Publications
1. Pabo, C.O., Sauer, R.T., Sturtevant, J.M. & Ptashne, M. (1979) The λ Repressor Contains Two Domains. Proc. Natl. Acad. Sci., USA 76, 1608-1612.
2. Sauer, R.T., Pabo, C.O., Meyer, B.J., Ptashne, M. & Backman, K.C. (1979) The Regulatory Functions of the λ Repressor Reside in the Amino-Terminal Domain. Nature 279, 396-400.
3. Johnson, A.D., Pabo, C.O. & Sauer, R. T. (1980) Bacteriophage λ Repressor and Cro Protein: Interactions with Operator DNA. Meth. Enz. 65, 839-856.
4. Ptashne, M., Jeffrey, A., Johnson, A.D., Mauer, R., Meyer, B.J., Pabo, C.O., Roberts, T.M. & Sauer, R.T. (1980) How the λ Repressor and Cro Work. Cell 19, 1-11.
5. Pabo, C.O., Krovatin, W., Jeffrey, A. & Sauer, R.T. (1982) The N-Terminal Arms of λ Repressor Wrap Around the Operator DNA. Nature 298, 441-443.
6. Pabo, C.O. & Lewis, M. (1982) The Operator-Binding Domain of λ Repressor: Structure and DNA Recognition. Nature 298, 443-447.
7. Sauer, R.T., Yocum, R.R., Doolittle, R.F., Lewis, M. & Pabo, C.O. (1982) Homology Among DNA-Binding Proteins Suggests Use of a Conserved Super-Secondary Structure. Nature 298, 447-451.
8. Ptashne, M., Johnson, A.D. & Pabo, C.O. (1982) A Genetic Switch in a Bacterial Virus. Scientific American 247, 128-140.
9. Lewis, M., Jeffrey, A., Wang, J-H., Ladner, R.C., Ptashne, M. & Pabo, C.O. (1983) Structure of the Operator-Binding Domain of λ Repressor: Implications for DNA Recognition and Gene Regulation. Cold Spring Harbor Symp. Quant. Biol. 47, 435-440.
10. Gussin, G., Johnson, A.D., Pabo, C.O. & Sauer, R.T. (1983) Repressor and Cro. Lambda II (J. Roberts, ed.) Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 93-121.
11. Ohlendorf, D.H., Anderson, W.F., Lewis, M., Pabo, C.O. & Matthews, B.W. (1983) Comparison of the Structures of Cro and λ Repressor Proteins from Bacteriophage λ. J. Mol. Biol. 169, 757-769.
12. Sauer, R.T. & Pabo, C.O. (1983) Protein-DNA Recognition: The λ Repressor- Operator Complex. American Society for Microbiology News 49, 131- 136.
13. Pabo, C.O. (1983) Designing Proteins and Peptides. Nature 301, 200.
14. Pabo, C.O., Jordan, S.R. & Frankel, A.D. (1983) Systematic Analysis of Possible Hydrogen Bonds Between Amino Acid Side Chains and B-Form DNA. J. Biomolecular Structure and Dynamics 1, 1039-1049.
15. Sauer, R.T. & Pabo, C.O. (1984) How λ Repressor Binds Operator DNA. Microbiology 1984.
16. Pabo, C.O. & Sauer, R.T. (1984) Protein-DNA Recognition. Ann. Rev. Biochem. 53, 293-321.
17. Pabo, C.O. (1984) DNA-Protein Interactions. Proceedings of the Robert A. Welch Foundation Conferences on Chemical Research XXVII Stereospecificity in Chemistry and Biochemistry Robert A. Welch Foundation, Houston, TX, 222-255.
18. Lewis, M., Wang, J. & Pabo, C.O. (1985) Structure of the Operator Binding Domain of λ Repressor. Biological Macromolecules and Assemblies, Volume 2 (Drs. Jurnak & McPherson, eds.) John Wiley and Sons, Inc., New York, 266-287.
19. Jordan, S.R., Pabo, C.O., Vershon, A.K. & Sauer, R.T. (1985) Crystallization of the Arc Repressor. J. Mol. Biol. 185, 445-446.
20. Jordan, S.R., Whitcombe, T.V., Berg, J.M. & Pabo, C.O. (1985) Systematic Variation in DNA Length Yields Highly Ordered Repressor-Operator Co-Crystals. Science 230, 1383-1385.
21. Pabo, C.O. & Suchanek, E.G. (1986) Computer-Aided Model-Building Strategies for Protein Design. Biochemistry 25, 5987-5991.
