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Year
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Publication
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2008
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Saraiya, A.A., Lamichhane, T. N., Chow, C.S., SantaLucia, J., Jr., and Cunningham, P.R. (2008) "Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA", J. Mol. Biol., 376, 645-657. Download PDF |
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2007
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Bevilacqua, P.C., SantaLucia, J., Jr. (2007) "The Biophysics of RNA", ACS Chem. Biol., 2, 440–444. Download PDF |
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2007
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Aduri, R., Psciuk, B.T., Saro, P., Taniga, H., Schlegel, H.B., SantaLucia, J., Jr. (2007) "AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA", J. Chem. Theory and Comput., 3, 1464 -1475. Download PDF |
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2007
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SantaLucia, J., Jr. (2007) "Physical Principles and Visual-OMP Software for Optimal PCR Design", Methods in Molecular Biology: PCR Primer Design, Anton Yuryev, Ed., Humana Press, Totowa, New Jersey, Methods Mol. Biol. |
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2006
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Dhimitruka, I., SantaLucia, J., Jr. (2006) "Investigation of the Yamaguchi Esterification Mechanism. Synthesis of a Lux-S Enzyme Inhibitor Using an Improved Esterification Method", Organic Letters, 2006, 8, 47-50. Download PDF |
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2005
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Watkins, N.E., Jr., SantaLucia, J., Jr. (2005) "Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes", Nucleic Acids Research, 2005, 33, 6258-6267. Download PDF |
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2004
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SantaLucia, J., Jr., Hicks, D. (2004) "The Thermodynamics of DNA Structural Motifs", Annu. Rev. Biophys. Biomol. Struct., 33, 415-40. Download PDF |
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2004
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Jang, S.B., Baeyens, K., Jeong, M.S., SantaLucia, J., Jr., Turner, D., Holbrook, S.R. (2004) "Structures of two RNA octamers containing tandem G-A base pairs", Acta Cryst., 60D, 829-835. Download PDF |
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2004
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Irani, R.J., SantaLucia, J., Jr. (2004) "Efficient preparation of 2-deoxy-3,5-di-O-p-toluoyl-a-D-ribofuranosyl chloride", SynLett, 2, 335-337. Download PDF |
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2002
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Irani, R.J., SantaLucia, J., Jr. (2002) "The Synthesis of Anti-fixed 3-Methyl-3-deaza-2'-deoxyadenosine and Other 3H-imidazo[4,5-c]pyridine Analogs", Nucleosides, Nucleotides & Nucleic Acids, 21, 737-751. Download PDF |
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2002
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Chow, C.S., Cunningham, P.R., Lee, K.S., Meroueh, M., SantaLucia, J., Jr., Varma, S. (2002) "Photoinduced cleavage by a rhodium complex at G-U mismatches and exposed guanines in large and small RNAs", Biochimie, 84, 859-868. Download PDF |
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2002
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Biswas, T., Clos, L.J., Santa Lucia, J., Jr., Mitra, S., Roy, R.J. (2002) "Binding of Specific DNA Base-pair Mismatches by N-Methylpurine-DNA Glycosylase and its implication in Initial Damage Recognition", Mol. Biol., 320, 503-513. Download PDF |
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2001
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Morosyuk, S.M., SantaLucia, J., Jr., Cunningham, P.R. (2001) "Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: III. Instant Evolution Studies", Mol. Biol., 307, 213-221. Download PDF |
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2001
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Morosyuk, S.M., Cunningham, P.R., SantaLucia, J., Jr. (2001) "Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: II. NMR Solution Structure", Mol. Biol., 307, 197-211. Download PDF |
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2000
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Morosyuk, S.V., Lee, K., SantaLucia, J., Jr., & Cunningham, P.R. J. (2000) "Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: Analysis of the stem nucleotides", Mol. Biol., 300, 113-126. Download PDF |
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2000
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Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia, J., Jr., Scaringe, S.A., Chow, C.S. (2000) "Unique Structural and Stabilizing Roles for the Individual Pseudouridine Residues in the 1920 Region of Escherichia coli 23S rRNA", Nucleic Acids Res., 28, 2075-2083. Download PDF |
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2000
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Bommarito, S., Peyret, N., SantaLucia, J., Jr. (2000) "Thermodynamic parameters for DNA sequences with dangling ends", Nucleic Acids Res., 28, 1929-1934. Download PDF |
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1999
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Irani, R., SantaLucia, J., Jr. (1999) "The Synthesis of 5-iodocytidine Phosphoramidite for Heavy Atom Derivatization of RNA", Tetrahedron Lett., 40, 8961-8964. Download PDF |
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1999
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Blake, R.D., Bizzaro, J.W., Blake, J.D., Day, G.R., Delcourt, S.G., Knowles, J., Marx, K. A., SantaLucia, J., Jr. (1999) "Statistical Mechanical Simulation of Polymeric DNA Melting with MELTSIM", Bioinformatics, 15, 370-375. Download PDF |
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1999
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Peyret, N., Seneviratne, P.A., Allawi, H.T., SantaLucia, J., Jr. (1999) "Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches", Biochemistry, 38, 3468-3477. Download PDF |
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1998
