WO2003058227A1 - Capillary electrophoresis chip apparatus for detecting polymorphism of nucleotide and mononucleotide - Google Patents

Capillary electrophoresis chip apparatus for detecting polymorphism of nucleotide and mononucleotide Download PDF

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Publication number
WO2003058227A1
WO2003058227A1 PCT/CN2002/000857 CN0200857W WO03058227A1 WO 2003058227 A1 WO2003058227 A1 WO 2003058227A1 CN 0200857 W CN0200857 W CN 0200857W WO 03058227 A1 WO03058227 A1 WO 03058227A1
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Prior art keywords
electrophoresis chip
layer
capillary electrophoresis
channel
capillary
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PCT/CN2002/000857
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English (en)
French (fr)
Inventor
Peng Liu
Wanli Xing
Dong Liang
Jing Cheng
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Capital Biochip Company, Ltd.
Tsinghua University
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Application filed by Capital Biochip Company, Ltd., Tsinghua University filed Critical Capital Biochip Company, Ltd.
Priority to US10/500,180 priority Critical patent/US7527719B2/en
Priority to EP02782653A priority patent/EP1464955A4/en
Priority to AU2002349465A priority patent/AU2002349465A1/en
Publication of WO2003058227A1 publication Critical patent/WO2003058227A1/zh

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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/416Systems
    • G01N27/447Systems using electrophoresis
    • G01N27/44756Apparatus specially adapted therefor
    • G01N27/44791Microapparatus

