Publications from the Kodadek Lab
148. Archer, C.T., Burdine, L., Liu, B., Ferdous, A., Johnston, S.A. and Kodadek,
T. (2008) Physical and functional interaction of mono-ubiquitylated
transactivators with the proteasome” J. Biol. Chem. 2008
May 30
147. Kodadek,
T. (2008) “Chemical cloaking devices” Nature 2008 Jun 12;453(7197):861-2.
146. Tan, N.C., Yu, P., Kwon, Y.-U. and Kodadek,
T. (2008) “High-throughput
evaluation of relative cell permeability between peptoids and peptides”
Bioorg. Med. Chem. 2008 Jun 1;16(11):5853-61.
145. Kodadek,
T. (2008) “Second generation reagents for activity based
protein profiling” Nature Chem. Biol. 4, In press.
144. Udugamasooriya, D.G., Ritchie, C., Brekken, R.A. and Kodadek,
T. (2008) “A peptoid antagonist of VEGF Receptor 2 recognizes a “hotspot”
in the extracellular domain distinct from the hormone-binding site”
Bioorg. & Med.
Chem. 2008 Jun 15;16(12):6338-43
143. Udugamasooriya,
D.G., Dineen, S.P., Brekken, R.A. and Kodadek, T. (2007) A peptoid
'antibody surrogate' that antagonizes VEGF Receptor 2 activity.
J Am Chem Soc. 2008 Apr 30;130(17):5744-52.
142. Archer, C.T., Delahodde, A., Gonzalez, F., Johnston, S.A. and Kodadek,
T. (2008) Activation domain-dependent mono-ubiquitylation of Gal4 protein
is essential for promoter binding in vivo J. Biol. Chem. 283, 12614-12623.
141. Hanaoka, K., Lubag, A.J.M., Castillo-Muzquiz, A., Kodadek,
T. and Sherry,
A.D. (2008) “The detection limit of a Gd3+-based T1 agent is substantially reduced
when targeted to a protein microdomain” Mag. Res. Imaging In press.
140. Friedberg,
E.C. and Kodadek,
T. (2008) “Chemical damage to nucleic acids”
in The Encylopedia of Chemical Biology, In press.
139. Lim,
H.-S., Archer, C.T., Kim, Y.-C., Hutchens, T. and Kodadek,
T. (2008)
“Rapid identification of the pharmacophore in a peptoid inhibitor of
the proteasome regulatory particle” Chem. Comm. (Camb).2008 Mar 7;(9):1064-6.
138. Shores, K.S., Udugamasooriya, D.G., Kodadek, T. and Knapp, D.R. (2008) “Use
of peptide analog diversity library beads for increased depth of
proteomic analysis: Application to cerebrospinal fluid” J. Proteome
Res., 7 (5),1922-1931, 2008. 10.1021/pr7066889.
137. Marthandan,
N., Klyza, S., Li, S., Kwon, Y.u., Kodadek, T. and Garner, H.R. (2008) "Construction and evaluation of an automated light directed protein-detecting
microarray synthesizer" IEEE Transactions in NanoBioscience, 7,20-27.
136. Lee,
J., Yu, P., Xiao, X. and Kodadek, T. (2008) "A General System for Evaluating the Efficiency of Chromophore-Assisted Light
Inactivation (CALI) of Proteins Reveals Ru(II)
tris-bipyridyl As An Unusually Efficient "Warhead", Molecular BioSystems 2008 Jan;4(1):59-65.
135. Yu, P. and Kodadek, T. (2007) "Dynamics of the Hypoxia-Inducible Factor-1-VEGF promoter complex" J. Biol. Chem. 282, 35035-35045.
134. Lim,
H.-S., Cai, D., Archer C.T. and Kodadek, T. (2007) "Periodate-triggered cross-linking reveals Sug2/Rpt4 as the molecular target of
a peptoid inhibitor of the 19S proteasome regulatory
particle" J. Amer. Chem. Soc. 129, 12936-12937.
133. Liu,
B., Archer, C.T., Burdine, L., Gillette, T.G.
and Kodadek, T. (2007)"Label transfer chemistry for the characterization of protein-protein interactions" J. Amer. Chem. Soc. 129, 12348-12349.
132. Kwon,
Y. U. and Kodadek, T. (2007) “Quantitative Comparison of the Relative Cell Permeability of Cyclic and Linear
Peptides” Chem. Biol. 2007, 14, 671-677.
