520-1531 (2010).

  35. "An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods," K. Reblova, Z. Strelcova, P. Kulhanek, I. Besseova, D.H. Mathews, K. Van Nostrand, I. Yildirim, D.H. Turner, and J. Sponer, J. Chem. Theory and Comput. 6, 910-929 (2010).

  36. "NNDB: The Nearest Neighbor Parameter Database for Predicting Stability of Nucleic Acid Secondary Structure," D.H. Turner and D.H. Mathews, Nucleic Acids Res. 38, D280-D282 (2010).

  37. "Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots," B. Liu, N. Shankar, and D.H. Turner, Biochemistry, 49, 623-634 (2010).

  38. "RNA Pseudoknots: Folding and Finding," B. Liu, D.H. Mathews, and D.H. Turner, F1000 Biology Reports, 2, 8 (2010).

  39. "Folding and Finding RNA Secondary Structure," D.H. Mathews, W.N. Moss, and D.H. Turner, in The RNA World, 4th edition, ed. By R. F. Gesteland, T. R Cech, and J. F. Atkins, Cold Spring Harbor Press, in press (2010).

  40. "The Chemical Synthesis of LNA-2-thiouridine and it's Influence on Stability and Selectivity of Oligonucleotide Binding to RNA," M. Carlucci, E. Kierzek, A. Marciniak, D.H. Turner, and R. Kierzek, Biochemistry 48, 10882-10893 (2009).

  41. "Optical Melting Measurements of Nucleic Acid Thermodynamics," S.J. Schroeder and D.H. Turner, in Methods in Enzymology, 468, 371-387, ed. by D. Herschlag, Academic Press, Burlington, (2009).

  42. "Effects of Restrained Sampling Space and Non-planar 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" I. Yildirim, H. Stern, J. Sponer, N. Spackova, and D.H. Turner, J. Chem. Theory and Comput. 5, 2088-2100 (2009).

  43. "Secondary Structures for 5' Regions of R2 Retrotransposon RNAs Reveal a Novel Conserved Pseudoknot and Regions that Evolve under Different Constraints" E. Kierzek, S.M. Christensen, T.H. Eickbush, R. Kierzek, D.H. Turner, and W.N. Moss, J. Mol. Biol. 390, 428-442 (2009).

  44. "A CA+ Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops" G. Chen, S.D. Kennedy, and D.H. Turner, Biochemistry 48, 5738-5752 (2009).

  45. "Contributions of Stacking, Preorganization, and Hydrogen Bonding to the Thermodynamic Stability of Duplexes between RNA and 2'-O-methyl RNA with Locked Nucleic Acids (LNA)" E. Kierzek, A. Pasternak, K. Pasternak, Z. Gdaniec, I. Yildirim, D. Turner, and R. Kierzek, Biochemistry, 48, 4377-4387 (2009).

  46. "NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon" J.M. Hart, S.D. Kennedy, D.H. Mathews, and D.H. Turner, J. Am. Chem. Soc. 130, 10233-10239 (2008).

  47. "The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure" A. Pasternak, E. Kierzek, K. Pasternak, A. Fratczak, D.H. Turner, and R. Kierzek, Biochemistry 47, 1249-1258 (2008).

  48. "Isoenergetic Penta- and Hexanucleotide Microarray Probing and Chemical Mapping Provide a Secondary Structure Model for an RNA Element Orchestrating R2 Retrotransposon Protein Function" E. Kierzek, R. Kierzek, W.N. Moss, S.M. Christensen, T.H. Eickbush, and D.H. Turner, Nucleic Acids Res. 36, 1770-1782 (2008).

  49. "Selective Nanoparticle Quenching of Fluorescence from Unbound Oligonucleotides as a Probe of RNA Structure" H. Li, R. Liang, D.H. Turner, L.J. Rothberg, and S. Duan, RNA, 13, 2034-2041 (2007).

  50. "NMR Reveals Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA" N. Shankar, T. Xia, S.D. Kennedy, T.R. Krugh, D.H. Mathews, and D.H. Turner, Biochemistry, 46, 12665-12678 (2007).

  51. "The Chemical Synthesis of 2'-O-methyl-2,6-diaminopurine Riboside and LNA-2,6-diaminopurine Riboside and their Influence on the Thermodynamic Properties of 2'-O-methyl RNA/RNA Heteroduplexes" A. Pasternak, E. Kierzek, K. Pasternak, D.H. Turner, and R. Kierzek, Nucleic Acids Res., 35, 4055-4063 (2007).