Definitions

  • Capillary electrophoresis chip device for detecting nucleotide and single nucleotide polymorphism
  • a capillary electrophoresis chip device for detecting single nucleotide polymorphism belongs to the technical field of capillary electrophoresis chip devices. Background technique
  • SNPs Single nucleotide polymorphisms
  • SNPs Single nucleotide polymorphisms
  • Finding and studying SNPs is one of the important contents and goals of the Human Genome Project.
  • SNP As a marker of polymorphism, SNP has great significance in anthropology, medical diagnosis, disease research, environmental susceptibility factor research, drug screening, and forensic identification.
  • Direct sequencing of DNA is the most direct method for detecting SNP, but it has a large workload and low efficiency. People are currently looking for high-throughput methods.
  • Detection methods based on DNA melting kinetics are a class of high-throughput methods that include gradient denaturing gel electrophoresis, constant denaturing gel electrophoresis, capillary denaturing gel electrophoresis, and denaturing high-performance liquid chromatography.
  • gradient denaturing gel electrophoresis constant denaturing gel electrophoresis
  • capillary denaturing gel electrophoresis capillary denaturing gel electrophoresis
  • denaturing high-performance liquid chromatography it is necessary to add a modifying agent, and the influence mechanism of the modifying agent on electrophoresis and chromatography is complicated.
  • the selection of the modifying agent, the setting of the electrophoresis or chromatography conditions, and the realization of the gradient are all major technical problems.
  • the object of the present invention is to provide a capillary electrophoresis chip device for detecting nucleotides and single nucleotide polymorphisms by replacing temperature with denaturant based on high-speed, high-efficiency, and low-consumption capillary electrophoresis.
  • the invention is characterized in that it comprises: an upper channel layer having a microfluidic channel and an electrode hole structure for sample application, a middle electrode layer that closes the upper microfluidic channel to form a complete capillary and provides a desired voltage to an electrophoresis chip, and electrophoresis A heating layer with a stable temperature gradient is provided.
  • the upper, middle and lower layers are thermally conductive and adhere to each other.
  • the microfluidic channel is any one of one-dimensional, two-dimensional, or multidimensional microfluidic channels.
  • the cross-sectional width or diameter of the microfluidic channel is between 5 and 200 ⁇ m, the depth of the fluid channel is between 5 and 200 ⁇ m, and the length of the electrophoretic separation channel is between 1 and 30 cm.
  • the material of the middle electrode layer is any one of gold, platinum or graphite.
  • the upper surface of the middle electrode layer is coated with a layer of polydimethylsiloxane (PDMS). All
  • PDMS polydimethylsiloxane
  • All The heating layer is provided with temperature control elements that are spaced apart into two or more groups and each maintain a different constant temperature in order to form a stable spatial temperature gradient.
  • the stable temperature gradient of the heating layer is a time temperature gradient formed by gradually increasing the temperature of the entire chip.
  • FIG. 1 is a schematic diagram of a capillary electrophoresis chip device for detecting nucleotide and single nucleotide polymorphisms proposed by the present invention.
  • FIG. 2 is a schematic top view of the upper channel layer of the preferred embodiment of the device for detecting nucleotide and single nucleotide polymorphisms proposed by the present invention.
  • FIG. 3 is a schematic plan view of an intermediate electrode layer of a preferred embodiment of the device for detecting nucleotide and single nucleotide polymorphisms according to the present invention.
  • FIG. 4 is a schematic top view of the lower heating layer of the preferred embodiment of the device for detecting nucleotide and single nucleotide polymorphisms proposed by the present invention.
  • Fig. 5 is a longitudinal sectional view in the direction of Figs. 1A-A of the preferred embodiment of the apparatus for detecting nucleotide and single nucleotide polymorphisms proposed by the present invention.
  • FIG. 6 is an enlarged schematic top view of a dotted frame in FIG. 2.
  • FIG. 7 is a schematic diagram of a pretreatment process of a sample used in a device according to a preferred embodiment of the present invention.
  • FIG. 1 is a schematic diagram of the upper and lower layers of FIG. 2 and FIG. 3.
  • 1 is an electrode hole
  • 2 is a first-dimensional electrophoresis separation channel
  • 3 is the second-dimensional electrophoretic separation channel, which has 50 channels in total, each tube is 100 ⁇ m wide, with a pitch of 100 ⁇ m, and a depth of 10 ⁇ m.
  • the total length of the electrophoretic separation channel is 30cm.
  • 4 is the upper fluid channel layer, that is, the channel layer.
  • the channel layer 4 is made of polydimethylsiloxane (PDMS), and any one of other silicone rubber, plastic, quartz, and glass can also be used.
  • PDMS polydimethylsiloxane
  • the microfabrication method of the electrode hole 1 includes casting, embossing, etching, or photolithography, and it depends on the material of the channel layer.
  • the cross section of the electrophoretic separation channel, that is, the microfluidic channel, on the channel layer 4 is rectangular, and may be any other geometric shape.
  • the electrophoretic separation channel is an open capillary groove, and the capillary groove is closed with a cover sheet to form a complete capillary.
