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Year |
Publications
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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,
3892–3895, 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.
Download
PDF |
| 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 |
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