131. Lim,
H.-Y., Archer, C.T. and Kodadek, T. (2007) "Identification of a Peptoid Inhibitor of the Proteasome 19S regulatory particle" J. Amer. Chem. Soc. 129, 7750-7751.
130. Xiao,
X., Yu, P., Lim, H.-Y., Sikder, S. and Kodadek, T. (2007) "Design and synthesis of a cell permeable transcription factor mimic" J. Comb. Chem. 9, 592-600.
129. Xiao,
X., Yu, P., Lim, H.-S., Sikder, D. and Kodadek, T. (2007) "A cell permeable transcription factor mimic" Angew. Chem. Intl. Ed. 46, 2865-2868.
128. Yu,
P. and Kodadek, T. (2007) "A convenient, high-throughput strategy for measuring the relative cell permeability
of synthetic compounds" Nature Protocols doi: 10.1038/nprot.2007.1
127. Kwon,
Y.-U. and Kodadek, T. (2007) "Quantitative evaluation of the relative cell permeability of peptoids and peptides" J. Amer. Chem. Soc. 129, 1508-1509.
126.
Ferdous, A., Sikder, D., Gillette, T.,
Nalley, K., Kodadek, T. and Johnston, S.A. (2007) "The Role of the Proteasomal ATPases and Activator Mono-Ubiquitylation in Regulating
Gal4 Binding to Promoters"Genes & Dev. 21, 112-123.
125. Kodadek,
T., Sikder, D. and Nalley, K. (2006) "Keeping transcriptional activators under control" Cell 127, 1-4.
124. Liu,
B., Burdine, L. and Kodadek, T. (2006) "Chemistry of periodate-mediated cross-linking of 3,4-dihydroxyphenlalanine (DOPA)-containing
molecules to proteins" J. Amer. Chem. Soc. 128, 15228-15235.
123. Alluri,
P., Liu, B., Yu, P., Xiao, X. and Kodadek, T. (2006) "Isolation and characterization of coactivator-binding peptoids from a combinatorial
library" Molecular BioSystems 2, 568-579.
122. Friedberg,
E.C. and Kodadek, T. (2006) "Chemical damage to nucleic acids" in The Encylopedia of Chemical Biology, In press.
121.
Sikder, D., Johnston, S.A.
and Kodadek, T. (2006) "Widespread, but non-identical, association of proteasomal 19S and 20S proteins
with yeast chromatin" J. J. Biol. Chem. 281, 27346-27355.
120. Nalley,
K., Johnston, S.A. and Kodadek, T. (2006) "Proteolytic turnover of Gal4 is not required for function in vivo" Nature 442, 1054-1057.
119. Page,
T., Sikder, D. Yang,
L. Pluta, L., Wolfinger,
R.D., Kodadek, T. and Thomas, R.S. (2006) "Genome-wide analysis of human HSF1 signaling reveals a transcriptional program
linked to cellular adaptation
and survival", Molecular BioSystems, 627-639.
118.
Sulahian, R., Sikder,
D., Johnston, S.A.
and Kodadek, T. (2006) "The Proteasomal ATPase Complex Is Required For Stress-Induced Transcription In
Yeast" Nucl. Acids Res. 34, 1351-1357.
117.
Sikder, K. and Kodadek, T. (2006) "Optimized protocols for the isolation of specific protein-binding peptides or
peptoids from combinatorial
libraries displayed on
beads" Molecular BioSystems 2, 25-35.
116. Kreishman-Deitrick,
M. Goley, E.D. Burdine,
L., Denison, C., Egile,
C. Murali, N. Kodadek, T., Welch, M.D. and Rosen, M.K. (2005) NMR analyses of the activation of Arp2/3
complex by N-WASP Biochemistry, 44, 15247-15256.
115.
Archer, C., Burdine,
L. and Kodadek, T. (2005) "Identification of Gal4 transactivation domain binding proteins in the 26S proteasome
by periodate-triggered
cross-linking" Molecular BioSystems, 1, 366-372.
114. Liu,
B., Yu, P., Alluri,
P. and Kodadek, T. (2005) "Simple reporter gene-based assays for hairpin polyamide conjugate permeability
and DNA-binding activity
in living cells" Molecular BioSystems 1, 307-317.
