Year
Publications
2008
SantaLucia, J., Jr., Machak, J., and Finzel, B. (2008) "Opportunities for RNA-Targeted Therapeutics", Next Gen. Pharm., Issue 13, 645-657, Download PDF
2008
Desaulniers, J. P., Chang, Y.-C., Aduri, R., Abeysirigunawardena, S. C., SantaLucia, J., Jr. and Chow, C. S. (2008) "Pseudouridines in rRNA helix 69 play a role in loop stacking interactions", Org. Biomol. Chem., 6, 38923895, Download PDF
2008
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
2007
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., 402, 3-34, Download PDF
2007
Bevilacqua, P. C. and SantaLucia, J., Jr. (2007) "The Biophysics of RNA", ACS Chem. Biol., 2, 440–444, Download PDF
2007
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
2006
Ilirian Dhimitruka and John SantaLucia, Jr. (2006) "Investigation of the Yamaguchi Esterification Mechanism. Synthesis of a Lux-S Enzyme Inhibitor Using an Improved Esterification Method", Organic Letters, 2006, Vol.8, No.1, 47-50.  Download PDF
2005
Norman E.Watkins, Jr. and John SantaLucia, Jr. (2005) "Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes", Nucleic Acids Research, 2005, Vol.33, No.19, 6258-6267.  Download PDF
2004
John SantaLucia, Jr. and Donald Hicks. (2004) "The Thermodynamics of DNA Structural Motifs", Annu. Rev. Biophys. Biomol. Struct. 33, 415-40.  Download PDF
2004
Jang, S.B., Baeyens, K., Jeong, M. S., SantaLucia, J., Jr., Turner, D. and Holbrook, S. R. (2004) "Structures of two RNA octamers containing tandem G-A base pairs", Acta Cryst. 60D, 829-835.  Download PDF
2004
Ilirian Dhimitruka and John SantaLucia,Jr. (2004) "Efficient preparation of 2-deoxy-3,5-di-O-p-toluoyl-a-D-ribofuranosyl chloride", SynLett (2), 335-337.  Download PDF
2003
Royce, R. D., SantaLucia, J., Jr. & Hicks, D. A. (2003) "Building an in silico laboratory for genomic assay design", Pharmaceutical Visions, 10-12.  Download PDF
2002
Irani, R.J. and 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
2002
Chow, C.S., Cunningham, P.R., Lee, K.S., Meroueh, M., SantaLucia, J., Jr., and 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
2002
Biswas, T., Clos, L.J., SantaLucia, J., Jr., Mitra, S., and Roy, R. J. (2002) "Binding of Specific DNA Base-pair Mismatches by N-Methylpurine-DNA Glycosylase and its implication in Initial Damage Recognition",J. Mol. Biol. 320, 503-513.  Download PDF
2001
Morosyuk, S.M., SantaLucia, J., Jr., and, Cunningham, P. R. J. (2001) "Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: III. Instant Evolution Studies", J. Mol. Biol. 307, 213-221.  Download PDF
2001
Morosyuk, S.M., Cunningham, P. R., and SantaLucia, J., Jr. J. (2001) "Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: II. NMR Solution Structure", J. Mol. Biol. 307, 197-211.  Download PDF
2000
John SantaLucia, Jr. (2000) "The use of Spectroscopic Techniques in the study of DNA stability", Chapter 13 in Spectrophotometry and Spectrofluorimetry, M.G.Gore(ed.), Oxford University Press, Oxford.  Download PDF
2000
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", J. Mol. Biol. 300, 113-126.  Download PDF
2000
Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia, J., Jr., Scaringe, S.A., and 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
2000
Bommarito, S., Peyret, N., SantaLucia, J., Jr. (2000) "Thermodynamic parameters for DNA sequences with dangling ends", Nucleic Acids Res. 28, 1929-1934.  Download PDF
1999
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
1999
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
1999
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
1998
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
1998
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
1998
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
1998
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
1998
Allawi, H. T. & SantaLucia, J., Jr. (1998), "Thermodynamics of Internal C-T Mismatches in DNA", Nucleic Acids Res. 26, 2694-2701.  Download PDF
1998
Allawi, H. T. & SantaLucia, J., Jr. (1998), "Nearest Neighbor Thermodynamic Parameters for Internal G-A Mismatches in DNA", Biochemistry 37, 2170-2179.  Download PDF
1998
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
1997
Leontis, N. B. & SantaLucia, J., Jr. (Eds.) (1997), "Molecular Modeling of Nucleic Acids", ACS Symposium Series vol. 682, ACS pub., Washington, DC.
1997
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
1997
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
1997
SantaLucia, J., Jr. & Turner, D. H. (1997), "Measuring the Thermodynamics of RNA Secondary Structure Formation", Biopolymers 44, 309-319.  Download PDF
1997
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
1997
Allawi, H. T. & SantaLucia, J., Jr. (1997), "Thermodynamics and NMR of Internal G-T Mismatches in DNA", Biochemistry 36, 10581-10594.  Download PDF
1996
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
1995
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
1993
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
1993
Jaeger, J. A., SantaLucia, J., Jr., and Tinoco, I., Jr.(1993), "Determination of RNA Structure and Thermodynamics", Ann. Rev. Biochem. 62, 255-287. Download PDF
1992
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
1991
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
1991
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
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
1990
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