22. Sauer, R.T., Hehir, K., Stearman, R.S., Weiss, M.A., Jeitler-Nilsson, A., Suchanek, E.G. & Pabo, C.O. (1986) An Engineered Intersubunit Disulfide Enhances the Stability and DNA Binding of the N-Terminal Domain of λ Repressor. Biochemistry 25, 5992-5998.
23. Weiss, M.A., Pabo, C.O., Karplus, M. & Sauer, R.T. (1986) Dimerization of the Operator-Binding Domain of Phage λ Repressor. Biochemistry 26, 897-904.
24. Pabo, C.O. (1987) Introductory chapter for Protein Engineering (D. L. Oxender & C. F. Fox, eds.) Alan R. Liss, Inc., New York, xv-xvii.
25. Berg, J.M., Jordan, S.R. & Pabo, C.O. (1987) The Structure and Function of Bacteriophage λ Repressor. DNA: Protein Interactions and Gene Regulation (E.B. Thompson & J. Papaconstantinou, eds.) University of Texas Press, Austin, 1-12.
26. Pabo, C.O. (1987) New Generation Databases for Molecular Biology. Nature 327, 467.
27. Frankel, A.D., Berg, J.M. & Pabo, C.O. (1987) Metal-Dependent Folding of a Single Zinc Finger from Transcription Factor IIIA. Proc. Natl. Acad. Sci., USA 84, 4841-4845.
28. Frankel, A.D., Bredt, D.S. & Pabo, C.O. (1988) Tat Protein from Human Immunodeficiency Virus Forms a Metal-Linked Dimer. Science 240, 70-73.
29. Frankel, A.D. & Pabo, C.O. (1988) Fingering Too Many Proteins. Cell 53, 675.
30. Frankel, A.D., Chen, L., Cotter, R.J. & Pabo C.O. (1988) Dimerization of the Tat Protein from HIV: A Cysteine-Rich Peptide Mimics the Normal Metal-Linked Dimer Interface. Proc. Natl. Acad. Sci., USA 85, 6297-6300.
31. Stearman, R.S., Frankel, A.D., Freire, E., Liu, B. & Pabo, C.O. (1988) Combining Thermostable Mutations Increases the Stability of λ Repressor. Biochemistry 27, 7571-7574.
32. Jordan, S.R. & Pabo, C.O. (1988) Structure of the λ Complex at 2.5 Å Resolution: Detailed View of the Repressor-Operator Interactions. Science 242, 893-899.
33. Frankel, A.D. & Pabo, C.O. (1988) Cellular Uptake of the Tat Protein from Human Immunodeficiency Virus. Cell 55, 1189-1193.
34. Sauer, R.T., Jordan, S.R. & Pabo, C.O. (1990) λ Repressor: A Model System for Understanding Protein-DNA Interactions and Protein Stability. Adv. Prot. Chem. 40, 1-61.
35. Bowie, J.U., Clarke, N.D., Pabo, C.O. & Sauer, R.T. (1990) Identification of Protein Folds: Matching Hydrophobicity Patterns of Sequence Sets with Solvent Accessibility Patterns of Known Structures. Proteins 7, 257-264.
36. Pabo, C.O., Aggarwal, A.K., Jordan, S.R., Beamer, L.J., Obeysekare, U. & Harrison, S.C. (1990) Conserved Residues Make Similar Contacts in Two Repressor- Operator Complexes. Science 247, 1210-1213.
37. Liu, B., Kissinger, C.R., Pabo, C.O., Martin-Blanco, E. & Kornberg, T.B (1990) Crystallization and Preliminary X-ray Diffraction Studies of the Engrailed Homeodomain and of an Engrailed Homeodomain/DNA Complex. Biochem. and Biophys. Res. Comm. 171, 257-259.
38. Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B. & Pabo, C.O. (1990) Crystal Structure of an Engrailed Homeodomain/DNA Complex at 2.8 Å Resolution: A Framework for Understanding Homeodomain/DNA Interactions. Cell 63, 579- 590.
39. Wolberger, C., Pabo, C.O., Vershon, A.K. & Johnson, A.D. (1991) Crystallization and Preliminary X-ray Diffraction Studies of a MATα2-DNA Complex. J. Mol. Biol. 217, 11-13.
40. Pavletich, N.P. & Pabo, C.O. (1991) Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 Å. Science 252, 809-817.
41. Wolberger, C. Vershon, A.K., Liu, B., Johnson, A.D. & Pabo, C.O. (1991) Crystal Structure of a MATα2 Homeodomain-Operator Complex Suggests a General Model for Homeodomain-DNA Interactions. Cell 67, 517-528.