113. Reddy,
M.M. and Kodadek, T. (2005) "Protein 'fingerprinting' in complex mixtures using peptoid microarrays" Proc. Natl. Acad. Sci. USA 102, 12672-12677.
112. Liu,
B., Alluri, P., Yu,
P. and Kodadek, T. (2005) "A KIX-binding peptoid functions as a transactivation domain in mammalian cells" J. Amer. Chem. Soc. 127, 8254-8255.
111.
Yu, P., Liu, B. and Kodadek, T. (2005) "A high-throughput assay for assessing the cell permeability of combinatorial
libraries"Nature Biotech. 23, 746-751.
110. Kodadek,
T., Duroux-Richard, I. And Bonnafous, J.-C. (2005) "Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated
signaling events" Trends In Pharm. Sci. 26, 210-217.
109. Li,
S., Marthandan, N.,
Bowerman, D., Garner,
H.R. and Kodadek, T. (2005) Photolithographic synthesis of cyclic peptide arrays using a differential
deprotection strategy" Chem. Comm., 581-583.
108. Cravatt,
B.F. and Kodadek, T. (2005) "A chemocentric view of genomics and proteomics" Curr. Opin. Chem. Biol. 9, 1-3.
107. Sikder,
D. and Kodadek, T. (2005) "Genomic studies of transcription factor-DNA interactions" Curr. Opin. Chem. Biol. 9, 38-45.
106. Lin,
H.-J. and Kodadek, T. (2005) "Photo-induced oxidative cross-linking as a method to evaluate the specificity
of protein-ligand interactions"J. Peptide Res. 65, 221-228.
105. Burdine,
L., Gillette, T.G.,
Lin, H.-J. and Kodadek, T. (2004) "Periodate-triggered cross-linking of DOPA-containing peptide-protein complexes" J. Amer. Chem. Soc. 126, 11442-11443.
104. Kodadek,
T., Reddy, M.M., Olivos, H.J., Bachhawat-Sikder , K. and Alluri, P.G. (2004) "Synthetic molecules as antibody replacements" Acc. Chem. Res. 37, 711-718.
103. Moola,
R., Bacchawat –Sikder,
K. and Kodadek, T. (2004) "Transformation of low affinity lead compounds into high affinity protein capture
agents"Chem. & Biol. 11, 1127-37.
101.
Burdine, L. and Kodadek, T. (2004) "Protein target identification: The (often) missing link in chemical genetics" Chem. & Biol. 11, 593-597.
100. Gillette,
T., Gonzalez, F.G.,
Delahodde, A., Johnston,
S.A. and Kodadek, T. (2004) "Physical and Functional Association of RNA Polymerase II and the Proteasome" Proc. Natl. Acad. Sci. USA 101, 5904-5909.
99. Li,
S., Bowerman, D.J.,
Marthandan, N., Garner,
H.R. and Kodadek, T. (2004) "Photolithographic synthesis of peptoids" J. Amer. Chem. Soc. 126, 4088-4089.
98. Smith,
A.H., Vrtis, J.M.
and Kodadek, T. (2004) "The Potential of Protein-Detecting Microrrays for Clinical Diagnostics" Clinical Chem 37, 217-238.
97. Denison,
C. and Kodadek, T. (2004) "Towards a general chemical method for mapping the architecture of multi-protein
complexes" J. Proteome Res. 3, 417-425.
96. Troitskaya,
L. and Kodadek, T. (2004) "Peptides as modulators of enzymes and regulatory proteins"Methods 32, 406-415.
95. Bacchawat-Sikder,
K. and Kodadek, T. (2003) "Protein detecting microarrays for diagnostics and basic research"Clin. Lab. Intl. 27, 16-18.
94. Alluri,
P.G. Reddy, M.M.,
Bacchawat-Sikder,
K., Olivos, H.J.
and Kodadek, T. (2003) "Isolation of protein ligands from large peptoid libraries" J. Amer. Chem. Soc. 125, 13995-14004.
93. Amini,
F., Denison, C.,
Lin, H.-J., Sun,
L. and Kodadek, T. (2003) "Quantitative analysis of protein-protein interactions using oxidative labeling
and cross-linking chemistry" Chem. & Biol. 10, 1115-1127.
