CN108893529A - 一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA - Google Patents

一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA Download PDF

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CN108893529A
CN108893529A CN201810664661.2A CN201810664661A CN108893529A CN 108893529 A CN108893529 A CN 108893529A CN 201810664661 A CN201810664661 A CN 201810664661A CN 108893529 A CN108893529 A CN 108893529A
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程诚
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Abstract

本发明公开了一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,其特征在于,包括CRISPR‑Cas13a***,还包括可与CRISPR‑Cas13a***结合的crRNA,所述crRNA序列格式为:5`‑Cas13a蛋白锚定序列‑crRNA向导序列‑3`,本发明的优点在于,所述检测结果可通过荧光读数直观判断人KRAS基因是否发生突变,而无需高通量测序,具有成本低、可多次重复检测、检测速度快,结果可直观分析等优势,适用于大规模的临床样本检测,本发明公开的核酸检测技术与以往的基于PCR技术的检测技术不同,反应全程无需复杂的温度控制仪器或***;通过将三步反应全部加入在一个反应体系中,进一步简化操作流程,可以在两个小时内检测出具有特异序列的核酸片段。

Description

一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子 突变的crRNA
技术领域
本发明涉及一种生物材料的检测,具体地说,涉及一种基于CRISPR-Cas13a技术适用于快速检测生物样本中特异性核酸片段的方法。
背景技术
从基因水平上对疾病进行研究和诊断,是实现个体化精准医疗这一医学概念的关键,Kras 是一种鼠类肉瘤病毒癌基因,ras基因家族与人类肿瘤相关的基因有三种—H-ras、K-ras和N-ras,分别定位在11、12和1号染色体上。K-ras因编码21kD的ras蛋白又名p21基因。在ras基因中,K-Ras对人类癌症影响最大,它好像分子开关:当正常时能控制调控细胞生长的路径;发生异常时,则导致细胞持续生长,并阻止细胞自我毁灭。它参与细胞内的信号传递,当K-ras基因突变时,该基因永久活化,不能产生正常的ras蛋白,使细胞内信号传导紊乱,细胞增殖失控而癌变。
目前常规的基因检测通过PCR技术实现,但现有的PCR技术存在一些缺陷如灵敏度不高、特异性不强、目的片段常采用DNA等,而造成成本高、重复性不强、检测耗时久等问题。
发明内容
为了解决现有技术中存在的问题,本发明的目的是提供一种检测人KRAS基因2号及3号外显子突变的crRNA。
一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,包括CRISPR-Cas13a***,还包括可与CRISPR-Cas13a***结合的crRNA,所述crRNA序列格式为:5`-Cas13a蛋白锚定序列-crRNA向导序列-3`。
所述Cas13a蛋白为Lw Cas13a,所述crRNA序列中的锚定序列为
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAAC,
所述crRNA序列分别为
KRAS-EXON2
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACCUUGCCUACGCCACCAGCUCC AACUA
KRAS-EXON3
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACGUACUCCUCUUGACCUGCUG UGUCGA;
所述用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC。
所述Cas13a蛋白为Lsh Cas13a,crRNA序列中的锚定序列为
CCACCCCAAUAUCGAAGGGGACUAAAAC,
所述crRNA序列分别为
KRAS-EXON2
CCACCCCAAUAUCGAAGGGGACUAAAACCUUGCCUACGCCACCAGCUCCAACUA KRAS-EXON3
CCACCCCAAUAUCGAAGGGGACUAAAACGUACUCCUCUUGACCUGCUGUGUCGA 用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC。
所述的一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA在人KRAS基因外显子2和外显子3突变检测中的应用。
本发明公开的一种基于CRIPSR-Cas13a的核酸检测技术,其最主要的机制是Cas13a蛋白可以在向导RNA的帮助下识别具有靶向序列的RNA片段,随后被激活的不受序列限制的RNA 酶活性,通过在反应体系中加入RNA链降解导致的信号报告分子,最终实现具有靶向序列的 RNA片段的信号识别。
本发明通过T7RNA聚合酶作用下合成的RNA,不仅使该检测技术的应用范围扩大到RNA 和DNA都可以检测,同时明显提高了检测的灵敏度,可以检测出阿摩尔级别的核酸。
由于Cas13a蛋白在识别靶向序列时,通常可以耐受一个碱基的错配,本发明通过提前在向导RNA的序列中加入人为错配碱基,使本检测技术的特异性达到可以识别具有单碱基差异的核酸序列。
相比之下本发明模板可以是DNA也可是RNA,检测结果可通过荧光读数直观判断人KRAS 基因是否发生突变,而无需高通量测序,具有成本低、可多次重复检测、检测速度快,结果可直观分析等优势,适用于大规模的临床样本检测。
本发明公开的核酸检测技术与以往的基于PCR技术的检测技术不同,反应全程无需复杂的温度控制仪器或***;通过将三步反应全部加入在一个反应体系中,进一步简化操作流程,可以在两个小时内检测出具有特异序列的核酸片段。
具体实施方式
为详细说明本发明之技术内容、构造特征、所达成目的及功效,以下兹例举实施例详予说明。
一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,包括CRISPR-Cas13a***,还包括可与CRISPR-Cas13a***结合的crRNA,所述crRNA序列格式为:5`-Cas13a蛋白锚定序列-crRNA向导序列-3`;所述Cas13a蛋白可以为Lw Cas13a,所述Cas13a蛋白亦可为Lsh Cas13a。
Cas13a蛋白为Lw Cas13a时
crRNA序列中的锚定序列为GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAAC 所述crRNA序列分别为
KRAS-EXON2
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACCUUGCCUACGCCACCAGC UCCAACUA
KRAS-EXON3
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACGUACUCCUCUUGACCUG CUGUGUCGA;
所述用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC。
所述Cas13a蛋白为Lsh Cas13a时
crRNA序列中的锚定序列为CCACCCCAAUAUCGAAGGGGACUAAAAC,
所述crRNA序列分别为
KRAS-EXON2
CCACCCCAAUAUCGAAGGGGACUAAAACCUUGCCUACGCCACCAGCUCCAACUA
KRAS-EXON3
CCACCCCAAUAUCGAAGGGGACUAAAACGUACUCCUCUUGACCUGCUGUGUCGA
用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC。
靶向人KRAS基因的crRNA设计原则
由于CRISPR-Cas13a***是一种新型的靶向RNA基因编辑***。其中Cas13a是一种双核糖核酸酶,Cas13a与crRNA结合形成监测复合物,crRNA的向导区域用互补序列识别目标RNA,并且Cas13a降解目标RNA链。目前由于没有明确的crRNA设计原则,根据前期工作和经验,靶向人KRAS基因的crRNA设计要求如下:
crRNA包括蛋白锚定序列和向导序列,序列格式为:5`-与Cas13a蛋白结合的锚定序列 -crRNA向导序列-3`,蛋白锚定序列需要根据Cas13a蛋白来确定,使其能够与选定的Cas13a 蛋白匹配并结合;向导序列则与靶向DNA中的片段匹配。
crRNA向导RNA的选择
根据NCBI查找人KRAS基因序列,确定外显子2和外显子3发生突变的位点;crRNA靶点不能离起始密码子(ATG)太近;长度为21-28个核苷酸;最终,设计出分别靶向人KRAS基因外显子2和外显子3的crRNA向导序列,其针对的靶位点DNA序列如表1所示,其中大写部分为会发生突变的密码子。
人KRAS基因的突变位点靶标序列
与Cas13a蛋白结合的锚定序列的设计:
当Cas13a蛋白选用Lw Cas13a时,crRNA序列中的锚定序列为
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAAC
当Cas13a蛋白选用Lsh Cas13a时,crRNA序列中的锚定序列为
CCACCCCAAUAUCGAAGGGGACUAAAAC
crRNA的合成
将化学合成的crRNA反转录成DNA并在5`添加T7启动子序列,所述的T7启动子序列为5`-TAATACGACTCACTATAGGG-3`;将上述带T7启动子DNA在T7RNA聚合酶作用下生成RNA,回收纯化,得到足量的crRNA,亦可根据设计的带T7启动子的crRNA转录模板 DNA在T7RNA聚合酶作用下生成RNA,回收纯化,得到足量的crRNA。
将合成的的靶向人KRAS基因的crRNA、样本DNA转录生成的RNA、相应的Cas13a蛋白、 RNA reporter(RNAse Alert V2,Thermo Scientfic)在核酸酶缓冲液中,37℃孵育1~3小时,通过荧光读数可以直观的分析KRAS基因外显子2和外显子3突变情况。所述的基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA可以应用于人KRAS 基因外显子2和外显子3突变的检测。
具体实施中,选用KRAS野生型基因片段和KRAS突变型基因片段作为检测模型,按照发明公布的核酸检测技术检测了两段基因,可以检测出约50aM的KRAS野生型基因片段,同时通过向导RNA的设计,可以区分出一个碱基差异的DNA核酸序列,即KRAS野生型基因片段和 KRAS-G12D突变型基因片段。
综上所述,仅为本发明之较佳实施例,不以此限定本发明的保护范围,凡依本发明专利范围及说明书内容所作的等效变化与修饰,皆为本发明专利涵盖的范围之内。

