Chimeric nucleases are an example of

engineered proteins Engineering is the use of scientific principles to design and build machines, structures, and other items, including bridges, tunnels, roads, vehicles, and buildings. The discipline of engineering encompasses a broad range of more speciali ...

which must comprise a

DNA-binding domain A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a genera ...

to give sequence specificity and a

nuclease A nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously effect single and double stranded breaks in their ta ...

domain for DNA cleavage.

DNA-binding domains

DNA-binding domains including the

basic helix-loop-helix BASIC (Beginners' All-purpose Symbolic Instruction Code) is a family of general-purpose, high-level programming languages designed for ease of use. The original version was created by John G. Kemeny and Thomas E. Kurtz at Dartmouth College ...

zinc finger A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold. It was originally coined to describe the finger-like appearance of a hypothesized struct ...

helix-turn-helix Helix-turn-helix is a DNA-binding protein (DBP). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of D ...

and

leucine zipper A leucine zipper (or leucine scissors) is a common three-dimensional structural motif in proteins. They were first described by Landschulz and collaborators in 1988 when they found that an enhancer binding protein had a very characteristic 30-amin ...

motifs have been used in construction of sequence-specific nucleases. Of these, zinc fingers have been suggested the most important due to their modularity, allowing construction of a tailor-made DNA-binding domain.

Nuclease domain

The nuclease domain is responsible for physical cleavage of DNA strands and may introduce either single stranded or double-stranded breaks.

FokI The restriction endonuclease ''Fok''1, naturally found in ''Flavobacterium okeanokoites'', is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non-specific DNA cleavage domain at the C-terminal. O ...

is an example of a sequence-specific

endonuclease Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases ...

whose non-specific nuclease domain introduces double stranded breaks and has been used in a variety of experiments including identification of high- and low-affinity binding sites of transcription factors ''in vitro'', to study recruitment of factors to promoter sites ''in vivo'' using protein position identification with a nuclease tail assay and to study proteins specific to interaction with DNA in the

Z-DNA Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form. Z-DNA is thought ...

conformation (Durai et al., 2005 and references therein).

References

Engineered proteins Protein engineering Genetics experiments {{hydrolase-stub

DNA-binding domains

Nuclease domain

See also

References