  • the channel layer running through the electrophoretic separation channel must also be Only the cover sheet forms a complete liquid pool structure.
  • 5 is an electrode on the middle electrode layer 6.
  • the electrode layer 6 can close the upper electrophoretic separation channel to form a complete capillary tube with an electrode that provides the required voltage for electrophoresis.
  • the electrode layer 6 can be formed by depositing metal on glass and then etching.
  • the metal layer is gold, or any one of platinum or graphite can be used.
  • An insulating layer is formed on the metal layer by an oxidation method.
  • the metal electrode is exposed only at the position corresponding to the electrode hole 1 on the channel layer, or the PDMS layer is directly coated. Only the metal electrode is exposed at the position of the electrode hole 1. After the channel layer 4 and the electrode layer 6 are adhered, the solution in the electrode hole 1 and the bottom of the hole formed by the electrode layer 6 expose the bottom electrode contact.
  • the electrode 5 can also be designed in a needle shape, inserted into the electrode hole 1 from above the channel layer 4 to be in contact with the solution, and then acting on the solution along the electrophoretic separation channel '.
  • the heating layer has two sets of temperature control elements for heating and cooling.
  • the heating element 7 maintains a constant bottom temperature and the cooling element 8 maintains a constant bottom temperature.
  • the heat between the two is conducted through the glass of the electrode layer 6 to form a stable bottom space temperature gradient in the glass.
  • a semiconductor temperature control element for heating and cooling elements may also be used as a resistor.
  • FIG. 6 is an enlarged schematic top view of the bottom of the dotted frame in FIG. 2.
  • FIG. 9 is the channel connected to electrode hole 1, and the width is 20 ⁇ .
  • 10 is the sample.
  • 2 is a first-dimensional electrophoretic separation pipe
  • 3 is a second-dimensional electrophoretic separation pipe. Arrows indicate corresponding electrophoretic separation directions.
  • the sample 10 can be prevented from penetrating into the second-dimensional electrophoretic separation pipe 3, and during the second-dimensional electrophoretic separation process, the second-dimensional electrophoretic separation pipe 3 and the channel 9 connecting the electrode hole 1 to the first Disturbance of the dimensional electrophoresis separation process. It can also make the band obtained by the first-dimensional electrophoretic separation completely enter the second-dimensional electrophoretic separation channel 3 without entering other adjacent pipelines at the same time.
  • FIG. 5 is a longitudinal cross-sectional view taken along the line AA of FIG. 1, and the structure is as described above.
  • FIG. 7 is a schematic diagram of a pretreatment process of a sample used in a device according to a preferred embodiment of the present invention.
  • 11 is a PCR polymerase chain reaction process
  • 12 is a denaturation and renaturation process.
  • B represents any base in AGCT
  • B * represents that the site is a SNP site
  • "+" and "one” are used to distinguish the two strands of DNA.
  • Figure 7 shows the case of SNP. Four DNA fragments of the same length were obtained, and some of them had mismatches. If no SNP is present, there can be only one type of DNA fragment. The process of detecting SNP by the present invention will be briefly described in conjunction with the figure.
  • First-dimensional electrophoresis allows efficient restriction of DNA fragments of different lengths. But the DNA with the SNP site and the same length of DNA fragment still exist in the same band.
  • a certain voltage is applied across the second-dimensional pipeline to prevent the sample from diffusing into the second-dimensional electrophoretic separation channel 3.
  • the second two-dimensional electrophoretic separation channel is a row of arrays. The bands separated by the first-dimensional electrophoresis enter the second-dimensional array electrophoresis channel 3 through voltage control to continue electrophoresis.
  • the heating layer provides a gradually increasing temperature gradient in the direction of electrophoresis.
  • the melting temperature of the mismatched DNA is lower than that of the non-mismatched DNA.
  • the temperature of the DNA is melted first, and then it is firstly subjected to a greater blocking force and separated from other DNA fragments of the same length that have not yet melted. As long as the system resolution is high enough, DNA fragments of the same length that have not yet been melted can be separated. If only one band is isolated, it can be concluded that there is no SNP site; if more than one band is isolated, it can be concluded that SNP exists. Based on the above information, it can also indicate which DNA restriction fragment the SNP exists on.
  • Temperature gradients can also be considered to achieve temperature gradients in time.
  • the electrophoresis chip is uniformly heated, and the heating rate is controlled, and the same purpose as the foregoing can be achieved.
  • ordinary capillary tubes can also be used for one-dimensional electrophoresis. DNA fragments of different lengths are separated, and then the time and temperature gradient is used to continue the electrophoresis.
  • the present application not only has the advantages of high speed, high efficiency, and few samples that are unique to capillary electrophoresis, but also avoids the use of denaturants, makes the detection process easy to control, and its gradient easy to implement.
  • the capillary electrophoresis chip device of the present invention can be widely used for detecting nucleotide and single nucleotide polymorphisms.

