Keyword Search
     Title   Author   Journal   Year
In order to help users find a particular paper, we offer this keyword search. By default, the search function checks your query against all of the fields in our publications database. If, however, you would like to refine your search so as to check only against paper title, author, year, or journal, or any combination of the five, simply select the criteria you want to the right of the form, and resubmit your search.
Journal Search
The journal names below are abbreviated; it may therefore be difficult to search for a specific journal. With this in mind, we have assembled a list of journals above. Select, and the search will return all matches.
No search terms have been entered.
Number
Title and Author(s)
Journal, Year, Volume, Pages
81
"Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome," Uemura S, Dorywalska M, Lee TH, Kim HD, Puglisi JD, Chu S
Nature, 2007, 446(7134), 454-7
Reprint Supp. Mat.
80
"Molecular framework for the activation of RNA-dependent protein kinase," McKenna SA, Lindhout DA, Kim I, Liu CW, Gelev VM, Wagner G, Puglisi JD
J. Biol. Chem., 2007 Feb 6, [Epub ahead of print],
Reprint
79
"Rapid purification of RNAs using fast performance liquid chromatography (FPLC)," Kim I, McKenna SA, Viani Puglisi E, Puglisi JD
RNA, 2007, 13(2), 289-94
Reprint
78
"Uncoupling of RNA Binding and PKR Kinase Activation," Sean A. McKenna, Insil Kim, Corey W. Liu and Joseph D. Puglisi
J. Mol. Biol., 2006, 358, 1270-1285
Reprint
77
"Specific Recognition of HIV TAR RNA by the dsRNA Binding Domains (dsRBD1-dsRBD2) of PKR," Kim I, Liu CW, and Puglisi JD
J. Mol. Biol., 2006, 358, 430-442
Reprint
76
"Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis," Kelly A. Underwood, James R. Swartz, Joseph D. Puglisi
Biotechnology & Engineering, 2005, 91, No. 4, 425-35
Reprint
75
"Structure Determination of Large Biological RNAs," Lukavsky PJ, Puglisi JD
Methods Enzymol., 2005, 394, 399-416
Reprint
74
"Site-specific labeling of the ribosome for single-molecule spectroscopy," Dorywalska M, Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD
Nucleic Acids Res., 2005, 33(1), 182-9
Reprint
73
"The Pathway of HCV IRES-Mediated Translation Initiation," Geoff A. Otto and Joseph D. Puglisi
Cell, 2004, 119, 369-380
Reprint
72
"tRNA selection and kinetic proofreading in translation," Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD
Nat. Struct. Mol. Biol., 2004, 11(10), 1008-14
Reprint
71
"tRNA dynamics on the ribosome during translation," Blanchard SC, Kim HD, Gonzalez RL Jr, Puglisi JD, Chu S
Proc. Natl. Acad. Sci. U.S.A., 2004, 101, 12893-12898
Reprint Supp. Mat.
70
"Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides," Lukavsky PJ, Puglisi JD
RNA, 2004, 10(5), 889-893
Reprint
69
"Design of a cyclic peptide that targets a viral RNA," Runyon ST, Puglisi JD
J. Am. Chem. Soc., 2003, 125(51), 15704-5
Reprint
68
"Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron," Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner, DH
Biochemistry, 2003, 42(48), 14184-96
Reprint Supp. Mat.
67
"Structure of HCV IRES domain II determined by NMR," Peter J Lukavsky, Insil Kim, Geoff A Otto & Joseph D. Puglisi
Nature Structural Biol., 2003, Advance Online Publication
Reprint Supp. Mat.
66
"Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein.," Li Q, Khosla C, Puglisi JD, Liu CW.
Biochemistry, 2003, 42(16), 4648-57
Reprint Supp. Mat.
65
"Comparison of x-ray Crystal Structure of the 30s Subunit-Antibiotic Complex with NMR Structure of Decoding Site Oligonucleotide-Paromomycin Complex," Lynch, S.R., Gonzalez, R.L., and Puglisi, J.D.