  52. "Stacking Effects on Local Structure in RNA: The Structure of Tandem GA Pairs Changes When Flanking GC Pairs are Replaced by isoG-isoC Pairs" G. Chen, R. Kierzek, I. Yildirim, T. R. Krugh, D. H. Turner, and S. D. Kennedy, J. Phys. Chem. B, 111, 6718-6727 (2007).

  53. "RNA Secondary Structure Prediction" D. H. Mathews*, D. H. Turner, and M. Zuker, Current Protocols in Nucleic Acid Chemistry, Supplement 28, 11.2.1 - 11.2.17 (2007).

  54. "A Set of Nearest Neighbor Parameters for Predicting the Enthalpy Change of RNA Secondary Structure Formation" Z. J. Lu, D. H. Turner, and D. H. Mathews, Nucleic Acids Res., 34, 4912-4924 (2006).

  55. "The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the Structural Features that Shape the Thermodynamic Stability of GA Pairs" B. S. Tolbert, S. D. Kennedy, S. J. Schroeder, T. R. Krugh, and D. H. Turner, Biochemistry, 46, 1511-1522 (2007).

  56. "The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from its Structure in Crystals of 50S Ribosomal Subunits" N. Shankar, S. D. Kennedy, G. Chen, T. R. Krugh, and D. H. Turner, Biochemistry, 45, 11776-11789 (2006).

  57. "Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA" S. Duan, D. H. Mathews, and D. H. Turner, Biochemistry, 45, 9819-9832 (2006).

  58. "Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides" E. Kierzek, D. H. Mathews, A. Ciesielska, D. H. Turner, and R. Kierzek, Nucleic Acids Res., 34, 3609-3614 (2006).

  59. "Prediction of RNA secondary structure by free energy minimization" D. H. Mathews and D. H. Turner, Curr Opin Struct Biol., 16, 270-278 (2006).

  60. "The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs" S. B. Jang, L. W. Hung, M. S. Jeong, E. L. Holbrook, X. Chen, D. H. Turner, and S. R. Holbrook, Biophys J., 90, 4530-4537 (2006).

  61. "An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA" G. Chen, S. D. Kennedy, J. Qiao, T. R. Krugh, D. H. Turner, Biochemistry, 45, 6889-6903 (2006).

  62. "Consecutive GA pairs stabilize medium size RNA internal loops" G. Chen, and D. H. Turner, Biochemistry, 45, 4025-4043 (2006).

  63. "Facilitating RNA Structure Prediction with Microarrays" E. Kierzek, R. Kierzek, D. H. Turner, and I. E. Catrina, Biochemistry, 45, 581-593 (2006).

  64. "RNA challenges for computational chemists" I. Yildirim and D. H. Turner, Biochemistry, 44, 13225-13234 (2005).

  65. "The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes" E. Kierzek, A. Ciesielska, K. Pasternak, D. H. Mathews, D. H. Turner, and R. Kierzek, Nucleic Acids Res., 33, 5082-5093 (2005).

  66. "Activity of Hoechst 33258 against Pneumocystis carinii f. sp. muris, Candida albicans, and Candida dubliniensis" M. D. Disney, R. Stephenson, T. W. Wright, C. G. Haidaris, D. H. Turner, F. Gigliotti, Antimicrob Agents Chemother, 49, 1326-1330 (2005).

  67. "Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs" G. Chen, B. M. Znosko, S. D. Kennedy, T. R. Krugh, and D. H. Turner, Biochemistry, 44, 2845 - 2856 (2005).

  68. "Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns" B. M. Znosko, S. D. Kennedy, P. C. Wille, T. R. Krugh, D. H. Turner, Biochemistry, 43, 15822-37 (2004).

  69. "Hoechst 33258 Selectively Inhibits Group I Intron Self-Splicing by Affecting RNA Folding," M. D. Disney, J. L. Childs, and D. H. Turner, Chembiochem., 5, 1-6 (2004).

  70. "Factors Affecting Thermodynamic Stabilities of RNA 3X3 Internal Loops," G. Chen, B. M. Znosko, X. Jiao, and D. H. Turner, Biochemistry, 43, 12865-12876 (2004).

  71. "Secondary Structure Models of the 3’ Untranslated Regions of Diverse R2 RNAs," A. M. Ruschak, D.H. Mathews, A. Bibillo, S. L. Spinelli, J. A. Childs, T. H. Eickbush, and D. H. Turner, RNA, 10, 978-987 (2004).