42. Clarke, N.D., Beamer, L.J., Goldberg, H.R., Berkower, C. & Pabo, C.O. (1991) The DNA Binding Arm of λ Repressor: Critical Contacts from a Flexible Region. Science 254, 267-270.
43. Godley, L., Pfeifer, J., Steinhauer, D., Ely, B., Shaw, G., Kaufmann, R., Suchanek, E., Pabo, C., Skehel, J.J., Wiley, D.C. & Wharton, S. (1992) Introduction of Intersubunit Disulfide Bonds In the Membrane-Distal Region of the Influenza Hemagglutinin Abolishes Membrane Fusion Activity. Cell 68, 635-645.
44. Pabo, C.O. & Sauer, R.T. (1992) Transcription Factors: Structural Families and Principles of DNA Recognition. Annu. Rev. Biochem. 61, 1053-1095.
45. Beamer, L.J. & Pabo, C.O. (1992) Refined 1.8 Å Crystal Structure of the λ Repressor-Operator Complex. J. Mol. Biol. 227, 177-196.
46. Pavletich, N.P. & Pabo, C.O. (1993) Crystal Structure of a Five Finger GLI-DNA Complex: New Perspectives on Zinc Fingers. Science 261, 1701-1707.
47. Pavletich, N.P., Chambers, K.A. & Pabo, C.O. (1993) The DNA-Binding Domain of p53 Contains the Four Conserved Regions and the Major Mutation Hot Spots. Genes & Development 7, 2556-2564.
48. Rebar, E.J. & Pabo, C.O. (1994) Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities. Science 263, 671-673.
49. Raumann, B.E., Rould, M.A., Pabo, C.O. & Sauer, R.T. (1994) DNA Recognition by β-sheets in the Arc Repressor-Operator Crystal Structure. Nature 367, 754-757.
50. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. & Pabo, C.O. (1994) Crystal Structure of the Oct-1 POU Domain Bound to an Octamer Site: DNA Recognition with Tethered DNA-Binding Modules. Cell 77, 21-32.
51. Ma, P.C.M., Rould, M.A., Weintraub, H. & Pabo, C.O. (1994) Crystal Structure of MyoD bHLH Domain-DNA Complex: Perspectives on DNA Recognition and Implications for Transcriptional Activation. Cell 77, 451-459.
52. Nekludova, L. & Pabo, C.O. (1994) Distinctive DNA Conformation with Enlarged Major Groove Is Found in Zn Finger-DNA and Other Protein-DNA Complexes. Proc. Natl. Acad. Sci., USA, 91, 6948-6952.
53. Clarke, N.D., Kissinger, C.R., Desjarlais, J., Gilliland, G.L., & Pabo, C.O. (1994) Structural Studies of the Engrailed Homeodomain. Prot. Sci. 3, 1779-1787.
54. Pomerantz, J.L., Sharp, P.A., & Pabo, C.O. (1995) Structure-Based Design of Transcription Factors. Science 267, 93-96.
55. Xu, W., Rould, M.A., Jun, S., Desplan, C., & Pabo, C.O. (1995) Crystal Structure of a Paired Domain-DNA Complex at 2.5 Å Resolution Reveals Structural Basis for Pax Developmental Mutations. Cell 80, 639-650.
56. Pomerantz, J.L., Pabo, C.O., & Sharp, P.A. (1995) Analysis of Homeodomain Function by Structure-Based Design of a Transcription Factor. Proc. Natl. Acad. Sci., USA 92, 9752-9756.
57. Klemm, J.D. & Pabo, C.O. (1996) Oct-1 POU Domain-DNA Interactions: Cooperative Binding of Isolated Subdomains and Effects of Covalent Linkage. Genes & Development 10, 27-36.
58. Rebar, E.J., Greisman, H.A., & Pabo, C.O. (1996) Phage Display Methods for Selecting Zinc Finger Proteins with Novel DNA-Binding Specificities. Methods In Enzymology 267, 129-149.
59. Elrod-Erickson, M., Rould, M.A., Nekludova, L., & Pabo, C.O. (1996) Zif268 Protein-DNA Complex Refined at 1.6 Å: A Model System for Understanding Zinc Finger-DNA Interactions. Structure 4, 1171-1180.
60. Greisman, H.A. & Pabo, C.O. (1997) A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites. Science 275, 657-661.
61. Kim, J.-S., Kim, J., Cepek, K.L., Sharp, P.A., & Pabo, C.O. (1997) Design of TATA Box-Binding Protein/Zinc Finger Fusions for Targeted Regulation of Gene Expression. Proc. Natl. Acad. Sci., USA 94, 3616-3620.
62. Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T., & Pabo, C.O. (1997) Engrailed (Gln 50 -> Lys) Homeodomain-DNA Complex at 1.9 Å Resolution: Structural Basis for Enhanced Affinity and Altered Specificity. Structure 5, 1047-1054.
63. Kim, J.-S. & Pabo, C.O. (1997) Transcriptional Repression by Zinc Finger Peptides. J. Biol. Chem. 272, 29795-29800.
64. Pomerantz, J.L., Wolfe, S.A., & Pabo, C.O. (1998) Structure-Based Design of a Dimeric Zinc Finger Protein. Biochemistry 37, 965-970.
65. Kim, J.-S. & Pabo, C.O. (1998) Getting a Handhold on DNA: Design of Poly-Zinc Finger Proteins with Femtomolar Dissociation Constants. Proc. Natl. Acad. Sci. USA 95, 2812-2817.
66. Elrod-Erickson, M., Benson, T.E., & Pabo, C.O. (1998) High-Resolution Structures of Variant Zif268-DNA Complexes: Implications for Understanding Zinc Finger-DNA Recognition. Structure 6, 451-464.
67. Fraenkel, E. & Pabo, C.O. (1998) Comparison of X-ray and NMR Structures for the Antennapedia Homeodomain-DNA Complex. Nature Struct. Bio. 5, 692- 697.
68. Fraenkel, E., Rould, M.A., Chambers, K.A., & Pabo, C.O. (1998) Engrailed Homeodomain-DNA Complex at 2.2 Å Resolution: A Detailed View of the Interface and Comparison with Other Engrailed Structures. J. Mol. Biol. 284, 351-361.
69. Wolfe, S.A., Greisman, H.A., Ramm, E.I., & Pabo, C.O. (1999) Analysis of Zinc Fingers Optimized Via Phage Display: Evaluating the Utility of a Recognition Code. J. Mol. Biol. 285, 1917-1934.
70. Zheng, N., Fraenkel, E., Pabo, C.O., & Pavletich, N.P. (1999) Structural Basis of DNA Recognition by the Heterodimeric Cell Cycle Transcription Factor E2F-DP. Genes & Development 13, 666-674.
71. Xu, H.E., Rould, M.A., Xu, W., Epstein, J.A., Maas, R.L., & Pabo, C.O. (1999) Crystal Structure of the Human Pax6 Paired Domain-DNA Complex Reveals Specific Roles for the Linker Region and Carboxy-terminal Subdomain in DNA Binding. Genes & Development 13, 1263-1275.
72. Ohndorf, U.-M., Rould, M.A., He, Q., Pabo, C.O., & Lippard, S.J. (1999) Basis for Recognition of Cisplatin-Modified DNA by High-Mobility-Group Proteins. Nature 399, 708-712.
73. Elrod-Erickson, M., & Pabo, C.O. (1999) Binding Studies with Mutants of Zif268: Contribution of Individual Side Chains to Binding Affinity and Specificity in the Zif268 Zinc Finger-DNA Complex. J. Biol. Chem. 274, 19281-19285.
74. Wang, B.S., & Pabo, C.O. (1999) Dimerization of Zinc Fingers Mediated by Peptides Evolved in vitro from Random Sequences. Proc. Natl. Acad. Sci., USA 96, 9568-9573.
75. Chasman, D., Cepek, K., Sharp, P.A., & Pabo, C.O. (1999) Crystal Structure of an OCA-B Peptide Bound to an Oct-1 POU Domain/Octamer DNA Complex: Specific Recognition of a Protein-DNA Interface. Genes & Development 13, 2650- 2657.
76. Wolfe, S.A., Nekludova, L., & Pabo, C.O. (2000) DNA Recognition by Cys2His2 Zinc Finger Proteins. Annual Review of Biophysics and Biomolecular Structure 29, 183-212.
77. Grant, R.A., Rould, M.A., Klemm, J.D., & Pabo, C.O. (2000) Exploring the Role of Glutamine 50 in the Homeodomain-DNA Interface: Crystal Structure of Engrailed (Gln50 -> Ala) Complex at 2.0 Å. Biochemistry 39, 8187-8192.
78. Wolfe, S.A., Ramm, E.I., & Pabo, C.O. (2000) Combining Structure-Based Design with Phage Display to Create New Cys2His2 Zinc Finger Dimers. Structure 8, 739-750.
79. Joung, J.K., Ramm, E.I., & Pabo, C.O. (2000) A Bacterial Two-Hybrid Selection System for Studying Protein-DNA and Protein-Protein Interactions. Proc. Natl. Acad. Sci., USA 97, 7382-7387.