Structure, 2003, 11, 43-53
Reprint
64
"NMR Study of 100 kDa HCV IRES RNA Using Segmental Isotope Labeling," ˇ Kim, I., Lukavsky, P.J., and Puglisi, J.D.
J. Am. Chem. Soc., 2002, 124, 9338-39
Reprint
63
"Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction.," ˇ Otto, G.A., Lukavsky, P.J., Lancaster, A.M., Sarnow, P. and Puglisi, J.D.
RNA, 2002, 8, 913-923
Reprint
62
"Sequence-Specific Recognition of the Major Groove of RNA by Deoxystreptamine.," Yoshizawa, S., Fourmy, D., Eason, R.G., and Puglisi, J.D.
Biochemistry, 2002, 41, 6263-70
Reprint
61
"RNAPack - An integrated NMR approach to RNA structure determination.," Lukavsky, P. J. and Puglisi, J. D.
Methods, 2001, 25, 316-332
60
"Aminoglycoside Resistance with Homogeneous and Heterogeneous Populations of Antibiotic-Resistant Ribosomes.," Recht, M. I. and Puglisi, J. D
AAC, 2001, 45, 2414-19
Reprint
59
"Solution structure of the A loop of 23S ribosomal RNA," Blanchard, S.C., and Puglisi, J.D.
Proc. Natl. Acad. Sci. U.S.A., 2001, 98(7), 3720-21
Reprint
58
"Structural origins of aminoglycoside specificity for prokaryotic ribosomes.," Lynch, S.R., and Puglisi, J.D.
J. Mol. Biol. , 2001, 306, 1037-58
Reprint
57
"Structure of a Eukaryotic Decoding Region A-site RNA ," Lynch, S.R., and Puglisi, J.D.
J. Mol. Biol. , 2001, 306, 1023-1035
Reprint
56
"Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function," Lukavsky, P.J., Otto, G.A., A.M. Lancaster, A.M., Sarnow, P. and Puglisi, J.D.
Nature Structural Biol.,, 2000, 7, 1105-1110
Reprint
55
"Approaching translation at atomic resolution," Puglisi, J. D., Blanchard, S. C., & Green
Nature, 2000, 7, 855-861
Reprint
54
"Application of Residual Dipolar Coupling Measurements to Identify Conformational Changes in RNA Induced by Antibiotics," Lynch, S. and Puglisi, J.D.
J. Am. Chem. Soc., 2000, 122, 7853-7854
Reprint
53
"Interaction of Translation Initiation Factor IF1 with the E. coli ribosomal A site," Dahlquist, K. and Puglisi, J. D.
J. Mol. Biol., 2000, 299, 1-15
Reprint
52
"mRNA processing: The 3'-end justifies the means," Puglisi, J.D.
Nature Struct. Biol., 2000, 4, 263-264
Reprint
51
"Aminoglycoside Antibiotics and Decoding," Puglisi, J. D., Blanchard, S. C., Dahlquist, K. D., Eason, R. G., Fourmy, D., Lynch, S., Recht, M. I., & Yoshizawa, S.
Ribosomes99, 1999, Chapter 34, 419-429
50
"The ribosome revealed," Green, R. and Puglisi, J. D.
Nature Structural Biol., 1999, 6, 999-1004
Reprint
49
"RNA helix recognition by ribosomal RNA," Yoshizawa, S., Fourmy, D., & Puglisi, J. D.
Science, 1999, 285, 1722-1725
Reprint
48
"Basis for prokaryotic specificity of action of aminoglycoside antibiotics," Recht, M. I., Douthwaite, S., & Puglisi, J. D.
EMBO J., 1999, 18, 3133-3138
Reprint
47
"Biochemical and NMR studies of aminoglycoside-RNA complexes," Lynch, S. R., Recht, M. I. & Puglisi, J. D.