  72. "Structures of Two RNA Octamers Containing Tandem GA Base Pairs," S. B. Jang, K. Baeyens, M. S. Jeong, J. SantaLucia, Jr., D. Turner, and S. R. Holbrook, Acta Cryst. D60, 829-835 (2004).

  73. "Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure," D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker, and D. H. Turner, Proc. Natl. Acad. Sci. USA, 101, 7287-7292 (2004).

  74. "New Approaches to Targeting RNA with Oligonucleotides: Inhibition of Group I Intron Self-Splicing," M. D. Disney, J. L. Childs, and D. H. Turner, Biopolymers, 73, 151-161 (2004).

  75. "Thermodynamic Stability and Structural Features of the J4/5 Loop in a Pneumocystis carinii Group I Intron," S. J. Schroeder, M. A. Fountain, S. D. Kennedy, P. J. Lukavsky, J. D. Puglisi, T. R. Krugh, and D. H. Turner, Biochemistry, 42, 14184-14196 (2003).

  76. "Inhibition of Escherichia coli RNase P by Oligonucleotide Directed Misfolding of RNA," J. L. Childs, A. W. Poole, and D. H. Turner, RNA, 9, 1437-1445 (2003).

  77. "NMR Studies of DNA Single Strands and DNA:RNA Hybrids with and without 1-Propynylation at C5 of Oligopyrimidines," B. M. Znosko, T. W. Barnes, III, T. R. Krugh, and D. H. Turner, J. Am. Chem. Soc., 125, 6090-6097 (2003).

  78. "Uptake and Antifungal Activity of Oligonucleotides in Candida albicans," M. D. Disney, C. G. Haidaris, and D. H. Turner, Proc. Natl. Acad. Sci. USA, 100, 1530-1534 (2003).

  79. "Oligonucleotide Directed Misfolding of RNA Inhibits Candida albicansGroup I Intron Splicing," J. L. Childs, M. D. Disney, and D. H. Turner, Proc. Natl. Acad. Sci. USA, 99, 11091-11096 (2002).

  80. "Dynalign: An Algorithm for Finding the Secondary Structure Common to Two RNA Sequences," D. H. Mathews and D. H. Turner, J. Mol. Biol., 317, 191-203 (2002).

  81. "Molecular Recognition in Purine-Rich Internal Loops: Thermodynamics, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2," B. M. Znosko, M. E. Burkard, T. R. Krugh, and D. H. Turner, Biochemistry, 41, 14978-14987 (2002).

  82. "Sheared Aanti•Aanti Base Pairs in a Destabilizing Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2," B. M. Znosko, M. E. Burkard, S. J. Schroeder, T. R. Krugh, and D. H. Turner, Biochemistry, 41, 14969-14977 (2002).

  83. "Molecular Recognition by the Candida albicans Group I Intron: Tertiary Interactions with an Imino G•A Pair Facilitate Binding of the 5' Exon and Lower the KM for Guanosine," M. D. Disney and D. H. Turner, Biochemistry, 41, 8113-8119 (2002).

  84. "Experimentally Derived Nearest Neighbor Parameters for the Stability of RNA Three- and Four-Way Multibranch Loops," D. H. Mathews and D. H. Turner, Biochemistry, 41, 869-880 (2002).

  85. "Long-Range Cooperativity due to C5-Propynylation of Oligopyrimidines Enhances Specific Recognition by Uridine of ribo-Adenosine Over ribo-Guanosine," T. W. Barnes III and D. H. Turner, J. Am. Chem. Soc., 123, 9186-9187 (2001b).

  86. "Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines," T. W. Barnes III, and D. H. Turner, J. Am. Chem. Soc., 123, 4107-4118 (2001a).

  87. "Stability and Structure of RNA Duplexes Containing Isoguanosine and Isocytidine," X. Chen, R. Kierzek, and D. H. Turner, J. Am. Chem. Soc., 123, 1267-1274 (2001).

  88. "The Energetics of Small Internal Loops in RNA," S. J. Schroeder, M. E. Burkard, and D. H. Turner, Biopolymers Nucleic Acid Sci., 52, 157-167 (2001).

  89. "Substrate Recognition by a Yeast 2'-Phosphotransferase Involved in tRNA Splicing and by its E. coli Homolog," M. A. Steiger, R. Kierzek, D. H. Turner, and E. M. Phizicky, Biochemistry, 40, 14098-14105 (2001).

  90. "C5-(1-Propynyl)-2'-deoxy-Pyrimidines Enhance Mismatch Penalties of DNA:RNA Duplex Formation," T. W. Barnes III and D. H. Turner, Biochemistry, 40, 12738-12745 (2001c).

