A method for finding zinc finger protein target sites in the genome

A technology of zinc finger protein and target site, which is applied in the field of genetic engineering, can solve problems such as spending a lot of time, and achieve the effects of improving efficiency, saving costs, and simplifying experimental procedures

Inactive Publication Date: 2018-08-07
SUN YAT SEN UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] However, most of the target sites obtained through the above-mentioned method and the zinc finger proteins constructed on this basis have a binding rate of less than 2, and it takes a lot of time and effort to screen those effective zinc fingers with a binding rate greater than 2. protein

Method used

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  • A method for finding zinc finger protein target sites in the genome
  • A method for finding zinc finger protein target sites in the genome
  • A method for finding zinc finger protein target sites in the genome

Examples

Experimental program
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Effect test

Embodiment 1

[0039] Example 1 Searching for zinc finger protein target sites in the silkworm partial genome sequence nscaf2681

[0040] 1. The search method is as follows: first, all 9 nucleotide sequences that can bind to zinc finger proteins and have a binding rate greater than 2 (that is, all zinc finger protein genes that can bind to 9 nucleotide sequences and have a binding rate greater than 2) Build a library; then design a software program, use the program to search for sites that match the 9 nucleotide sequences in the library described in step S1 at intervals in the double strand of the target genome, and obtain the corresponding Zinc finger protein target sites.

[0041]2. The specific operation method is as follows (operating system requirements: Windows system):

[0042] (1) Name the genome sequence nscaf2681 as seqnscaf2681.txt;

[0043] (2) Name the file name of the library consisting of all 9 nucleotide sequences whose binding rate to the zinc finger protein is greater tha...

Embodiment 2

[0057] Example 2 Searching for zinc finger protein target sites in the silkworm partial genome sequence nscaf1705

[0058] The basic requirements and process are the same as those in Embodiment 1, and the system requirements: Windows system.

[0059] The specific operation method is as follows:

[0060] (1) Name the genome sequence nscaf2681 as seqnscaf1705.txt

[0061] (2) Name the file name of the library composed of all 9 nucleotide sequences whose binding rate to zinc finger protein is greater than 2 motifs.txt

[0062] (3) Set the number of base distances between the forward and reverse motifs of the zinc finger protein target site to be 7;

[0063] (4) The program runs the command Mptif_finder.exe

[0064] The prompt is as follows: Enter your motif file name and fasta file name that contains all the primers and target sequences, specifically:

[0065] Type motifs.txt seqnscaf1705.txt, press enter, click the Run button, and the program starts to run;

[0066] (5) Pre...

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Abstract

The invention discloses a novel method for finding zinc finger protein target loci from a genome. The method comprises the following steps: firstly, building all 9-nucleotide sequences which can be bound with zinc finger proteins at a binding rate of greater than 2 into a pool; and then, designing a program for finding loci which exist at certain intervals in double chains and are matched with corresponding 9-nuclieotide sequences in the pool from the genome in order to obtain corresponding zinc finger protein target loci. Compared with a conventional method, the novel method has the advantages that constructed zinc finger proteins can be directly applied without being detected or screened, so that an experimental procedure is simplified greatly; the cost is reduced; and the efficiency is increased.

Description

technical field [0001] The invention belongs to the technical field of genetic engineering. More specifically, it relates to a new method for finding target sites of zinc finger proteins in the genome. Background technique [0002] Zinc finger nuclease (zinc finger nuclease, ZFN) is mainly composed of zinc finger protein and nuclease, through the binding of zinc finger protein to a specific DNA site, the nuclease is brought into the site, and the nearby DNA strand is enzymatically cut , so as to induce double-strand breaks at specific sites in DNA, and greatly increase the probability of homologous recombination. This technique has attracted extensive attention and research due to its high efficiency and specificity, and has been applied in various species (Drosophila, C. elegans, zebrafish, rats, etc.). In recent years, many research results have been published in journals such as Nature, Science, and Nature Biotechnology. [0003] The most important step in the construc...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 王方海程中山
Owner SUN YAT SEN UNIV
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