A recent study of significant research value carried out at the State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China-Research, and published in the May 2011 issue of Science China Life Sciences (Issue 54) described a novel method using FoldX force field based protein modeling that can be applied in zinc finger nucleases design.
Zinc finger nucleases (ZFNs) can actively introduce a double-strand break (DSB) at target loci in eukaryotic genomes and this can improve the efficiency of gene knock-out or knock-in by several orders of magnitude. Therefore, ZFN is becoming a promising novel tool for genomic editing. However, most current strategies for developing zinc finger nucleases with customized sequence specificities require the construction of numerous tandem arrays of zinc finger proteins (ZFPs), and the subsequent large-scale in vitro validation of their DNA binding affinities and specificities using bacterial selection. The labor and expertise required in this complex process limits the broad adoption of the ZFN technology.
In this work, an effective computational assisted design strategy was introduced to lower the complexity of the production of a pair of functional ZFNs. Dr. He and Prof. Chen used the FoldX force field to build 3D models of 420 ZFP-DNA complexes based on zinc finger arrays developed by the Zinc Finger Consortium using OPEN (oligomerized pool engineering). Using nonlinear and linear regression analysis, they found that the calculated protein-DNA binding energy in a modeled ZFP-DNA complex strongly correlates to the failure rate of the zinc finger array to show significant ZFN activity in human cells. In their models, less than 5% of the three-finger arrays with calculated protein-DNA binding energies lower than -13.132 kcal mol−1 failed to form active ZFNs in human cells. By contrast, for arrays with calculated protein-DNA binding energies higher than -5 kcal mo
|Contact: ZuYong He|
Science in China Press