  91. "Thermodynamic Stabilities of Internal Loops with GU Closing Pairs in RNA," S. J. Schroeder and D. H. Turner, Biochemistry, 40, 11509-11517 (2001).

  92. "Thermodynamics of Three-Way Multibranch Loops in RNA," J. M. Diamond, D. H. Turner, and D. H. Mathews, Biochemistry, 40, 6971-6981 (2001).

  93. "Binding Enhancement by Tertiary Interactions and Suicide Inhibition of a Candida albicans Group I Intron by Phosphoramidate and 2'-O-Methyl Hexanucleotides," M. D. Disney, T. Matray, S. M. Gryaznov, and D. H. Turner, Biochemistry, 40, 6520-6526 (2001).

  94. "Recognition Elements for 5' Exon Substrate Binding to the Candida albicansGroup I Intron," M. D. Disney, C. G. Haidaris, and D. H. Turner, Biochemistry, 40, 6507-6519 (2001).

  95. "Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair," M. E. Burkard, T. Xia, and D. H. Turner, Biochemistry, 40, 2478-2483 (2001).

  96. "Use of Chemical Modification to Elucidate RNA Folding Pathways," D. H. Mathews and D. H. Turner, in Current Protocols in Nucleic Acid Chemistry, ed. by S. Beaucage, D. E. Bergstrom, G. D. Glick, and R. A. Jones, John Wiley & Sons, p. 11.9.1-11.9.4.

  97. "Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways," P. C. Bevilacqua and D. H. Turner, in Current Protocols in Nucleic Acid Chemistry, ed. by S. Beaucage, D. E. Bergstrom, G. D. Glick, and R. A. Jones, John Wiley & Sons, p. 11.8.1-11.8.6.

  98. "Contributions of Individual Nucleotides to Tertiary Binding of Substrate by a Pneumocystis carinii Group I Intron," M. D. Disney, S. M. Gryaznov, and D. H. Turner, Biochemistry, 39, 14269-14278 (2000).

  99. "NMR Structures of r(GCAGGCGUGC)2 and Determinants of Stability for Single Guanosine-Guanosine Base Pairs," M. E. Burkard and D. H. Turner, Biochemistry, 39, 11748-11762 (2000).

  100. "Factors Affecting the Thermodynamic Stability of Small Asymmetric Internal Loops in RNA," S. J. Schroeder and D. H. Turner, Biochemistry, 39, 9257-9274 (2000).

  101. "Nuclear Magnetic Resonance Spectroscopy and Molecular Modeling Reveal that Different Hydrogen Bonding Patterns are Possible for G∙U Pairs: One Hydrogen Bond for each G∙U Pair in r(GGCGUGCC)2 and Two for each G∙U Pair in r(GAGUGCUC)2," X. Chen, J. A. McDowell, R. Kierzek, T. R. Krugh, and D. H. Turner, Biochemistry, 39, 8970-8982 (2000).

  102. "Targeting a Pneumocystis carinii Group I Intron with Methylphosphonate Oligonucleotides: Backbone Charge is Not Required for Binding or Reactivity," M. D. Disney, S. M. Testa, and D. H. Turner, Biochemistry, 39, 6991-7000 (2000).

  103. "The Chemical Synthesis of Oligoribonucleotides with Selectively Placed 2'-O-Phosphates, " R. Kierzek, M. A. Steiger, S. L. Spinelli, D. H. Turner, and E. M. Phizicky, Nucleosides, Nucleotides & Nucleic Acids 19, 917-933 (2000).

  104. "Conformational Changes," D. H. Turner, chapter 8 in Nucleic Acids: Structures, Properties and Functions ed. by V. A. Bloomfield, D. M. Crothers and I. Tinoco, Jr. with chapters by J. Hearst, P. Kollman, D. Wemmer and D. H. Turner, University Science Press (2000).

  105. "Expanded CUG Repeat RNAs form Hairpins that Activate the Double-Stranded-RNA-Dependent Protein Kinase PKR," B. Tian, R. J. White, T. Xia, S. Welle, D. H. Turner, M. B. Mathews, and C. A. Thornton, RNA, 6, 79-87 (2000).

  106. "RNA Secondary Structure Prediction," D. H. Mathews, D. H. Turner, and M. Zuker, in Current Protocols in Nucleic Acid Chemistry, ed. by S. Beaucage, D. E. Bergstrom, G. D. Glick, and R. A. Jones, John Wiley & Sons, p. 11.2.1-11.2.10 (2000).

