Potential application of FoldX force field based protein modeling in zinc finger nucleases design

Engineered sequence-specific zinc finger nucleases (ZFNs) make the highly efficient modification of eukaryotic genomes possible.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 subsequent largescale in vitro validation of their DNA binding affinities and specificities via bacterial selection.The labor and expertise required in this complex process limits the broad adoption of ZFN technology.An effective computational assisted design strategy will lower the complexity of the production of a pair of functional ZFNs.Here we 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,we 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 our models,less than 5% of the three-finger arrays with calculated protein-DNA binding energies lower than 13.132 kcal mol 1 fail to form active ZFNs in human cells.By contrast,for arrays with calculated protein-DNA binding energies higher than 5 kcal mol 1,as many as 40% lacked ZFN activity in human cells.Therefore,we suggest that the FoldX force field can be useful in reducing the failure rate and increasing efficiency in the design of ZFNs.

Application of Artificially Induced Double-strand Breaks (DSB) and Triplex-forming Oligonucleotides (TFO) in the Improvement of Gene Targeting Efficiency

Gene targeting technology is an important means to investigate gene functions, but its efficiency of gene targeting is very low, especially for somatic cell targeting. Artificially induced double-strand breaks （DSB） and triplex forming oligonucleotide （TFO） are currently developed methods to improve the targeting efficiency. This paper summarized the basic principles, design ideas and application in gene targeting efficiency improvement of these two methods, analyzed and com- pared their characteristics, and finally proposed prospects for their future development.

Mitochondrial diseases and mtDNA editing

Mitochondrial diseases are a heterogeneous group of inherited disorders character-ized by mitochondrial dysfunction,and these diseases are often severe or even fatal.Mito-chondrial diseases are often caused by mitochondrial DNA mutations.Currently,there is no curative treatment for patients with pathogenic mitochondrial DNA mutations.With the rapid development of traditional gene editing technologies,such as zinc finger nucleases and tran-scription activator-like effector nucleases methods,there has been a search for a mitochon-drial gene editing technology that can edit mutated mitochondrial DNA;however,there are still some problems hindering the application of these methods.The discovery of the DddA-derived cytosine base editor has provided hope for mitochondrial gene editing.In this paper,we will review the progress in the research on several mitochondrial gene editing technologies with the hope that this review will be useful for further research on mitochondrial gene editing technologies to optimize the treatment of mitochondrial diseases in the future.