Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains 1 1Edited by M. Yaniv

2000 ◽  
Vol 303 (4) ◽  
pp. 489-502 ◽  
Author(s):  
Birgit Dreier ◽  
David J Segal ◽  
Carlos F Barbas
Keyword(s):  
Molecular Recognition ◽  
Zinc Finger ◽  
Dna Sequences ◽  
Zinc Finger Domains

scholarly journals Development of Zinc Finger Domains for Recognition of the 5′-CNN-3′ Family DNA Sequences and Their Use in the Construction of Artificial Transcription Factors

2005 ◽  
Vol 280 (42) ◽  
pp. 35588-35597 ◽  
Author(s):  
Birgit Dreier ◽  
Roberta P. Fuller ◽  
David J. Segal ◽  
Caren V. Lund ◽  
Pilar Blancafort ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Dna Sequences ◽  
Artificial Transcription Factors ◽  
Zinc Finger Domains

The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites

2011 ◽  
Vol 39 (2) ◽  
pp. 584-588 ◽  
Author(s):  
Stephen E. Halford ◽  
Lucy E. Catto ◽  
Christian Pernstich ◽  
David A. Rusling ◽  
Kelly L. Sanders
Keyword(s):  
Zinc Finger ◽  
Dna Sequences ◽  
Catalytic Domain ◽  
Dna Recognition ◽  
Zinc Finger Nucleases ◽  
Target Sequence ◽  
Base Pairs ◽  
Catalytic Domains ◽  
Zinc Finger Domains ◽  
Better Than

The FokI endonuclease is a monomeric protein with discrete DNA-recognition and catalytic domains. The latter has only one active site so, to cut both strands, the catalytic domains from two monomers associate to form a dimer. The dimer involving a monomer at the recognition site and another from free solution is less stable than that from two proteins tethered to the same DNA. FokI thus cleaves DNA with two sites better than one-site DNA. The two sites can be immediately adjacent, but they can alternatively be many hundreds of base pairs apart, in either inverted or repeated orientations. The catalytic domain of FokI is often a component of zinc finger nucleases. Typically, the zinc finger domains of two such nucleases are designed to recognize two neighbouring DNA sequences, with the objective of cutting the DNA exclusively between the target sequences. However, this strategy fails to take account of the fact that the catalytic domains of FokI can dimerize across distant sites or even at a solitary site. Additional copies of either target sequence elsewhere in the chromosome must elicit off-target cleavages.

Towards understanding the molecular recognition process in prokaryotic zinc-finger domain

2015 ◽  
Vol 91 ◽  
pp. 100-108 ◽  
Author(s):  
Luigi Russo ◽  
Maddalena Palmieri ◽  
Jolanda Valentina Caso ◽  
Gianluca D' Abrosca ◽  
Donatella Diana ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Zinc Finger ◽  
Zinc Finger Domain ◽  
Recognition Process

scholarly journals Determination of DNA binding specificities of mutated zinc finger domains

FEBS Letters ◽  
1991 ◽  
Vol 283 (1) ◽  
pp. 23-26 ◽  
Author(s):  
Hans-Jürgen Thiesen ◽  
Christian Bach
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Domains

scholarly journals Biochemical Activities of Highly Purified, Catalytically Active Human APOBEC3G: Correlation with Antiviral Effect

2006 ◽  
Vol 80 (12) ◽  
pp. 5992-6002 ◽  
Author(s):  
Yasumasa Iwatani ◽  
Hiroaki Takeuchi ◽  
Klaus Strebel ◽  
Judith G. Levin
Keyword(s):  
Zinc Finger ◽  
Cytidine Deaminase ◽  
Antiviral Effect ◽  
Minimum Length ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Pure System ◽  
Dna And Rna ◽  
Catalytically Active ◽  
Zinc Finger Domains

ABSTRACT APOBEC3G (APO3G), a cytidine deaminase with two zinc finger domains, inhibits human immunodeficiency virus type 1 replication in the absence of Vif. Here, we provide a comprehensive molecular analysis of the deaminase and nucleic acid binding activities of human APO3G using a pure system containing only one protein component, i.e., highly purified, catalytically active enzyme expressed in a baculovirus system. We demonstrate that APO3G deaminates cytosines in single-stranded DNA (ssDNA) only, whereas it binds efficiently to ssDNA and ssRNA, about half as well to a DNA/RNA hybrid, and poorly to double-stranded DNA and RNA. In addition, the base specificities for deamination and binding of ssDNA are not correlated. The minimum length required for detection of APO3G binding to an ssDNA oligonucleotide in an electrophoretic mobility shift assay is 16 nucleotides. Interestingly, if nucleocapsid protein and APO3G are present in the same reaction, we find that they do not interfere with each other's binding to RNA and a complex containing the RNA and both proteins is formed. Finally, we also identify the functional activities of each zinc finger domain. Thus, although both zinc finger domains have the ability to bind nucleic acids, the first zinc finger contributes more to binding and APO3G encapsidation into virions than finger two. In contrast, deamination is associated exclusively with the second zinc finger. Moreover, zinc finger two is more important than finger one for the antiviral effect, demonstrating a correlation between deaminase and antiviral activities.

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