Methods in Enzymology, 2000, 317, 240-61
Reprint
46
"Effect of mutations in the A site of 16S rRNA on aminoglycoside antibiotic-ribosome interaction," Recht, M. I., Douthwaite, S., Dahlquist, K. D., & Puglisi, J. D.
J. Mol. Biol., 1999, 286, 33-43
Reprint
45
"RNA interaction with small ligands and peptides," Puglisi, J. D. & Williamson, J. R.
RNA World II, 1999, T. Cech & R. Gesteland, eds., pp 403-425
44
"HIV-1 A-rich RNA loop mimics the tRNA anticodon structure," Puglisi, E. V. & Puglisi, J. D.
Nature Struct. Biol., 1998, 5, 1033-1036
Reprint
43
"Structural origins of gentamicin antibiotic action," Yoshizawa, S., Fourmy, D. & Puglisi, J. D.
EMBO J., 1998, 17, 6437-6448
Reprint
42
"NMR structure determination of an antibiotic-RNA complex," Yoshizawa, S. & Puglisi, J. D.
NATO ASI series., 1998, 301, 173-182
41
"rRNA chemical groups required for aminoglycoside binding," Blanchard, S. C., Fourmy, D., Eason, R. G., & Puglisi, J. D.
Biochemistry, 1998, 37, 7716-7724
Reprint
40
"Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16S rRNA," Fourmy, D., Recht, M. I., & Puglisi, J. D.
J. Mol. Biol., 1998, 277, 347-362
Reprint
39
"Paromomycin binding induces a local conformational change in the A site of 16S rRNA," Fourmy, D., Yoshizawa, S. & Puglisi, J. D.
J. Mol. Biol., 1998, 277, 333-345
Reprint
38
"Nuclear magnetic resonance spectroscopy of RNA," Puglisi, E. V. & Puglisi, J. D.
RNA Structure and Function, 1998, R. W. Simons & M. Grunberg-Manago, eds., pp. 117-146
37
"Structural basis for aminoglycoside antibiotic action," Puglisi, J. D.
Many Faces of RNA, 1997, pp. 97-111
36
"Structure of a conserved RNA component of the peptidyl transferase center," Puglisi, E. V., Noller, H. F., & Puglisi, J. D.
Nature Struct. Biol., 1997, 4, 775-778
35
"RNA structure," Puglisi, E. Viani & Puglisi, J. D.
Post Transcriptional Gene Regulation, 1997, D. Morris & J. Harford, eds., N.Y. Wiley & sons, pp. 1-22
34
"Structure of the A site of E. coli 16S rRNA complexed with an aminoglycoside antibiotic," Fourmy, D., Recht, M., Blanchard, S. D., & Puglisi, J. D.
Science, 1996, 274, 1367-1371
33
"RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide," Recht, M., Fourmy, D., Blanchard, S., Dahlquist, K., & Puglisi, J. D.
J. Mol. Biol., 1996, 262, 421-436
Reprint
32
"Solution structure of an RNA-peptide complex," Puglisi, J. D., Chen, L., Blanchard, S., & Frankel, A.
Science:1995, 270, 1200-1203,
31
"Welcome guests to the RNA World: Proteins that interact with RNA," Puglisi, J. D.
Book Review Chemistry & Biology, 1995, 2, 581
30
"Biochemical and NMR studies of RNA conformation," Puglisi, J. D. & Wyatt, J. R.
in Methods in Enzymology, 1995, 261, 323-350
29
"NMR Analysis of tRNA acceptor stem microhelices: Discriminator base changes affect tRNA conformation at the 3'-end," Puglisi, E. V., Puglisi, J. D., Williamson, J. R., & RajBhandary, U. L.
Proc. Nat'l Acad. Sci. U. S. A., 1994, 91, 11467-11471
Reprint
28
"Role of RNA Structure in Arginine Binding to TAR RNA," Puglisi, J. D., Chen, L. Frankel, A. D., & Williamson, J. R.