  107. "The Application of Thermodynamics to the Modeling of RNA Secondary Structure," D. H. Mathews, J. M. Diamond, and D. H. Turner, in Thermodynamics in Biology, ed. by E. Di Cera, Oxford University Press, pp. 177-201 (2000).

  108. "Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide," M. Zuker, D. H. Mathews, and D. H. Turner, in RNA Biochemistry and Biotechnology, ed. by J. Barciszewski and B. F. C. Clark, Kluwer Academic Publishers, p. 11-43 (1999).

  109. "Predicting Oligonucleotide Affinity to Nucleic Acid Targets," D. H. Mathews, M. E. Burkard, S. M. Freier, J. R. Wyatt, and D. H. Turner, RNA, 5, 1458-1469 (1999).

  110. "Thermodynamics of RNA-RNA Duplexes with 2- or 4-Thiouridines: Implications for Antisense Design and Targeting a Group I Intron," S. M. Testa, M. D. Disney, D. H. Turner, and R. Kierzek, Biochemistry, 38, 16655-16662 (1999).

  111. "Thermodynamics of Single Mismatches in RNA Duplexes," R. Kierzek, M. E. Burkard, and D. H. Turner, Biochemistry, 38, 14214-14223 (1999).

  112. "Thermodynamics of Unpaired Terminal Nucleotides on Short RNA Helixes Correlates with Stacking at Helix Termini in Larger RNAs," M. E. Burkard, R. Kierzek, and D. H. Turner, J. Mol. Biol., 290, 967-982 (1999).

  113. "Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure," D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol., 288, 911-940 (1999).

  114. "In vitro Suicide Inhibition of Self-Splicing of a Group I Intron from Pneumocystis carinii by an N3¢®P5¢Phosphoramidate Hexanucleotide," S. M. Testa, S. M. Gryaznov, and D. H. Turner, Proc. Natl. Acad. Sci. U.S.A., 96, 2734-2739 (1999).

  115. "Thermodynamics of RNA Secondary Structure Formation," T. Xia, D. H. Mathews, and D. H. Turner, in Prebiotic Chemistry, Molecular Fossils, Nucleosides, and RNA, ed. by D. G. Söll, S. Nishimura, and P. B. Moore, Elsevier, p. 21-48 (1999) (reprinted in paperback as RNA (2001)).

  116. "Transient ADP-ribosylation of a 2¢-phosphate Implicated in its Removal from Ligated tRNA during Splicing in Yeast," S. L. Spinelli, R. Kierzek, D. H. Turner, and E. M. Phizicky, J. Biol. Chem., 274, 2637-2644 (1999).

  117. "Schematic Diagrams of Secondary and Tertiary Structure Elements," M. E. Burkard, D. H. Turner, and I. Tinoco, Jr., in The RNA World, Appendix 2, 2nd edition, ed. by R. F. Gesteland, T. R. Cech, and J. F. Atkins, Cold Spring Harbor Press, 681-685 (1999).

  118. "Structures of Base Pairs Involving at Least Two Hydrogen Bonds," M. E. Burkard, D. H. Turner, and I. Tinoco, Jr., in The RNA World, Appendix 1, 2nd edition, ed. by R. F. Gesteland, T. R. Cech, and J. F. Atkins, Cold Spring Harbor Press, 675-680 (1999).

  119. "The Interactions that Shape RNA," M. E. Burkard, D. H. Turner, and I. Tinoco, Jr., in The RNA World, 2nd edition, ed. by R. F. Gesteland, T. R. Cech and J. F. Atkins, Cold Spring Harbor Press, p. 233-264 (1999).

  120. "Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs," T. Xia, J. SantaLucia, Jr., M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry, 37, 14719-14735 (1998).

  121. "Antisense Binding Enhanced by Tertiary Interactions: Binding of Phosphorothioate and N3'®P5' Phosphoramidate Hexanucleotides to the Catalytic Core of a Group I Ribozyme from the Mammalian Pathogen Pneumocystis carinii," S. M. Testa, S. M. Gryaznov, and D. H. Turner, Biochemistry, 37, 9379-9385 (1998).

  122. "An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Thermodynamic Parameters," D. H. Mathews, T. C. Andre, J. Kim, D. H. Turner, and M. Zuker in Molecular Modeling of Nucleic Acids (Leontis, N. B., and SantaLucia, J., Jr., eds.), Am. Chem. Soc. Pub., New York p. 246-257 (1998).

