| Year |
Publication
|
2006 |
SantaLucia, J., Jr. (2006) "Physical
Principles and Visual-OMP Software for Optimal PCR Design",
Methods in Molecular Biology: PCR Primer Design, 2006,
Anton Yuryev, Ed., Humana Press, Totowa, New Jersey (2006)
in press. 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.
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| 2004 |
Irani,
R.J. and SantaLucia, J., Jr. (2004) "Efficient
preparation of 2-deoxy-3,5-di-O-p-toluoyl-a-D-ribofuranosyl
chloride", SynLett (2), 335-337.
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| 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., Santa Lucia, 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",
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", 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", Mol.
Biol. 307, 197-211. 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", 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", Biochemistry29,
8813-8819.
Download PDF |
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