92. Liu,
B., Han, Y. Ferdous,
A., Corey, D.R. and Kodadek, T. (2003) "Transcription Activation by a PNA-Peptide Chimera In A Mammalian Cell Extract" Chem. & Biol. 10, 909-916.
91. Olivos,
H.J., Bacchawat-Sikder,
K. and Kodadek, T. (2003) "Quantum dots as a visual aid for screening bead-bound combinatorial libraries" ChemBiochem 4, 1242-1245.
90. Sikder,
K. and Kodadek, T. (2003) "Mixed Element Capture Agents (MECAs): A Simple Strategy For the Construction
of Synthetic, High Affinity
Protein Capture Ligands" J. Amer. Chem. Soc. 125, 9550-9551.
89. Naffin,
J.L., Han, Y. Sun,
T., Reddy, M.M.,
Olivos,
H.J., and Kodadek, T. (2003) "Immobilized peptides as high affinity capture agents for self-associating proteins" Chem. & Biol. 10, 251-259.
88. Olivos,
H.J., Alluri. P.G,
Reddy, M.M., Saloney,
D. and Kodadek, T. (2002) "Microwave-assisted solid phase synthesis of peptoids" Organic Letters 4, 4057-4059.
87. Ferdous,
A., Kodadek, T. and Johnston, S.A. (2002) "A nonproteolytic function of the 19S regulatory subunit of the 26S proteasome
is required for efficient
activated transcription
by human RNA polymerase
II" Biochemistry 41, 12798-12805.
86. Sun,
L., Johnston, S.A.
and Kodadek, T. (2002) "Physical association of the APIS complex and general transcription factors" Biochem. Biophys. Res. Comm. 296, 991-999.
85. Sun,
L. and Kodadek, T. (2002) "Removal of impurities from transcription factor preparations that alter their
DNA-binding properties" Nucl. Acids Res. 30, e88.
84. Kodadek,
T. (2002) "Inhibition of proteolysis and other post-translational modifications with substrate-targeted
inhibitors" Biopolymers - Peptide Science, 66, 134-140.
83. De
León, L.M.Weiner,
A., Zhang, S., Kovacs,
Z., Kodadek, T. and Sherry, A.D. (2002) "Magnetic Resonance Imaging Detects a Specific Peptide-Protein Binding Event" J. Amer. Chem. Soc. 124, 3514-3515.
82. Kodadek,
T. (2002) "Development of protein-detecting microarrays and related devices" Trends In Biochem. Sci. 27, 295-300.
81. Gonzalez,
F., Delahoude, A., Kodadek, T. and Johnston, S.A. (2002)" A sub-complex of the 19S proteasome regulatory complex is recruited to an activated
promoter" Science, 296, 548-550.
80. Liu,
B., Han, Y., Corey,
D.R. and Kodadek, T. (2002) "Toward synthetic transcription activators: recruitment of transcription factors
to DNA by a PNA-peptide
chimera" J. Amer. Chem. Soc., 124, 1838-1839.
79. Amini,
F., Kodadek, T. and Brown, K.C. (2002) "Protein affinity labeling mediated by genetically-encoded peptide tags" Angew. Chem. Intl. Ed. 41, 356-359.
78. Chang,
C., Gonzalez, F.,
Rothermel, B., Sun,
L., Johnston,
S.A. and Kodadek, T. (2001) "The Gal4 activation domain binds the Sug2 protein, a proteasome component, in
vivo and in vitro" J. Biol. Chem. 276, 30956-30963.
77. Jeong,
C.-J., Yang, S.H.,
Xie, Y., Zhang, L.,
Johnston,
S.A. and Kodadek, T. (2001) "Evidence that Gal11 protein is a target of the Gal4 activation domain in the
mediator" Biochemistry, 40, 9421-9427.
76. Ferdous,
A., Gonzalez, F.,
Sun, L., Kodadek, T. and Johnston, S.A. (2001) "The 19S regulatory particle of the proteasome is required for efficient transcription
elongation by RNA polymerase
II" Mol. Cell 7, 981-991.
75. Zhang,
Z., Li, T. and Kodadek, T. (2001) "An inhibitor of sequence-specific proteolysis that targets the substrate rather
than the enzyme" Chem. & Biol. 8, 391-397.
74. Kodadek,
T. (2001) "Protein microarrays: Prospects and problems" Chem. & Biol. 8, 105-116.
73.
