Part:BBa_K364101

Zinc Finger Protein AAA

This part codes for a Cys2His2 zinc finger protein to be used in assembly of zinc finger polymers (to be continued).

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]

Zinc finger Biology

The Cys2His2-like fold group is by far the best-characterized class of zinc fingers and are extremely common in mammalian transcription factors. These domains adopt a simple ββα fold and have the amino acid Sequence motif: X2-Cys-X2,4-Cys-X12-His-X3,4,5-His. This class of zinc fingers can have a variety of functions such as binding RNA and mediating protein-protein interactions, but is best known for its role in sequence specific DNA-binding proteins such as Zif268. In such proteins, individual zinc finger domains typically occur as tandem repeats with two, three, or more fingers comprising the DNA-binding domain of the protein. These tandem arrays can bind in the major groove of DNA and are typically spaced at 3-bp intervals. The α-helix of each domain (often called the "recognition helix") can make sequence-specific contacts to DNA bases; residues from a single recognition helix can contact 4 or more bases to yield an overlapping pattern of contacts with adjacent zinc fingers. Adapted from [http://en.wikipedia.org/wiki/Zinc_fingers#Cys2His2 Wikipedia]

Engineered Zinc fingers and their applications

Various strategies have been developed to engineer Cys2His2 zinc fingers to bind desired sequences. The majority of engineered zinc finger arrays are based on the zinc finger domain of the murine transcription factor Zif268, although some groups have generated zinc finger arrays based on the human transcription factor SP1. Zif268 has three individual zinc finger motifs that collectively bind a 9 bp sequence with high affinity. The structure of this protein bound to DNA was solved in 1991 and stimulated a great deal of research into engineered zinc finger arrays. In 1994 and 1995, a number of groups used phage display to alter the specificity of a single zinc finger of Zif268. Typical engineered zinc finger arrays have between 3 and 6 individual zinc finger motifs and bind target sites ranging from 9 basepairs to 18 basepairs in length. Arrays with 6 zinc finger motifs are particularly attractive because they bind a target site that is long enough to have a good chance of being unique in a mammalian genome. Adapted from [http://en.wikipedia.org/wiki/Zinc_fingers#Engineered_zinc_finger_arrays Wikipedia]

Engineered zinc finger arrays can then be used in numerous applications such as artificial transcription factors, zinc finger methylases, zinc finger recombinases, and Zinc finger nucleases. Artificial transcription factors with engineered zinc finger arrays have been used in numerous scientific studies, and an artificial transcription factor that activates expression of VEGF is currently being evaluated in humans as a potential treatment for several clinical indications. Zinc finger nucleases have become useful reagents for manipulating genomes of many higher organisms including Drosophila melanogaster, Caenorhabditis elegans, tobacco, corn[23], zebrafish, various types of mammalian cells, and rats. An ongoing clinical trial is evaluating Zinc finger nucleases that disrupt the CCR5 gene in CD4+ human T-cells as a potential treatment for HIV/AIDS. Adapted from [http://en.wikipedia.org/wiki/Zinc_fingers#Applications Wikipedia]

Using this part to design a DNA binding Domain

Zinc Finger coding standard biobrick parts may be used to assemble in silico a polydactyl zinc finger polymer (see BBF RFC ??? for more data).
The following parts are available as well for the construction:
1. Zinc finger proteins with helices able to bind: 16 GNN triplets, 15 ANN triplets (ATC not represented), 15 CNN triplets (CTC not represented), TGA, TGG and TAG
2. Constant 5 prime and 3 prime regions, which must be used in assembly of every polydactyl zinc finger polymer.
3. Constant Linker segment, linking adjacent zinc fingers in polymers.