  123. "Measuring the Thermodynamics of RNA Secondary Structure Formation," J. SantaLucia, Jr. and D. H. Turner, Biopolymers, 44, 309-319 (1997).

  124. "A Pneumocystis carinii Group I Intron Ribozyme that Does Not Require 2' OH Groups on its 5' Exon Mimic for Binding to the Catalytic Core," S. M. Testa, C. G. Haidaris, F. Gigliotti, and D. H. Turner, Biochemistry, 36, 15303-15314 (1997).

  125. "The Crystal Structure of an RNA Oligomer Incorporating Tandem Adenosine-Inosine Mismatches," R. J. Carter, K. J. Baeyens, J. SantaLucia, D. H. Turner and S. R. Holbrook, Nucleic Acids Res., 25, 4117-4122 (1997).

  126. "Thermodynamics of Nonsymmetric Tandem Mismatches Adjacent to G×C Base Pairs in RNA," T. Xia, J. A. McDowell, and D. H. Turner, Biochemistry, 36, 12486-12497 (1997).

  127. "Guanosine Binds to the Tetrahymena Ribozyme in More than One Step, and its 2'-OH and the Nonbridging pro-SpPhosphoryl Oxygen at the Cleavage Site Are Required for Productive Docking," L. A. Profenno, R. Kierzek, S. M. Testa, and D. H. Turner, Biochemistry, 36, 12477-12485 (1997).

  128. "Effects of Mg2+and the 2' OH of Guanosine on Steps Required for Substrate Binding and Reactivity with the Tetrahymena Ribozyme Reveal Several Local Folding Transitions," Y. Li and D. H. Turner, Biochemistry, 36, 11131-11139 (1997).

  129. "Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Wobble Pairs: NMR Structures of (rGGAGUUCC)2and (rGGAUGUCC)2," J. A. McDowell, L. He, X. Chen, and D. H. Turner, Biochemistry, 36, 8030-8038 (1997).

  130. "Solution Structure of (rGGCAGGCC)2by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach," M. Wu, J. SantaLucia, Jr., and D. H. Turner Biochemistry, 36, 4449-4460 (1997).

  131. "Secondary Structure Model of the RNA Recognized by the Reverse Transcriptase from the R2 Retrotransposable Element," D. H. Mathews, A. R. Banerjee, D. D. Luan, T. H. Eickbush, and D. H. Turner, RNA, 3, 1-16 (1997).

  132. "G×A and U×U Mismatches Can Stabilize RNA Internal Loops of Three Nucleotides," S. Schroeder, J. Kim, and D. H. Turner, Biochemistry, 35, 16105-16109 (1996).

  133. "An Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Mismatches: Solution Structure of (rGAGGUCUC)2by Two-Dimensional NMR and Simulated Annealing," J. A. McDowell and D. H. Turner, Biochemistry, 35, 14077-14089 (1996).

  134. "Thermodynamics of Coaxially Stacked Helixes with GA and CC Mismatches," J. Kim, A. E. Walter, and D. H. Turner, Biochemistry, 35, 13753-13761 (1996).

  135. "Dynamics of a Group I Ribozyme Detected by Spectroscopic Methods," D. H. Turner, Y. Li, M. Fountain, L. Profenno, and P. C. Bevilacqua, Nucleic Acids and Molecular Biology, 10, 19-32 (1996).

  136. "Thermodynamics of Base Pairing," D. H. Turner, invited review, Current Opinion in Structural Biology, 6, 299-304 (1996).

  137. "Solution Structure of (rGCGGACGC)2by Two-Dimensional NMR and the Interative Relaxation Matrix Approach," M. Wu and D. H. Turner, Biochemistry, 35, 9677-9689 (1996).

  138. "Structural Features of a Six-Nucleotide RNA Hairpin Loop Found in Ribosomal RNA," M. A. Fountain, M. J. Serra, T. R. Krugh, and D. H. Turner, Biochemistry, 35, 6539-6548 (1996).

  139. "A Mechanistic Framework for the Second Step of Splicing Catalyzed by the Tetrahymena Ribozyme," P. C. Bevilacqua, N. Sugimoto, and D. H. Turner, Biochemistry, 35, 648-658 (1996).

  140. "Predicting Thermodynamic Properties of RNA," M. J. Serra and D. H. Turner, Methods in Enzymology, 259, 242-261 (1995).

  141. "Thermodynamic and Activation Parameters for Binding of a Pyrene-Labeled Substrate by the Tetrahymena Ribozyme: Docking is Not Diffusion Controlled and is Driven by a Favorable Entropy Change," Y. Li, P. C. Bevilacqua, D. H. Mathews, and D. H. Turner, Biochemistry, 34, 14394-14399 (1995).