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Description

检测核苷酸和单核苷酸多态性用的毛细管电泳芯片装置
技术领域
一种检测单核苷酸多态性 (Single Nucleotide Polymorphism, 简称 SNP) 用的毛细管电泳芯片装置, 属于毛细管电泳芯片装置技术领域。 背景技术
在基因组中普遍存在着单核苷酸多态性(SNP) , 据估计人类基因组中 有 300万个 SNP位点。 SNP在基因组中数量巨大、 分布频密并且有二态性, 这 些性质决定了它成为第三代遗传标记。 寻找和研究 SNP是人类基因组计划的 重要内容和目标之一。 作为多态性标记, SNP在人类学、 医疗诊断、 疾病研 究、 环境易感因子研究、 药物筛选以及法医鉴定等方面具有重大意义。 对 脱氧核糖核酸 (DNA ) 直接测序是检测 SNP的最直接的方法, 但其工作量 大, 效率低。 目前人们致力于寻找高通量的方法。 基于 DNA解链动力学的检 测方法就是一类高通量的方法, 它包括梯度变性胶电泳、 恒变性胶电泳、 毛细管变性胶电泳和变性高效液相层析。 但是在这些方法中都需要加入变 性剂, 而变性剂对电泳、 色谱等的影响机制比较复杂, 变性剂的选择、 电 泳或色谱条件的设置以及梯度的实现等都是比较大的技术难题。
发明公开
本发明的目的是提供一种基于高速、 高效、 耗样量少的毛细管电泳之 上的以温度来代替变性剂的检测核苷酸和单核苷酸多态性用的毛细管电泳 芯片装置。
本发明的特征在于, 它含有: 具有微流体通道和加样用的电极孔结构 的上层通道层, 封闭上层微流体通道以构成起完整毛细管且为电泳芯片提 供所需电压的中层电极层以及电泳提供稳定温度梯度的加热层, 其中, 上、 中、 下三层是可导热且相互粘合的。 所述的微流体通道是一维、 或二 维、 或多维微流体通道中的任何一种。 所述的微流体通道的截面宽度或直 径在 5— 200 μ ιη之间, 流体通道深度在 5— 200 μ ηι之间, 电泳分离通道的 长度在 1 30cm之间。 所述中层电极层的材料是金或铂或石墨中的任何一 种。 所述的中层电极层的上表面涂布着一层聚二甲基硅氧垸(PDMS ) 。 所 述的加热层带有相间隔地分成二组或多组且各自分别保持不同的恒定温度 以便形成稳定的空间温度梯度的温控元件。 所述加热层的稳定温度梯度是 一种把芯片整体均勾逐渐升温而形成的时间温度梯度。
使用证明: 它可以达到预期目的。
附图说明
图 1 为本发明提出的检测核苷酸和单核苷酸多态性用的毛细管电泳芯 片装置的原理示意图。
图 2 为本发明提出的检测核苷酸和单核苷酸多态性用的优选实施例装 置的上层通道层的俯视示意图。
图 3 为本发明提出的检测核苷酸和单核苷酸多态性用的优选实施例装 置的中间层电极层的俯视示意图。
图 4为本发明提出的检测核苷酸和单核苷酸多态性用的优选实施例装 置的下层加热层的俯视示意图。
图 5 为本发明提出的检测核苷酸和单核苷酸多态性用的优选实施例装 置中图 1A-A向的纵剖视图。
图 6为图 2中虚线框的俯视放大示意图。
图 7为本发明优选实施例装置所用样品的预处理过程示意图。
实施发明的最佳方式
如图 1—图 6。 图 1是图 2、 图 3上、 下层叠后的原理示意图。 1是电 极孔, 2 是第一维电泳分离通道。 3 是第二维电泳分离通道, 它共有 50 条, 每条管宽 ΙΟΟ μ πι, 间距 ΙΟΟ μ ιη, 深为 ΙΟ μ πι, 电泳分离通道的总长度 为 30cm, 与电极孔 1 的连接管道宽 20 μ ιη, 4是上层流体通道层, 即通道 层。 本优选实施例装置种, 通道层 4用聚二甲基硅氧烷 (PDMS)制成, 也 可以用其他硅橡胶、 塑料、 石英和玻璃中的任何一种, 其电泳分离通道和 加样用电极孔 1 的微加工方法有浇注、 模压、 蚀刻或光刻, 随通道层材料 而异。 通道层 4上的电泳分离通道即微流体通道的横截面呈矩形, 也可以 是任何其他几何形状。 上述电泳分离通道是开放的毛细槽, 用一片盖片把 毛细槽封闭就形成完整的毛细管。 同样, 贯穿电泳分离通道的通道层也要 加盖片才形成完整的液池结构。 5 是在中层电极层 6上的电极。 电极层 6 可以封闭上层电泳分离通道以形成完整毛细管又带有为电泳提供所需电压 的电极。 从图 1 中可知: 电极 5的裸露部分只在必要处与电极分离通道中 的流体接触, 提供所需电压, 并能根据计算机控制按程序变换电压。 电极 层 6可以通过在玻璃上沉积金属再蚀刻而成。 金属层采用金, 也可用铂或 石墨中的任何一种, 再金属层上利用氧化方法形成绝缘层, 只在与通道层 上电极孔 1对应位置把金属电极暴露出来, 或者直接涂布 PDMS层, 只在 电极孔 1的位置裸露金属电极。 当通道层 4与电极层 6粘合后, 电极孔 1 中的溶液与电极层 6形成的孔底暴露出底电极接触。 这些暴露底电极为电 泳提供电泳所需电压。 电极 5也可设计成针状, 从通道层 4上面插入电极 孔 1 中与溶液接触, 再沿着电泳分离通道对溶液起作用'。 加热层有加热和 冷却两组温控元件。 加热元件 7保持较高底恒定温度, 冷却元件 8保持较 低底恒定温度, 两者间热量通过电极层 6底材料玻璃传导, 从而再玻璃中 形成稳定底空间温度梯度。 本实施例中加热和冷却元件用半导体温控元 件, 也可用电阻。 图 6是图 2中虚线框底俯视放大示意图。 9是与电极孔 1 连接的通道, 宽 20 μ ΐϋ, 10是样品。 2是第一维电泳分离管道, 3是第二维 电泳分离管道, 箭头表示相应的电泳分离方向。 在第一维电泳分离过程中 可以防止样品 10渗入第二维电泳分离管道 3, 也可在第二维电泳分离过程 中防止第二维电泳分离管道 3和连接电极孔 1的通道 9对第一维电泳分离 过程的干扰。 它还可使第一维电泳分离得到的区带完整进入第二维电泳分 离通道 3, 而不致同时进入相邻的其他管道。 图 5是图 1的 Α— Α向纵剖视 图, 其构成已如上述。
图 7 为本发明优选实施例装置所使用样品的预处理过程原理示意图。 11是 PCR聚合酶链式反应过程, 12是变性、 复性过程。 其中, B代表 AGCT 中任一碱基, B*代表该位点为 SNP点, " + "、 "一"用以区分 DNA的两 条链。 图 7为存在 SNP的情况, 得到相同长度的 4种 DNA片段, 有的存在 错配。 若不存在 SNP, 则只能有一种 DNA片段。 现结合该图简要描述用本 发明检测 SNP的过程。 对于可能存在 SNP位点的待分析样品进行预处理, 使得 DNA在存在 SNP位点的地方发生错配, 具体方法见图 7。 第一维电泳 使不同长度的 DNA 限制性内切片段得到有效分离。 但是存在 SNP位点的 DNA和与其长度相同的 DNA片段仍然存在于同一区带中。 在第一维分离 时, 第二维管道两端加一定电压, 防止样品扩散到第二维电泳分离通道 3 中。 第二维电泳分离通道是一排阵列。 第一维电泳分离出的各区带通过电 压控制进入第二维阵列电泳通道 3 中继续进行电泳, 在这个电泳过程中, 加热层在电泳前进方向上提供了逐渐升高的温度梯度。 有错配的 DNA解链 温度较无错配的低, 在电泳前进不断升温的过程中首先解链, 从而首先受 到更大的阻滞力, 与其他尚未解链的相同长度的 DNA片段分离。 只要系统 分辨率足够高, 就可以把尚未解链的相同长度的 DNA片段分离。 若只分离 得到 1条区带, 就可以断定无 SNP位点; 若分离得到多于一条的区带, 则 可以断定存在 SNP。 综合以上信息还可以指出 SNP存在于哪一段 DNA限制 性片段上。
温度梯度也可以考虑在时间上实现温度梯度。 在第二维电泳分离时, 对电泳芯片均匀加热, 控制好升温速率, 可以达到与前述相同的目的。 只 要分离通道足够长, 电泳分离效率足够高, 也可用普通毛细管作一维电泳 分离.分离出不同长度的 DNA片段, 然后采用时间温度梯度继续电泳。
由此可见, 本申请既有毛细管电泳技术所特有的高速、 高效、 消耗样 品少的优点, 又可避免使用变性剂, 使检测过程易于控制, 其梯度也易于 实现。
工业应用
本发明的毛细管电泳芯片装置可以广泛应用于检测核苷酸和单核苷酸 多态性。