Proc. Nat'l Acad. Sci. U. S. A., 1993, 90, 3680-3684
Reprint
27
"Additive, Cooperative and Anticooperative Effects between Identity Nucleotides of a tRNA," Pütz, J., Puglisi, J. D., Florentz, C., & Giegé, R.
EMBO J., 1993, 12, 2949-2957
26
"Influence of tRNA Tertiary Structure and Stability on Aminoacylation by yeast Aspartyl-tRNA Synthetase," Puglisi, J. D., Pütz, J., Florentz, C., & Giegé, R.
Nucleic Acids Res., 1993, 21, 41-49
25
"tRNA Structure and Aminoacylation Efficiency," Giegé, R., Florentz, C., & Puglisi, J. D.,
Prog. Nucl. Acids Res. Molec. Biol., 1993, 45, 129-206
24
"Structure and Function of HIV TAR RNA," Puglisi, J. D., Tan, R., Frankel, A. D., Williamson, J. R.
in Structural Tools for the Analysis of Protein-Nucleic Acid Complexes Advances in Life Sciences, 1992, D. Lilley, H. Heumann, D. Suck, eds., pp. 269-285
23
"Preparation of Isotopically Labeled Ribonucleotides for Multidimensional NMR Spectroscopy of RNA," Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., & Williamson, J. R.
Nucleic Acids Res., 1992, 20, 4515-4523
22
"Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy," Puglisi, J. D., Tan, R., Calnan, B. J.,Frankel, A. D. & Williamson, J. R.
Science, 1992, 257, 76-80
21
"Effect of Conformational Features on the Aminoacylation of tRNAs and Consequences on the Permutation of tRNA Specificities," Perret, V., Florentz, C., Puglisi, J. D., & Giegé, R.
J. Mol. Biol., 1992, 226, 323-333
20
"Determinant Nucleotides of Yeast tRNA Asp Interact Directly with Aspartyl-tRNA Synthetase," Rudinger, J., Puglisi, J. D., Pütz, J., Schatz, D., Eckstein, F., Florentz, C. & Giegé, R.
Proc. Natl. Acad. Sci. U.S.A., 1992, 89, 5882-5886
19
"Synthesis and Purification of Large Amounts of RNA Oligonucleotides," Wyatt, J. R., Chastain, M. & Puglisi, J. D.
BioTechniques, 1991, 11, 764-769
18
"Identity Elements for Specific Aminoacylation of Yeast tRNA Asp by Cognate Aspartyl-tRNA Synthetase," Pütz, J., Puglisi, J. D., Florentz, C. & Giegé, R.
Science, 1991, 252, 1696-1699
17
"RNA Pseudoknots," Puglisi, J. D., Wyatt, J. R. & Tinoco, I., Jr
Accts Chem. Res., 1991, 24, 152-158
16
"Conformation in Solution of tRNA Asp Transcripts Deprived of Modified Nucleotides," Perret, V., Garcia, A., Puglisi, J., Grosjean, H., Ebel, J.-P. & Giegé, R.
Biochimie, 1990, 72, 735-744
15
"Exploring the Aminoacylation Function of transfer RNA by Macromolecular Engineering Approaches. Involvement of conformational features in the charging process of yeast tRNA Asp," Giegé, R., Florentz, C., Garcia, A., Grosjean, H., Perret, V., Puglisi, J., Theobald-Dietrich, A., & Ebel, J.-P.
Biochimie, 1990, 72, 735-747
14
"Conformation of an RNA Pseudoknot," Puglisi, J. D., Wyatt, J. R. & Tinoco, I., Jr.
J. Mol. Biol., 1990, 214, 437-453
13
"RNA Pseudoknots: Stability and Loop Size Requirements," Wyatt, J. R., Puglisi, J. D. & Tinoco, I., Jr.
