Publications

Year
Publication
2014
Zemtsova, G. E., Watkins, N. E. Jr.and Levin, M.L. "Multiplex qPCR assay for identification and differentiation of Amblyomma americanum, Amblyomma cajennense, and Amblyomma maculatum (Ixodida:Ixodidae) tick species in the Eastern United States", J. Med. Entomol., 2014, 51(4), 795-803.  PMID: 25118411
2014
Madani, TA, Azhar El, Abuelzein el-TM,  Kao M, Al-Bar HM, Farraj, SA, Masri BE, Al-Kaiedi NA, Shakil S, Sohrab, SS, SantaLucia, J. Jr. and Ksiazek TG "Complete genome sequencing and genetic characterization of Alkhumra Hemorrhagic Fever virus isolated from Najron, Saudi Arabia", Intervirology, 2014, 57(5), 300-310. PMID: 25096447. 
2013
Jiang, J., Aduri, R., Chow, C.S. and SantaLucia, J. Jr.  "Structure modulation of helix 69 from Escherichia Coli 23S ribosomal RNA by pseudouridylations", Nucleic Acids Research, 2013, 1-11. PMID: 24371282. 
2012
Sumitaa, M., Jiang, J., SantaLucia, J., Jr., and Chow, C.S.  "Comparison of Solution Conformations and Stabilities of Modified Helix 69 rRNA Analogues from Bacteria and Human", Biopolymers, 97, 94-106. 
2012
Cruz, J.A., Blanchet, M.-F., et al. (2012) "RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure", Biopolymers, RNA 18, 610-625. 
2012
Rothe, J., Watkins, N.E., Jr, Nagy, M.  (2012) "New Prediction Model for Probe Specificity in an Allele-Specific Extension Reaction for Haplotype-Specific Extraction (HSE) of Y Chromosome Mixtures", PLOS ONE, 7(9), e45955. 
2011
Zazantsev, A.V., Rambo, R.P., Karimpour, S. SantaLucia, J., Jr., Tainer, J.A., and Pace, N.R.(2011) "Solution structure of RNase P RNA", RNA, 17, 1159-1171. 
2011
Sijenyi, F., Saro, P., Ouyang, Z., Damm-Ganamet, K., Wood, M., Jiang, J., and SantaLucia, J., Jr. (2011) "The RNA Folding Problems: Different Levels of RNA Structure Prediction", in RNA 3D Structure Analysis and Prediction (Leontis, N, and Westhof, E., eds.) Series "Nucleic Acids and Molecular Biology", Springer
2011
Watkins, N.E., Kennelly, W.J., Tsay, M.J., Tuin, A., Lee, H.R., Morosyuk, S.M., Hicks, D.A., and SantaLucia, J., Jr. (2011) "Thermodynamic Contributions of Single Internal rA-dA, rC-dC, rG-dG, and rU-dT Mismatches in DNA/RNA Duplexes", Nucleic Acids Res ., 39, 1894-1902. 
2011
Medina, R.A., Rojas, M., Tuin, A., Huff, S., Ferres, M., Martines-Valdebenito, C., Godoy, P., Garcia-Sastre, A., Fofanov, Y., and SantaLucia, J., Jr. (2011) "Development and Characterization of a Highly Specific and Sensitive SYBR Green RT-PCR Assay for Detection of the 2009 Pandemic H1N1 Influenza Virus Based on Sequence Signatures", J. Clin. Microbiol., 49, 335-344. 
2010
SantaLucia, J., Jr., Boggy, G., Tuin, A., Lee, S. Sekinger, E., and Robertson, G.  (2010) "Design Tools for Use in Assay Optimization", Gen. Eng. Biotech. News 30, 28-29
2008
Desaulniers, J.P., Chang, Y.-C., Aduri, R., Abeysirigunawardena, S.C., SantaLucia, J., Jr., and Chow, C.S. (2008) "Pseudouridines in rRNA Helix Play a Role in Loop Stacking Interactions", Org. Biomol.Chem., 6, 3892-3895. 
