Which genome editing platform uses protein-DNA interactions to determine specificity?
Genome editing specificity can derive from protein-DNA contacts versus RNA-DNA base pairing. CRISPR Cas9 relies on guide RNA pairing and PAM. RNA interference uses small RNA-mRNA complementarity. Zinc finger nucleases use engineered arrays of Cys2His2 zinc finger domains, each recognizing three nucleotides via alpha helix contacting major groove. Tandem fingers create specific protein-DNA interface fused to FokI nuclease. Thus ZFN specificity is entirely determined by protein side chain interactions with DNA bases, requiring modular assembly and selection to achieve desired target without RNA
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.