80. Pabo, C.O., & Nekludova, L. (2000) Geometric Analysis and Comparison of Protein-DNA Interfaces: Why Is There No Simple Code for Recognition? J. Mol. Biol. 301, 597-624.
81. Pabo, C.O., Peisach, E., & Grant, R.A. (2001) Design and Selection of Novel Cys2His2 Zinc Finger Proteins. Ann. Rev. Biochem. 70, 313-340.
82. Wang, B.S., Grant, R.A., Pabo, C.O. (2001) Selected Peptide Extension Contacts Hydrophobic Patch on Neighboring Zinc Finger and Mediates Dimerization on DNA. Nature Struct. Bio. 8, 589-593.
83. Wolfe, S.A., Grant, R.A., Elrod-Erickson, M., & Pabo, C.O. (2001) Beyond the "Recognition Code": Structures of Two Cys2His2 Zinc Finger/TATA Box Complexes. Structure 9, 717-723.
84. Miller, J.C., & Pabo, C.O. (2001) Rearrangement of Side-chains in a Zif268 Mutant Highlights the Complexities of Zinc Finger-DNA Recognition. J. Mol. Biol. 313, 309-315.
85. Snowdon, A.W., Gregory, P.D., Case, C.C., & Pabo, C.O. (2002) Gene-Specific Targeting of H3K9 Methylation Is Sufficient for Initiating Repression in Vivo. Current Biology 12, 2159-2166.
86. Jamieson, A.C., Miller, J.C., & Pabo, C.O. (2003) Drug Discovery with Engineered Zinc Finger Proteins. Nature Reviews: Drug Discovery 2, 361-368.
87. Peisach, E., & Pabo, C.O. (2003) Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes. J. Mol. Biol., 330, 1-7.
88. Tan, S. et al (2003) Zinc-Finger Protein-Targeted Gene Regulation: Genomewide Single-Gene Specificity. Proc. Natl. Acad. Sci., USA 100, 11997-12002.
89. Hurt, J.A., Thibodeau, S.A., Hirsh, A.S., Pabo, C.O. & Joung, J.K. (2003) Highly Specific Zinc Finger Proteins Obtained by Directed Domain Shuffling and Cell-Based Selection. Proc. Natl. Acad. Sci., USA 100, 12271-12276.
90. Bartsevich, V.V., Miller, J.C., Case, C.C. & Pabo, C.O. (2003) Engineered Zinc Finger Proteins for Controlling Stem Cell Fate, Stem Cells 21, 632-637.
91. Wolfe, S.A., Grant, R.A., & Pabo, C.O. (2003) Structure of a Dimeric Zinc Finger Protein Bound to DNA. Biochemistry 42, 13401-13409.
92. Snowden, A.W., Zhang, L., Urnov, F. Dent, C. Jouvenot, Y., Zhong, X., Rebar, E.J., Jamieson, A.C., Zhang, H.S., Tan, S., Case, C.C., Pabo, C.O., Wolffe, A.P., and Gregory, P.D. (2003) Repression of Vascular Endothelial Growth Factor A in Glioblastoma Cells Using Engineered Zinc Finger Transcription Factors. Cancer Res. 63, 8968-8976.
93. Liu, P.Q., Morton, M.F., Reik, A., de la Rosa, R., Mendel, M.C., Li, Y.Y., Case, C.C., Pabo, C.O., Moreno, V., Kempf, A., Pyati, J. & Shankley, N.P. (2004) Cell Lines for Drug Discovery: Elevating Target-protein Levels Using Engineered Transcription Factors. J. Biomol. Screen. 9, 44-51.
94. Nguyen-Hackley, D.H., Ramm, E., Taylor, C.M., Joung, K.C., Dervan, P.B. & Pabo, C.O. (2004) Allosteric Inhibition of Zinc-Finger Binding in the Major Groove of DNA by Minor-Groove Binding Ligands. Biochemistry 43, 3880-3890.
95. Pabo, C.O. (2006) Specificity by Design. Nature Biotechnology 24, 954-955.
96. Miller, J.C., Holmes, M.C., Wang, J., Guschin, D.Y., Lee, Y.L., Rupniewski, I., Beausejour, C.M., Waite, A.J., Wang, N.S., Kim, K.A., Gregory, P.D., Pabo, C.O., and Rebar, E.J. (2007) An Improved Zinc-finger Nuclease Architecture for Highly Specific Genome Editing, Nature Biotechnology 25, 778-785.