Claims (4)

1.一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,其特征在于,包括CRISPR-Cas13a***,还包括可与CRISPR-Cas13a***结合的crRNA,所述crRNA序列格式为:5`-Cas13a蛋白锚定序列-crRNA向导序列-3`。
2.根据权利要求1所述的一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,其特征在于:所述Cas13a蛋白为LwCas13a,所述crRNA序列中的锚定序列为GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAAC,所述crRNA序列分别为
KRAS-EXON2
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACCUUGCCUACGCCACCAGCUCCAACUA
KRAS-EXON3
GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACGUACUCCUCUUGACCUGCUGUGUCGA;
所述用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGTTTTTGGGGTAGTCTAAATCCCCTATAGTGAGTCGTATTAATTTC。
3.根据权利要求1所述的一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA,其特征在于:所述Cas13a蛋白为LshCas13a,crRNA序列中的锚定序列为CCACCCCAAUAUCGAAGGGGACUAAAAC,所述crRNA序列分别为
KRAS-EXON2
CCACCCCAAUAUCGAAGGGGACUAAAACCUUGCCUACGCCACCAGCUCCAACUA
KRAS-EXON3
CCACCCCAAUAUCGAAGGGGACUAAAACGUACUCCUCUUGACCUGCUGUGUCGA
用于转录crRNA的脱氧核酸序列为
KRAS-EXON2
TAGTTGGAGCTGGTGGCGTAGGCAAGGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC
KRAS-EXON3
TCGACACAGCAGGTCAAGAGGAGTACGTTTTAGTCCCCTTCGATATTGGGGTGGCCCTATAGTGAGTCGTATTAATTTC。
4.权利要求1-3所述的一种基于CRISPR技术特异性检测人KRAS基因2号及3号外显子突变的crRNA在人KRAS基因外显子2和外显子3突变检测中的应用。
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