Brown, K.C. and Kodadek, T. (2001) "Protein Cross-linking mediated by metal ion complexes" in "Probing proteins by metal ions and their low-molecular-weight complexes", Vol. 38 of Metal Ions In Biological Systems, pages 351-384, A. Sigel and H.
Sigel, eds., M. Dekker,
New York.
72. Xie,
Y., Sun, L. and Kodadek, T. (2000) "Cooperative binding of the Gal4 and TATA-binding proteins to promoters does not
contribute substantially
to activated transcription" J. Biol. Chem., 275, 40797-40803.
71. Xie,
Y., Denison, C.,
Yang, S., Fancy,
D.A. and Kodadek, T. (2000) "Biochemical characterization of the TATA-binding protein-Gal4 activation domain
complex" J. Biol. Chem. 275, 31914-31920.
70. Zhu,
W., Williams, R.S.
and Kodadek, T. (2000) "A Cdc6-binding peptide selected using a bacterial two-hybrid-like system is a
cell cycle inhibitor" J. Biol. Chem. 275, 32098-32105.
69. Fancy,
D.A., Denison, C.,
Kim, K., Xie, Y.,
Holdeman,
T., Amini, F. and Kodadek, T. (2000) "Scope, limitations and mechanistic aspects of the photo-induced cross-linking
of proteins by water-soluble
metal complexes" Chem. & Biol. 7, 697-708.
68. Han,
Y. and Kodadek, T. (2000) "Peptides selected to bind the Gal80 repressor are potent transcriptional activation
domains in yeast" J. Biol. Chem. 275, 14979-14984.
67.
Brent, R. and Kodadek, T. (2000) "Analysis and Manipulation of Proteins and Protein Complexes: A New Frontier In
Chemical Biology and
Biotechnology" Curr. Op. Chem. Biol. 4, 13-15.
66.
Kodadek, T. (2000) "Chemistry & Biology: A challenging balancing act" Chem. & Biol. 7, R1-R2.
65. Zhang,
Z., Zhu, W. and Kodadek, T. (2000) "Selection and practical applications of peptide-binding peptides" Nature Biotech. 18, 71-74.
64. Patikoglou,
G.A., Kim, J.L.,
Sun, L., Yang, S.-H., Kodadek, T. and Burley, S.K. (1999) "TATA element recognition by the TATA box-binding protein has been conserved throughout
evolution" Genes & Dev. 13, 3217-3230.
63. Kim,
K., Fancy, D.A. and Kodadek, T. (1999) "Photo-induced protein cross-linking mediated by palladium porphyrins" J. Amer. Chem. Soc. 121, 11896-11897.
62. Fancy,
D.A., Kodadek, T. (1999) "Chemistry for the analysis of protein-protein interactions: Rapid and efficient
cross-linking triggered
by long wavelength light" Proc. Natl. Acad. Sci. USA 96, 6020-6024. Also see correction, Vol. 97, Issue 3, 1317a-1317a, February 1, 2000.
61. Zhang,
Z., Murphy, A., Hu,
J.C. and Kodadek, T. (1999) "Genetic selection of short peptides that support protein oligomerization in vivo" Current Biol. 9, 417-420.
60. Vashee,
S., Willie, J. and Kodadek, T. (1998) "Synergistic activation of transcription by physiologically unrelated transcription
factors through cooperative
DNA-binding" Biochem Biophys. Res. Comm. 247, 530-535.
59. Campbell,
L., Kodadek, T., and Brown, K.C. (1998) "Protein cross-linking mediated by metalloporphyrins" Bioorg Med. Chem. 6, 1301-1307.
58. Denison,
C. and Kodadek, T. (1998) "Small molecule control of gene expression" Chem. & Biol. 5, R129-R145.
57. Fancy,
D.A. and Kodadek, T. (1998) "A critical role for tyrosine residues in His6-Ni-mediated protein cross-linking" Biochem. Biophys. Res. Comm. 247, 420-426.
56. Vashee,
S., Melcher, K.,
Ding, W., Johnston,
S.A. and Kodadek, T. (1998) "Evidence for two modes of cooperative DNA binding in vivo that do not involve
direct protein-protein
interactions" Curr. Biol. 8, 452-458.
55. Kodadek,
T. (1998) "Mechanistic parallels between DNA replication, recombination and transcription" Trends In Biochem. Sci. 23, 79-83.
