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    METHODS AND SYSTEMS FOR QUANTIFYING GENE EXPRESSION IN SYNTHETIC GENE CIRCUITS AND FOR TUNING SYNTHETIC GENE CIRUITS
    3.
    发明申请
    METHODS AND SYSTEMS FOR QUANTIFYING GENE EXPRESSION IN SYNTHETIC GENE CIRCUITS AND FOR TUNING SYNTHETIC GENE CIRUITS 审中-公开

    公开(公告)号：US20190221281A1

    公开(公告)日：2019-07-18

    申请号：US16248720

    申请日：2019-01-15

    Applicant: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY

    Inventor： Xiao Wang ,  Qi Zhang ,  Fuqing Wu

    IPC: G16B5/00 ,  C12N15/63

    CPC classification number: G16B5/00 ,  C12N15/635

    Abstract: A method of tuning the performance of a synthetic gene circuit comprising a plurality of genes is disclosed. The method includes quantifying, for each gene, a relative gene expression metric. The metric is quantified by determining a number of nucleotides in a 5′ adjacent transcriptional region (ATR) of the gene, a number of nucleotides in a 3′ ATR, a minimum free energy of a mRNA secondary structure around a ribosome binding site of the gene, a total folding energy for the 5′ ATR, and a folding energy for the first 100 nucleotides of the 3′ ATR, and then summing sequence-dependent energy changes, the terms including scaling coefficients and an average energy cost for synthesizing a nucleotide. The method further includes simulating, through application of the relative gene expression metrics of the plurality of genes to a deterministic model, the performance of an intended function of the synthetic gene circuit.

    Methods and systems for quantifying gene expression in synthetic gene circuits and for tuning synthetic gene circuits
    4.
    发明授权
    Methods and systems for quantifying gene expression in synthetic gene circuits and for tuning synthetic gene circuits 有权

    公开(公告)号：US11276478B2

    公开(公告)日：2022-03-15

    申请号：US16248720

    申请日：2019-01-15

    Applicant: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY

    Inventor： Xiao Wang ,  Qi Zhang ,  Fuqing Wu

    IPC: G16B5/00 ,  C12N15/63 ,  G16B5/30

    Abstract: A method of tuning the performance of a synthetic gene circuit comprising a plurality of genes is disclosed. The method includes quantifying, for each gene, a relative gene expression metric. The metric is quantified by determining a number of nucleotides in a 5′ adjacent transcriptional region (ATR) of the gene, a number of nucleotides in a 3′ ATR, a minimum free energy of a mRNA secondary structure around a ribosome binding site of the gene, a total folding energy for the 5′ ATR, and a folding energy for the first 100 nucleotides of the 3′ ATR, and then summing sequence-dependent energy changes, the terms including scaling coefficients and an average energy cost for synthesizing a nucleotide. The method further includes simulating, through application of the relative gene expression metrics of the plurality of genes to a deterministic model, the performance of an intended function of the synthetic gene circuit.

    TARGETED REMODELING OF PROKARYOTIC GENOMES USING CRISPR-NICKASES
    5.
    发明申请
    TARGETED REMODELING OF PROKARYOTIC GENOMES USING CRISPR-NICKASES 审中-公开
    使用CRISPR-NICKASES进行重新定型

    公开(公告)号：US20170073663A1

    公开(公告)日：2017-03-16

    申请号：US15260788

    申请日：2016-09-09

    Applicant: Arizona Board of Regents on behalf of Arizona State University

    Inventor： Xiao Wang ,  Kylie Standage-Beier

    IPC: C12N15/01 ,  C12N9/22

    CPC classification number: C12N15/01 ,  C12N9/22

    Abstract: The present invention relates to kits and methods of modifying the prokaryotic genome a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system that utilized one nicking Cas nuclease and crRNAs. The kid and methods delete or replace portions of the prokaryotic genome. In some embodiments, an entire gene or multiple genes may be deleted or replaced.

    Abstract translation: 本发明涉及使用一个切口的Cas核酸酶和crRNAs来调节原核基因组的聚簇定期间隔短回归重复（CRISPR）-Cas系统的试剂盒和方法。 孩子和方法删除或替换原核基因组的部分。 在一些实施方案中，可以缺失或替换整个基因或多个基因。

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