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Xia, T., SantaLucia, J., Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., Turner, D.H. (1998) "Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs", Biochemistry, 37, 14719-14735. Download PDF |
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1998
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Allawi, H.T., SantaLucia, J., Jr. (1998) "NMR Solution Structure of a DNA dodecamer containing single G-T Mismatches", Nucleic Acids Res., 26, 4925-4934. Download PDF |
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1998
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SantaLucia, J., Jr. (1998) "A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics", Proc. Natl. Acad. Sci. USA, 95, 1460-1465. Download PDF |
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1998
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Allawi, H.T., SantaLucia, J., Jr. (1998) "Nearest-Neighbor Thermodynamics of Internal A-C Mismatches in DNA: Sequence Dependence and pH Effects", Biochemistry, 37, 9435-9444. Download PDF |
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1998
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Allawi, H.T., SantaLucia, J., Jr. (1998) "Thermodynamics of Internal C-T Mismatches in DNA", Nucleic Acids Res., 26, 2694-2701. Download PDF |
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1998
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Allawi, H.T., SantaLucia, J., Jr. (1998) "Nearest Neighbor Thermodynamic Parameters for Internal G-A Mismatches in DNA", Biochemistry, 37, 2170-2179. Download PDF |
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1998
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Arghavani, M.B., SantaLucia, J., Jr., Romano, L.J. (1998) "Effect of Mismatched Complementary Strands and 5'-Change in Sequence Context on the Thermodynamics and Structure of Benzo[a]pyrene-Modified Oligonucleotides", Biochemistry, 37, 8575-8583. Download PDF |
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1997
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Leontis, N.B., SantaLucia, J., Jr. (Eds.) (1997) "Molecular Modeling of Nucleic Acids", ACS Symposium Series, 682, ACS pub., Washington, DC. |
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1997
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Wu, M., SantaLucia, J., Jr., Turner, D.H. (1997) "Solution Structure of (rGGCAGGCC)2 by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach", Biochemistry, 36, 4449-4460. Download PDF |
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1997
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Carter, R.J., Baeyens, K.J., SantaLucia, J., Jr., Turner, D.H., Holbrook, S.R. (1997) "The Crystal Structure of an RNA Oligomer Incorporating Tandem Adenosine-Inosine Mismatches", Nucleic Acids Res., 25, 4117-4122. Download PDF |
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1997
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SantaLucia, J., Jr., Turner, D.H. (1997) "Measuring the Thermodynamics of RNA Secondary Structure Formation", Biopolymers, 44, 309-319. Download PDF |
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1997
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Lee, K., Varma, S., SantaLucia, J., Jr., Cunningham, P.R. (1997) "In Vivo Determination of RNA Structure-Function Relationships: Analysis of the 790 Loop in Ribosomal RNA", J. Mol. Biol., 269, 732-743. Download PDF |
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1997
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Allawi, H.T., SantaLucia, J., Jr. (1997) "Thermodynamics and NMR of Internal G-T Mismatches in DNA", Biochemistry, 36, 10581-10594. Download PDF |
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1996
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SantaLucia, J., Jr., Allawi, H.T., Seneviratne, P.A. (1996) "Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability", Biochemistry, 35, 3555-3562. Download PDF |
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1995
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SantaLucia, J., Jr., Shen, L., Cai, Z., Lewis, H., Tinoco, I., Jr. (1995) "Synthesis and NMR of RNA with Isotopic Enrichment in the Bases", Nucleic Acids Res., 23, 4913-4921. Download PDF |
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1993
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SantaLucia, J., Jr., Turner, D.H. (1993) "Structure of (rGGCGAGCC)2 in Solution from NMR and Restrained Molecular Dynamics", Biochemistry, 32, 12612-12623. Download PDF |
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1993
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Jaeger, J.A., SantaLucia, J., Jr., Tinoco, I., Jr. (1993) "Determination of RNA Structure and Thermodynamics", Ann. Rev. Biochem., 62, 255-287. Download PDF |
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1992
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SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1992) "Context Dependence of Hydrogen Bond Free Energy Revealed by Substitutions in an RNA Hairpin", Science, 256, 217-219. Download PDF |
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1991
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He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A.E., Turner, D.H. (1991) "Nearest-Neighbor Parameters for GU Mismatches: GU/UG Is Destabilizing in the Contexts CGUG, UGUA, and AGUU but Stabilizing in GGUC", Biochemistry, 30, 11124-11132. Download PDF |
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1991
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SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1991) "Stabilities of Consecutive AC, CC, GG, UC, and UU Mismatches in RNA Internal Loops: Evidence for Stable Hydrogen-Bonded UU and CC+ Pairs", Biochemistry, 30, 8242-8251.
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1991
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SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1991) "Functional Group Substitutions as Probes of Hydrogen Bonding between GA Mismatches in RNA Internal Loops", J. Am. Chem. Soc., 113, 4313-4322. Download PDF |
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1990
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SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1990) "Effects of GA Mismatches on the Structure and Thermodynamics of RNA Internal Loops", Biochemistry, 29, 8813-8819. Download PDF |
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