54. Dresser,
M., Ewing, D., Conrad, M.,
Dominguez, A., Barstead,
R., Jiang, H. and Kodadek, T. (1997) "DMC1 functions in a meiotic pathway that is largely independent of the RAD51
pathway" Genetics 147, 533-544.
53. Fancy,
D.A. and Kodadek, T. (1997) "Site-directed, metal-catalyzed oxidative protein crosslinking" Tetrahedron 53, 11953-11960.
52. Barry,
J.F., Campbell, L.,
Smith, D.W. and Kodadek, T. (1997) "Synthesis and Catalytic Epoxidation Activity of Terpene-Derived D4-Symmetric
Metalloporphyrins" Tetrahedron 53, 7753-7776.
51.
Jiang, H., Salinas,
F. and Kodadek, T. (1997) "The gene 32 single-stranded DNA-binding protein does not associate stably with
the phage T4 presynaptic
filament" Biochem. Biophys. Res. Comm. 231, 600-605.
50.
Campbell, L. and Kodadek, T. (1997) "Chiral porphyrins as catalysts for the asymmetric oxidation of hydrocarbons" J. Mol. Catal. A: Chemical 113, 293-310.
49. Jiang,
H., Xie, Y., Stemke-Hale,
K., Houston, P.,
Mortensen, U.H.,
Rothstein, R. and Kodadek, T. (1996) "Direct Association Between the Yeast Rad51 and Rad54 Recombination Proteins" J. Biol. Chem. 271, 33181-33186.
48. Fancy,
D.A., Melcher, K.;
Johnston, S.A. and Kodadek, T. (1996) "New chemistry for the study of multiprotein complexes: The six histidine tag
as a receptor for a protein
cross-linking reagent" Chem. & Biol. 3, 551-559.
47. Sessler,
J.L., Lisowski, J.,
Boudreaux, K., Lynch,
V., Barry,
J. and Kodadek, T. (1995) "Synthesis and characterization of di-aryl sapphyrins prepared under Lindsey-type
conditions" J. Org. Chem. 60, 5975-5978.
46. Vashee,
S. and Kodadek, T. (1995) "The activation domain of GAL4 protein mediates cooperative promoter binding with
general transcription
factors in vivo" Proc. Natl. Acad. Sci. USA 92, 10683-10687.
45. Robbins
Wolf, J., Hamaker,
C.G., Djukic, J.-P., Kodadek, T. and Woo, L.K. (1995) "Shape and stereoselective cyclopropanation of alkenes catalyzed by iron porphyrins" J. Amer. Chem. Soc. 117, 9194-9199.
44.
Xu, H.E., Kodadek, T. and Johnston, S.A. (1995) "A single dimer of GAL4 protein can maximally stimulate transcription under physiological
conditions" Proc. Natl. Acad. Sci. USA 92, 7677-7680.
43. Salinas,
F. and Kodadek, T. (1995) "Phage T4 homologous strand exchange: A DNA helicase, not the strand transferase,
drives polar branch migration" Cell 82, 111-119.
42. Kodadek,
T. (1995) "From carpet bombing to cruise missiles: 'Second-order' mechanisms of transcription
factor-DNA binding in
vivo" .
41. Brown,
K.C., Yang, S.-H.
and Kodadek, T. (1995) "Highly specific oxidative protein crosslinking mediated by a nickel peptide complex" Biochemistry 34, 4733-4739.
40. Salinas,
F., Jiang, H. and Kodadek, T. (1995) "Homology dependence of uvsX protein-catalyzed joint molecule formation" J. Biol. Chem. 270, 5181-5186.
39. Kodadek,
T. and Johnston, S.A. (1995) "The dangers of ‘splicing and dicing’: On the use of chimeric transcriptional
activators in vitro" Chem. & Biol. 2, 187-194.
38. Salinas,
F. and Kodadek, T. (1994) "Strand exchange through a DNA-protein complex requires a DNA helicase" Biochem. Biophys. Res. Comm. 205, 1004-1009.
37. Maine,
I.P. and Kodadek, T. (1994) "Efficient unwinding of triplex DNA by a DNA helicase" Biochem. Biophys. Res. Comm. 204, 1119-1124.
36. Houston,
P. and Kodadek, T. (1994) "Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA" Proc. Natl. Acad. Sci. USA 91, 5471-5474.
