Zinc Fingers, TAL Effectors, or Cas9-Based DNA Binding Proteins： What＇s Best for Targeting Desired Genome Loci？

ZINC FINGER- AND TAL EFFECTOR- BASED DNA BINDING PROTEINS
Programmable DNA binding proteins （PDPs） that selectively bind user-defined nucleotide sequences can navigate protein domains to any desired target within the genome. Different functional domains can be fused to PDPs to achieve （1） acti- vation or repression of transcription, （2） nicking or cleavage of DNA, or （3） modification or removal of epigenetic marks at the targeted genome spot. Given their broad applicabil- ity, the development of highly specific, easy-to-use PDPs has been a holy grail of biotechnology since the determination of the 3-D structure of zinc fingers （ZFs） bound to DNA in 1991 （Pavletich and Pabo, 1991）. This structure suggested that tandemly arranged ZFs act as functionally independ- ent modules with each finger binding three bases. However, the combination of fingers with experimentally defined base specificities into arrays revealed that ZFs are not function- ally independent. Instead, they were found to behave in a context-dependent, and often unpredictable fashion requir- ing iterative cycles of selection to get ZF arrays with desired specificity （Joung and Sander, 2013）.