EENdb - Utilities  >  ZFP construction strategies
This page describes and compares the ZFN/ZFP construction strategies and methods.
For web-tools and resources of ZFN/ZFP engineering, see the page of Engineering Resource.

List of ZFP construction strategies
ClassificationStrategyDescriptionFeaturesReference
Direct assembly MA
(Modular Assembly)
MA considers each zinc fingers as an independent module, and directly assembles 3 (or more) fingers according to the target site sequence into a ZFP/ZFN.
There are many sets of modules for selection.
> Quick and straightforward.
> Reported low success rate.
9843940 (Original)
17406455 (Protocol)

ZFNs by MA
CoDA
(Context-Dependent Assembly)
CoDA is also a direct assembly strategy, but the 3 fingers, especially the relatively important F2, were selected from effective ZFPs by OPEN, which showed robust efficiency in different contexts. > Quick and easy.
> Reported ~50% success rate.
21151135

ZFNs by CoDA
"2F-MA"
(Named by EENdb)
S. Wolfe's group (authors of "PRS") also developed a 2-finger modular assembly system mainly covering GRNNYG. Combined with 1-finger modules, this system can be used to construct 3-finger or 4-finger ZFPs/ZFNs. > Quick and easy.
> Reported ~80% success rate.
22543349

ZFNs by "2F-MA"
Screening-based OPEN
(Oligomerized Pool ENgineering)
OPEN employs a two-step screening. the first step is to establish pre-screened pools of single zinc fingers targeting a specific triplet from a pool of nearly randomized oligos by using a phage-display system; The second step is to assemble 3 pre-screened pools into a ZFP pool to perform the second screening. > Time- and labor-consuming for the first screening step, or need to reuqest the pre-screened pools.
> Reported high success rate.
17406455
19798082 (Protocol)

ZFNs by OPEN
"PRS"
("Partially-Randomized Screening")
(Named by EENdb)
"PRS" relies on one-step or two-step screening. The initial zinc finger pools (library) are designed to be patially randomized regarding the coding potentials for each zinc finger, some residues are fixed (especially for G and A in the triplet targets) and others are randomized.
"PRS" is named by EENdb; some review articles call it as "B1H" strategy, but it may cause confusion with the ZFP screening method.
> The size of the library for screening is relatively more controllable and easier to handle than OPEN.
> Reported high success rate.
18500337

ZFNs by "PRS"
Commercial service Sangamo 2-finger module based assembly and/or screening strategy is initially developed by A. Klug and M. Isalan (reviewed by 20478078). The non-public, commercial strategy used by Sangamo BioSciences Inc. (or Sigma Aldrich Inc.) is mainly based on this work.
ToolGen Inc. also employs a public 2-finger based MA strategy (noted as "MA(2F)" by EENdb).
ZFNs by Sangamo


Relationship of different strategies

This figure is modified from 22049679 (A review in Chinese).



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