Probing the DNA-binding affinity and specificity of designed zinc finger proteins.

[1]  A. Scharenberg,et al.  Zinc-finger nucleases: a powerful tool for genetic engineering of animals , 2010, Transgenic Research.

[2]  Y. Doyon,et al.  Precise genome modification in the crop species Zea mays using zinc-finger nucleases , 2009, Nature.

[3]  Ronnie J Winfrey,et al.  High frequency modification of plant genes using engineered zinc finger nucleases , 2009, Nature.

[4]  J. Gall,et al.  Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases , 2008, Proceedings of the National Academy of Sciences.

[5]  Drena Dobbs,et al.  An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins , 2008, Nucleic acids research.

[6]  Ronnie J Winfrey,et al.  Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. , 2008, Molecular cell.

[7]  T. Hocking,et al.  Heritable Targeted Gene Disruption in Zebrafish Using Designed Zinc Finger Nucleases , 2008, Nature Biotechnology.

[8]  Yukio Sugiura,et al.  New redesigned zinc-finger proteins: design strategy and its application. , 2008, Chemistry.

[9]  Daniel F. Voytas,et al.  Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool , 2007, Nucleic Acids Res..

[10]  David J Segal,et al.  Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. , 2006, Journal of molecular biology.

[11]  Dana Carroll,et al.  Design, construction and in vitro testing of zinc finger nucleases , 2006, Nature Protocols.

[12]  Jeremy M Berg,et al.  Reduction in DNA-binding affinity of Cys2His2 zinc finger proteins by linker phosphorylation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Jeremy M Berg,et al.  The design of functional DNA-binding proteins based on zinc finger domains. , 2004, Chemical reviews.

[14]  Scot A Wolfe,et al.  Structure of a designed dimeric zinc finger protein bound to DNA. , 2003, Biochemistry.

[15]  David Baltimore,et al.  Chimeric Nucleases Stimulate Gene Targeting in Human Cells , 2003, Science.

[16]  S. Biswas,et al.  Affinity and sequence specificity of DNA binding and site selection for primer synthesis by Escherichia coli primase. , 2002, Biochemistry.

[17]  Yan Huang,et al.  Induction of angiogenesis in a mouse model using engineered transcription factors , 2002, Nature Medicine.

[18]  C. Barbas,et al.  Regulation of transgene expression in plants with polydactyl zinc finger transcription factors , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  E. Margeat,et al.  Equilibrium Binding Assays Reveal the Elevated Stoichiometry and Salt Dependence of the Interaction between Full-length Human Sex-determining Region on the Y Chromosome (SRY) and DNA* , 2002, The Journal of Biological Chemistry.

[20]  R. Beerli,et al.  Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.

[21]  C C Case,et al.  Regulation of an Endogenous Locus Using a Panel of Designed Zinc Finger Proteins Targeted to Accessible Chromatin Regions , 2001, The Journal of Biological Chemistry.

[22]  Dana Carroll,et al.  Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases , 2001, Molecular and Cellular Biology.

[23]  Catherine A. Royer,et al.  Quantitative characterization of the interaction between purified human estrogen receptor and DNA using fluorescence anisotropy , 2000, Nucleic Acids Res..

[24]  C. Pabo,et al.  Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. , 2000, Structure.

[25]  A Klug,et al.  Zinc finger peptides for the regulation of gene expression. , 1999, Journal of molecular biology.

[26]  D J Segal,et al.  Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[27]  C. Pabo,et al.  Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. , 1999, Journal of molecular biology.

[28]  D. Hart,et al.  The salt dependence of DNA recognition by NF-kappaB p50: a detailed kinetic analysis of the effects on affinityand specificity. , 1999, Nucleic acids research.

[29]  D J Segal,et al.  Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[30]  M. S. Ozers,et al.  Equilibrium Binding of Estrogen Receptor with DNA Using Fluorescence Anisotropy* , 1997, The Journal of Biological Chemistry.

[31]  S. Melcher,et al.  Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. , 1997, Journal of molecular biology.

[32]  Carl O. Pabo,et al.  A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites , 1997, Science.

[33]  J. Berg,et al.  A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA , 1996, Nature Structural Biology.

[34]  Z. X. Wang,et al.  An exact mathematical expression for describing competitive binding of two different ligands to a protein molecule , 1995, FEBS letters.

[35]  J R Desjarlais,et al.  Length-encoded multiplex binding site determination: application to zinc finger proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[36]  C. Pabo,et al.  Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. , 1994, Science.

[37]  V. LeTilly,et al.  Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. , 1993, Biochemistry.

[38]  J R Desjarlais,et al.  Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[39]  J R Desjarlais,et al.  Toward rules relating zinc finger protein sequences and DNA binding site preferences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[40]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[41]  J. Lee,et al.  Application of fluorescence energy transfer and polarization to monitor Escherichia coli cAMP receptor protein and lac promoter interaction. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[42]  P E Wright,et al.  Three-dimensional solution structure of a single zinc finger DNA-binding domain. , 1989, Science.

[43]  R. Burgess,et al.  Use of difference boundary sedimentation velocity to investigate nonspecific protein-nucleic acid interactions. , 1980, Biochemistry.

[44]  P. Dehaseth,et al.  Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. , 1977, Biochemistry.

[45]  D. Carroll,et al.  Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases. , 2008, Methods in molecular biology.

[46]  D. Hart,et al.  Distamycin A affects the stability of NF‐κB p50‐DNA complexes in a sequence‐dependent manner , 2002, Journal of molecular recognition : JMR.

[47]  C. Pabo,et al.  Design and selection of novel Cys2His2 zinc finger proteins. , 2001, Annual review of biochemistry.

[48]  C. Pabo,et al.  DNA recognition by Cys2His2 zinc finger proteins. , 2000, Annual review of biophysics and biomolecular structure.

[49]  R. Ebright,et al.  Fluorescence anisotropy: rapid, quantitative assay for protein-DNA and protein-protein interaction. , 1996, Methods in enzymology.

[50]  C. Pabo,et al.  Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities. , 1996, Methods in Enzymology.

[51]  M. Record,et al.  Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. , 1991, Methods in enzymology.

[52]  J. Berg,et al.  Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. , 1988, Proceedings of the National Academy of Sciences of the United States of America.