Claims

权利要求书
1、 一种检测核苷酸和单核苷酸多态性用的毛细管电泳芯片装置, 含有 电泳芯片, 其特征, 它含有: 具有微流体通道和加样用的电极孔结构的上 层通道层, 封闭上层微流体通道以构成起完整毛细管且为电泳芯片提供所 需电压的中层电极层以及电泳提供稳定温度梯度的加热层, 其中, 上、 中、 下三层是可导热且相互粘合的。
2、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述的微流体通道是一维、 或二维、 或多维微 流体通道中的任何一种。
3、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述的微流体通道的截面宽度或直径在 5— 200 u m之间, 流体通道深度在 5— 200 μ ιη之间, 电泳分离通道的长度在 1 - 30cm之间。
4、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述中层电极层的材料是金或铂或石墨中的任 何一种。
5、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述的中层电极层的上表面涂布着一层聚二甲 基硅氧垸(PDMS) 。
6、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述的加热层带有相间隔地分成二组或多组且 各自分别保持不同的恒定温度以便形成稳定的空间温度梯度的温控元件。
7、 根据权利要求 1所述的检测核苷酸和单核苷酸多态性用的毛细管电 泳芯片装置, 其特征在于: 所述加热层的稳定温度梯度是一种把芯片整体 均勾逐渐升温而形成的时间温度梯度。
PCT/CN2002/000857 2001-11-30 2002-11-29 Capillary electrophoresis chip apparatus for detecting polymorphism of nucleotide and mononucleotide WO2003058227A1 (en)

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US20050161335A1 (en) 2005-07-28
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