  142. "The Time Dependence of Chemical Modification Reveals Slow Steps in the Folding of a Group I Ribozyme," A. R. Banerjee and D. H. Turner, Biochemistry, 34, 6504-6512 (1995).

  143. "A Periodic Table of Symmetric Tandem Mismatches in RNA," M. Wu, J. A. McDowell, and D. H. Turner, Biochemistry, 34, 3204-3211 (1995).

  144. "Replacement of the Conserved G.U with a G-C Pair at the Cleavage Site of the Tetrahymena Ribozyme Decreases Binding, Reactivity, and Fidelity," A. M. Pyle, S. Moran, S. A. Strobel, T. Chapman, D. H. Turner, and T. R. Cech, Biochemistry, 33, 13856-13863 (1994).

  145. "A Model for the Stabilities of RNA Hairpins Based on a Study of the Sequence Dependence of Stability for Hairpins of Six Nucleotides," M. J. Serra, T. J. Axenson, and D. H. Turner, Biochemistry, 33, 14289-14296 (1994).

  146. "Sequence Dependence of Stability for Coaxial Stacking of RNA Helixes with Watson-Crick Base Paired Interfaces," A. E. Walter and D. H. Turner, Biochemistry, 33, 12715-12719 (1994).

  147. "The Stability and Structure of Tandem GA Mismatches in RNA Depend on Closing Base Pairs," A. E. Walter, M. Wu, and D. H. Turner, Biochemistry, 33, 11349-11354 (1994).

  148. "Fluorescence-Detected Stopped Flow with a Pyrene Labeled Substrate Reveals that Guanosine Facilitates Docking of the 5' Cleavage Site into a High Free Energy Binding Mode in the Tetrahymena Ribozyme," P. C. Bevilacqua, Y. Li, and D. H. Turner, Biochemistry, 33, 11340-11348 (1994).

  149. "Coaxial Stacking of Helixes Enhances Binding of Oligoribonucleotides and Improves Predictions of RNA Folding," A. E. Walter, D. H. Turner, J. Kim, M. H. Lyttle, P. Müller, D. H. Mathews, and M. Zuker, Proc. Natl. Acad. Sci. U.S.A., 91, 9218-9222 (1994).

  150. "Structure of (rGGCGAGCC)2in Solution from NMR and Restrained Molecular Dynamics," J. SantaLucia, Jr. and D. H. Turner, Biochemistry, 32, 12612-12623 (1993).

  151. "A Novel NAD Derivative Produced During tRNA Splicing: ADP-ribose 1”-2” Cyclic Phosphate," G. M. Culver, S. M. McCraith, M. Zillman, R. Kierzek, N. Michaud, R. D. LaReau, D. H. Turner, and E. M. Phizicky, Science, 261, 206-208 (1993).

  152. "Cooperative and Anticooperative Binding to a Ribozyme," P. C. Bevilacqua, K. A. Johnson, and D. H. Turner, Proc. Natl. Acad. Sci. U.S.A., 90, 8357-8361 (1993).

  153. "RNA Hairpin Loop Stability Depends on Closing Base Pair," M. J. Serra, M. H. Lyttle, T. J. Axenson, C. A. Schadt, and D. H. Turner, Nucleic Acids Res., 21, 3845-3849 (1993).

  154. "Effect of a 5'-Phosphate on the Stability of Triple Helix," K. Yoon, C. A. Hobbs, A. E. Walter, and D. H. Turner, Nucleic Acids Research, 21, 601-606 (1993).

  155. "Binding of Guanosine and 3' Splice Site Analogues to a Group I Ribozyme: Interactions with Functional Groups of Guanosine and with Additional Nucleotides," S. Moran, R. Kierzek, and D. H. Turner, Biochemistry, 32, 5247-5256 (1993).

  156. "5’-Amino Pyrene Provides a Sensitive, Non-Perturbing Fluorescent Probe of RNA Secondary and Tertiary Structure Formation," R. Kierzek, D. H. Turner, Y. Li, and P. C. Bevilacqua, J. Am. Chem. Soc., 115, 4985-4992 (1993).

  157. "Thermal Unfolding of a Group I Ribozyme: The Low Temperature Transition is Primarily Disruption of Tertiary Structure," A. R. Banerjee, J. A. Jaeger, and D. H. Turner, Biochemistry, 32, 153-163 (1993).

