Year Publication
2021 2021 Sun, Y., Patel, A., SantaLucia, J., Jr., Roberts, E., Zhao, L.L., Kaye, K., Rao, K., and Bachman, M.A. “Measurement of Klebsiella Intestinal Colonization Density To Assess Infection Risk,” Mpshere 6, e00500-21 (2021).
2021 2021 Rao, K., Patel, A.R., Seekatz, A.M., Bassis, C.M., Sun, Y., Henig, O., Albin, O.R., SantaLucia, J., Jr., Woods, R., and Bachman, M.A. “Gut microbiome features are associated with sepsis onset and outcomes,” bioRxiv (2021) doi:
2020 2020 SantaLucia, J., Jr., Sozhamannan, S., Gans, J.D., Koehler, J.W., Soong, R., Lin, N.J., Xie, G., Olson, V. Roth, K., Beck, L.S.  “Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches,” J. AOAC Int.103, 882-899 (2020).
2019 David M. Mauger , B. Joseph Cabral, Vladimir Presnyak , Stephen V. Su, David W. Reid , Brooke Goodman , Kristian Link , Nikhil Khatwani, John Reynders, Melissa J. Moore, and Iain J. McFadyen, “mRNA structure regulates protein expression through changes in functional half-life,” PNAS, 24075–24083
2019 Hoshika, S., Leal, N.A., Kim, M.-J., Karalkar, N.B., Kim, M.-S., Bates, A.M., Watkins, N.E., Jr., SantaLucia, H.A., Meyer, A.J., DasGupta, S., Piccirilli, J.A., Ellington, A.D., SantaLucia, J., Jr., Georgiadis, M.M., Benner, S.A. “Hachimoji DNA and RNA: A Genetic System with Eight Building Blocks,” Science, 363, 884-887 (2019).
2018 Arjang Hassibi, Arun Manickam, Rituraj Singh, Sara Bolouki, Ruma Sinha, Kshama B Jirage, Mark W McDermott, Babak Hassibi, Haris Vikalo, Gelareh Mazarei, Lei Pei, Luc Bousse, Mark Miller, Mehrdad Heshami, Michael P Savage, Michael T Taylor, Nader Gamini, Nicholas Wood, Pallavi Mantina, Patrick Grogan, Peter Kuimelis, Piyush Savalia, Scott Conradson, Yuan Li, Rich B Meyer, Edmond Ku, Jessica Ebert, Benjamin A Pinsky, Gregory Dolganov, Tran Van, Kirsten A Johnson, Pejman Naraghi-Arani, Robert G Kuimelis & Gary Schoolnik , “Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip,” Nature Biotechnology
2018 SantaLucia, J., Jr., “How Much Free Energy is Absorbed Upon Breaking DNA Base Pairs?”, Physics of Life Reviews, (2018)
2017 “RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme,” Miao, Z. et al. RNA, 23, 655-672 (2017).
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”, inRNA 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.