35. Barry,
J. and Kodadek, T. (1994) "A new route '5+1' route to arenes. Application to the facile synthesis of D4-symmetric
chiral porphyrins" Tetrahedron Letters 35, 2465-2468.
34. Qui,
H., Kodadek, T., and Giederoc, D.P. (1994) "Zinc-free and reduced T4 gene 32 protein binds single-stranded DNA weakly and
fails to stimulate UvsX-catalyzed
homologous pairing" J. Biol. Chem. 269, 2773-278.
33. Maine,
I.P. and Kodadek, T. (1994) "Inhibition of the DNA unwinding and ATP hydrolysis activities of the bacteriophage
dda helicase by a sequence
specific DNA-protein
complex" Biochem. Biophys. Res. Comm. 198, 1070-1077.
32. Kodadek,
T.J. (1994) "Protein-protein interactions in transcriptional activation " in" Transcription", Conaway, R. and Conaway, J., Eds., Raven Press, NY.
31.
Kodadek, T. (1993) "How does the GAL4 transcription factor recognize the appropriate DNA binding
sites in vivo?" Cell. Mol. Biol. Res. 39, 355-360.
30. Vashee,
S., Xu, H., Johnston,
S.A. and Kodadek, T. (1993) "How do Zn2Cys6 proteins distinguish between similar upstream activation sites?
Comparison of the in
vivo and in vitro DNA-binding
specificities of the
GAL4 protein". J. Biol. Chem. 268, 24699-24706.
29. Van
Hoy, M., Leuther,
K.K., Kodadek, T. and Johnston, S.A. (1993) "The acidic activation domains of the GCN4 and GAL4 proteins are not ?-helical,
but form ?-sheets" Cell 72, 587-594.
28.
Bartley, D.W. and Kodadek, T. (1993) "Identification of the active catalyst in the rhodium porphyrin-mediated cyclopropanation
of alkenes" J. Amer. Chem. Soc. 115, 1656-1660.
27. Jiang,
H., Geideroc, D. and Kodadek, T. (1993) "The Role of Protein-Protein Interactions in the Assembly of the Presynaptic Filament
for T4 Homologous Recombination" J. Biol. Chem. 268, 7904-7911.
26. Kodadek,
T. (1992) "The molecular basis of sequence-specific DNA-protein interactions" in "Nucleic Acid Targeted Drug Design", Propst, C. and Perun, T., Eds., Marcel Dekker, NY, ppg. 196-299.
25. Brown,
K.C. and Kodadek, T. (1992) "A transition state model for the rhodium-catalyzed cyclopropanation of alkenes
by diazo esters" J. Amer. Chem. Soc. 114, 8336-8338.
24. Maxwell,
J.L., Brown, K.C.,
Bartley, D.W. and Kodadek, T. "Mechanism of the rhodium porphyrin-catalyzed cyclopropanation of alkenes" (1992) Science 256, 1544-1547.
23.
O'Malley, S. and Kodadek, T. (1992) "Asymmetric cyclopropanation of alkenes catalyzed by a rhodium 'chiral fortress'
porphyrin" Organometallics 11, 2299-2302.
22. Maine,
I.P., Sun, D., Hurley,
L. and Kodadek, T. (1992) "The antitumor agent CC-1065 inhibits helicase-catalyzed unwinding of duplex DNA" Biochemistry 31, 3968-3975.
21. Maxwell,
J.L., O'Malley, Brown,
K.C. and Kodadek. T. (1992) "Shape selective and asymmetric cyclopropanation of alkenes catalyzed by rhodium
porphyrins" Organometallics 11, 645-652.
20. VanHoy,
M., Hansen, A. and Kodadek, T. (1992) "Spectroscopic studies of a transcriptional activation peptide" J. Amer. Chem. Soc. 114, 362-363.
19.
Kodadek, T. (1991) "Inhibition of protein-mediated homologous pairing by a DNA helicase" J. Biol. Chem. 266, 9712-9718.
18. O'Malley,
S. and Kodadek, T. (1991) "Asymmetric cyclopropanation of alkenes catalyzed by a 'chiral wall' porphyrin" Tetrahedron Letters 32, 2445-2448.
17. Hansen,
A., VanHoy, M. and Kodadek, T. (1991) "Spectroscopic studies of the DNA binding site for the GAL4 zinc finger protein" Biochem. Biophys. Res. Comm. 175, 492-499.