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. 
2008
SantaLucia, J., Jr., Machak, J., and Finzel, B., "Opportunities for RNA-Targeted Therapeutics", Next Gen. Pharm., Issue 13 (2008)
2007
Bevilacqua, P.C., SantaLucia, J., Jr. (2007) "The Biophysics of RNA", ACS Chem. Biol., 2, 440–444. 
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. 
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.   
2006
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. 
2005
Watkins, N.E., Jr., SantaLucia, J., Jr. (2005) "Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes", Nucleic Acids Research, 2005, 33, 6258-6267. 
2004
SantaLucia, J., Jr., Hicks, D. (2004) "The Thermodynamics of DNA Structural Motifs", Annu. Rev. Biophys. Biomol. Struct., 33, 415-40. 
2004
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. 
2004
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. 
2002
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. 
2002
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. 
2002
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.  
2001
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. 
2001
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. 
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", Mol. Biol., 300, 113-126. 
2000
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. 
2000
Bommarito, S., Peyret, N., SantaLucia, J., Jr. (2000) "Thermodynamic parameters for DNA sequences with dangling ends", Nucleic Acids Res., 28, 1929-1934. 
2000
SantaLucia, J., Jr. (2000) "Determination of Nucleic Acid Thermodynamics by UV Absorbance Melting Curves", in Spectrophotometry and Spectrofluorimetry: A Practical Approach (M.G. Gore, ed.), Oxford U. Press
1999
Irani, R., SantaLucia, J., Jr. (1999)  "The Synthesis of 5-iodocytidine Phosphoramidite for Heavy Atom Derivatization of RNA", Tetrahedron Lett., 40, 8961-8964. 
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. 
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. 
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. 
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. 
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. 
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. 
1998
Allawi, H.T., SantaLucia, J., Jr. (1998) "Thermodynamics of Internal C-T Mismatches in DNA", Nucleic Acids Res., 26, 2694-2701. 
1998
Allawi, H.T., SantaLucia, J., Jr. (1998) "Nearest Neighbor Thermodynamic Parameters for Internal G-A Mismatches in DNA", Biochemistry, 37, 2170-2179. 
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. 
1997
Leontis, N.B., SantaLucia, J., Jr. (Eds.) (1997) "Molecular Modeling of Nucleic Acids", ACS Symposium Series, 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. 
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. 
1997
SantaLucia, J., Jr., Turner, D.H. (1997) "Measuring the Thermodynamics of RNA Secondary Structure Formation", Biopolymers, 44, 309-319. 
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. 
1997
Allawi, H.T., SantaLucia, J., Jr. (1997) "Thermodynamics and NMR of Internal G-T Mismatches in DNA", Biochemistry, 36, 10581-10594. 
1996
SantaLucia, J., Jr., Allawi, H.T., Seneviratne, P.A. (1996) "Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability", Biochemistry, 35, 3555-3562. 
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. 
1994
Tinoco, I., Jr., Cai, Z., Chang, K.Y., Chen, X., Hines, J.V., James, J., Jaeger, J.,Molinaro, M., SantaLucia, J., Jr., Shen, L., Variani, G., and Wimberly, B. (1994) "RNA Structural Elements - Loops and Pseudoknots", FASEB J, 8, A1262.
1993
SantaLucia, J., Jr., Turner, D.H. (1993) "Structure of (rGGCGAGCC)2 in Solution from NMR and Restrained Molecular Dynamics", Biochemistry, 32, 12612-12623. 
1993
Jaeger, J.A., SantaLucia, J., Jr., Tinoco, I., Jr. (1993) "Determination of RNA Structure and Thermodynamics", Ann. Rev. Biochem., 62, 255-287. 
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. 
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.  
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.
 
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. 
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. 
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