  158. "Thermodynamic Considerations for Evolution by RNA," D. H. Turner and P. C. Bevilacqua, invited chapter in The RNA World, ed. by R. F. Gesteland and J. F. Atkins, Cold Spring Harbor Press, p. 447-464 (1993).

  159. "Dynamics of Ribozyme Binding of Substrate Revealed by Fluorescence Detected Stopped-Flow," P. C. Bevilacqua, R. Kierzek, K. A. Johnson, and D. H. Turner, Science, 258, 1355-1358 (1992).

  160. "Context Dependence of Hydrogen Bond Free Energy Revealed by Substitutions in an RNA Hairpin," J. SantaLucia, Jr., R. Kierzek, and D. H. Turner, Science, 256, 217-219 (1992).

  161. "Bulges in Nucleic Acids," D. H. Turner, invited review for Current Opinion in Structural Biology, 2, 334-337 (1992).

  162. "Association of 2'-5' Oligoribonucleotides," R. Kierzek, L. He, and D. H. Turner, Nucleic Acids Res., 20, 1685-1690 (1992).

  163. "Nearest Neighbor Parameters for GU Mismatches: 5'GU3'/3'UG5' is Destabilizing in the Contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGA,but Stabilizing in GGUC/CUGG." L. He, R. Kierzek, J. SantaLucia, Jr., A. Walter, and D. H. Turner, Biochemistry, 30, 11124-11132 (1991).

  164. "Comparison of Binding of Mixed Ribose-Deoxyribose Analogues of CUCU to a Ribozyme and to GGAGAA by Equilibrium Dialysis: Evidence for Ribozyme Specific Interactions with 2' OH Groups," P. C. Bevilacqua and D. H. Turner, Biochemistry, 30, 10632-10640 (1991).

  165. "Stabilities of Consecutive A•C, C•C, G•G, U•C, and U•U Mismatches in RNA Internal Loops: Evidence for Stable Hydrogen Bonded U•U and C•C+ Pairs," J. SantaLucia, Jr., R. Kierzek, and D. H. Turner, Biochemistry, 30, 8242-8251 (1991).

  166. "A Comparison of Optimal and Suboptimal RNA Secondary Structures Predicted by Free Energy Minimization with Structures Determined by Phylogenetic Comparison," M. Zuker, J. A. Jaeger, and D. H. Turner, Nucleic Acids Res., 19, 2707-2714 (1991).

  167. "Thermodynamic Study of Internal Loops in Oligoribonucleotides: Symmetric Loops are More Stable than Asymmetric Loops," A. E. Peritz, R. Kierzek, N. Sugimoto, and D. H. Turner, Biochemistry, 30, 6428-6436 (1991).

  168. "Functional Group Substitutions as Probes of Hydrogen Bonding Between GA Mismatches in RNA Internal Loops," J. SantaLucia, Jr., R. Kierzek, and D. H. Turner, J. Am. Chem. Soc., 113, 4313-4322 (1991).

  169. "Melting and Chemical Modification of a Cyclized Self-Splicing Group I Intron: Similarity of Structures in 1 M Na+, in 10 mM Mg2+, and in the Presence of Substrate," J. A. Jaeger, M. Zuker, and D. H. Turner, Biochemistry, 29, 10147-10158 (1990).

  170. "Effects of GA Mismatches on the Structure and Thermodynamics of RNA Internal Loops," J. SantaLucia, Jr., R. Kierzek, and D. H. Turner, Biochemistry, 29, 8813-8819 (1990).

  171. “Thermodynamics and Kinetics of Base-Pairing and of DNA and RNA Self-Assembly and Helix-Coil Transition,” D. H. Turner, N. Sugimoto, and S. M. Freier, in "Nucleic Acids," Vol. 1c by W. Saenger, Landolt-Bornstein series, Springer-Verlag, Berlin, p. 201-227 (1990).

  172. "Thermodynamic and Spectroscopic Study of Bulge Loops in Oligoribonucleotides," C. E. Longfellow, R. Kierzek, and D. H. Turner, Biochemistry, 29, 278-285 (1990).

  173. "Predicting Optimal and Suboptimal Secondary Structure for RNA," J. A. Jaeger, D. H. Turner, and M. Zuker, Methods in Enzymology, Vol. 183, 280-305 (1990).

  174. "Inhibition of Deoxyribo Oligonucleotides on the Circle Opening Reaction of the Intervening Sequence from Tetrahymena thermophila," N. Sugimoto, M. Sasaki, R. Kierzek, and D. H. Turner, Chemistry Letters, 747-748 (1990).

 

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