16.
Maxwell, J. and Kodadek, T. (1991) "Organometallic chemistry of porphyrins: Spectroscopic and chemical characterization
of a rhodium porphyrin/ethyldiazo
acetate adduct" Organometallics 10, 4-6.
15. Bartley,
D.W. and Kodadek, T. (1990) "Catalysis of Diels-Alder reactions by metalloporphyrins" Tetrahedron Letters 44, 6303-6306.
14. Kodadek,
T. (1990) "Functional interactions between phage T4 and E. coli DNA-binding proteins during
the presynapsis phase
of homologous recombination" Biochem. Biophys. Res. Commun. 172, 804-10.
13. Kodadek,
T. and Wong, M.-L. (1990) "Homologous pairing in vitro initiated by DNA synthesis" Biochem. Biophys. Res. Comm. 169, 302-309.
12. Rodriguez,
M., Kodadek, T., Torres, M. and Bard, A.J. (1990) "Cleavage of DNA by electrochemically activated Mn(III) and Fe(III) complexes
of meso-tetrakis (N-methyl-4-pyridiniumyl)
porphine" Bioconjugate Chem. 2, 123-131.
11. Kodadek,
T. (1990) "The role of the bacteriophage gene 32 protein in homologous pairing" J. Biol. Chem. 265, 20966-20969.
10.
Kodadek, T.; Gan, D. C. and Stemke-Hale, K. (1989) "The phage T4 uvs Y recombination protein stabilizes presynaptic filaments" J. Biol. Chem. 264, 16451-16457.
9. O'Malley,
S. and Kodadek, T. (1989) "Synthesis and characterization of the 'chiral wall porphyrin'" J. Amer. Chem. Soc. 111, 9116-9117.
8.
Kodadek, T. and Gamper, H. (1988) "Efficient synthesis of a supercoiled M13 DNA molecule containing a site-specifically
placed psoralen adduct
and its use as a substrate
for DNA replication" Biochemistry 27, 3210-3215.
7.
Kodadek, T.; Wong, M. L.; Alberts, B. M. (1988) "Mechanism of strand exchange catalyzed by the bacteriophage uvsX protein" J. Biol. Chem. 263, 9427-9436.
6.
Kodadek, T.; Alberts, B. M. (1987) "Stimulation of protein-directed strand exchange by a DNA helicase" Nature 326, 312-314.
5. Collman,
J.P., Kodadek, T. and Brauman, J.I. (1986) "Oxygenation of styrene by cytochrome P-450 model systems: A mechanistic study" J. Amer. Chem. Soc. 108, 2588-2594.
4. Collman,
J.P., Kodadek, T., Raybuck, S.A., Brauman, J.I. and Papazian, L.M. (1986) "" J. Amer. Chem. Soc. 107, 4343-4344.
3. Collman,
J.P., Brauman, J.I.,
Meuneier, B., Hayashi,
T., Kodadek, T. and Raybuck, S.A. (1985) "Epoxidation of olefins by cytochrome P-450 model compounds: Kinetics and stereochemistry
of oxygen atom transfer
and origin of shape selectivity" J. Amer. Chem. Soc. 107, 2000-2005.
2. Collman,
J.P., Brauman, J.I.,
Meunier, B., Raybuck,
S.A. and Kodadek, T. (1984) "Epoxidation of olefins by cytochrome P-450 model compounds: Mechanism of oxygen
atom transfer" Proc. Natl. Acad. Sci. USA 81, 3245-3248.
1. Collman,
J.P., Kodadek, T., Raybuck, S.A. and Meunier, B. (1983) "Oxygenation of hydrocarbons by cytochrome P-450 model compounds: Modification
of reactivity by axial
ligands" Proc. Natl. Acad. Sci. USA 80, 7039-7041.
Patents
1. Kodadek,
T.J., Barry, J.F. (1996) U.S. Patent N-7376. "D4-symmetric porphyrin-based catalysts. Processes for preparing same and processes
for using same".
2. Kodadek,
T.J., Fancy, D.A., Johnston, S.A. (2003) U.S. Patent No. 6,613,582. "Methods for rapid and efficient protein cross-linking".
3. Kodadek,
T. (2006) U.S. Patent no. 7,018,801. "Selection of peptides with antibody-like properties".