J. Mol. Biol., 1990, 214, 455-470
12
"Solution Conformation of an RNA Hairpin Loop," Puglisi, J. D., Wyatt, J. R. & Tinoco, I., Jr.
Biochemistry, 1990, 29, 4215-4226
11
"RNA Folding," Tinoco, I. Jr., Puglisi, J. D. & Wyatt, J. R.
Nucleic Acids and Molecular Biology, 1990, 4, F. Eckstein & D. Lilley, eds., Springer-Verlag, Berlin, pp. 205-226
10
"RNA Folding: Pseudoknots, Loops and Bulges," Wyatt, J. R., Puglisi, J. D. & Tinoco, I. Jr.
Bioessays, 1989, 11, 100-106
9
"Nucleic Acids from A to Z," Tinoco, I.,Jr., Aboul-ela, F., Hardin, C.C., Puglisi, J.D., Varani, G.,Walker, G.T., Wolk, S. & Wyatt, J. R.
Frontiers of Macromolecular Science, 1989, T. Saegusa, T. Higashimura & A. Abe, eds. pp. 519- 524, Blackwell Scientific Publications, Oxford
8
"Absorbance Melting Curves of RNA," Puglisi, J. D. & Tinoco, I.,Jr.
Methods in Enzymology, RNA Processing 180, 1989, J. E. Dahlberg & J. N. Abelson, eds, Academic Press, New York,
7
"A Pseudoknotted RNA Oligonucleotide," Puglisi, J. D., Wyatt, J. R. & Tinoco, I.,Jr.
Nature, 1988, 331, 283-286
6
"Pseudoknotted RNA Oligonucleotides," Wyatt, J. R., Puglisi, J. D.& Tinoco, I., Jr.
Molecular Biology of RNA, (T. Cech, ed.) U.C.L.A Symposia Series, 1988, 94, 25-32, Alan. R. Liss, Inc., New York, N.Y
5
"RNA Structure from A to Z," Tinoco, I., Jr., Davis, P.W., Hardin, C.C., Puglisi, J.D.,Walker, G.T. & Wyatt, J.R.
Cold Spring Harbor Symp. Quant. Biol., 1988, 52, 135-146
4
"Raman Spectroscopic Study of Left-Handed Z-RNA," Trulson, M.O., Cruz, P., Puglisi, J.D., Tinoco, I., Jr. & Mathies, R.A.
Biochemistry, 1987, 26, 8624-8630
3
"Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies," Hardin, C.C., Zarling, D.A., Puglisi, J.D., Trulson, M. O., Davis, P.D. & Tinoco, I.,Jr.
Biochemistry, 1987, 26, 5191-5199
2
"The Left-Handed Z-Form of Double-Stranded RNA," Cruz, P., Hall, K., Puglisi, J., Davis, P., Hardin, C., Trulson, M., Mathies, R., Tinoco, I.,Jr., Johnson, W.,Jr. & Neilson, T.1986
Biomolecular Stereodynamics, IV, 1986, Adenine Press, New York , pp 179-200
1
"Z-RNA: A Left-Handed Double Helix," Tinoco, I.,Jr., Cruz, P., Davis, P., Hall, K., Hardin, C.C., Mathies, R. A., Puglisi, J. D., Trulson, M. O., Johnson, W. C., & Neilson, T.
Structure and Dynamics of RNA, 1986, Plenum Press, New York, pp. 55-68
Joseph Puglisi
Professor and Chair, Department of Structural Biology
Director, Stanford Magnetic Resonance Laboratory
ph.650-498-4397
fx.650-723-8464
e-m.puglisi@stanford.edu

Mailing Address:
Stanford University School of Medicine
D105 Fairchild Science Building
299 Campus Drive West
Stanford, CA 94305-5126
Manolia Margaris
Administrative Associate

ph.650-723-9151
fx.650-723-8464
e-m.manolia@stanford.edu