生物技术通报 ›› 2018, Vol. 34 ›› Issue (9): 149-162.doi: 10.13560/j.cnki.biotech.bull.1985.2018-0568
刘晓, 朱鹏宇, 王垚, 朱水芳, 付伟
收稿日期:
2018-06-21
出版日期:
2018-09-26
发布日期:
2018-10-10
作者简介:
刘晓,硕士研究生,研究方向:转基因成分新型检测技术的开发;E-mail:1092681247@qq.com
基金资助:
LIU Xiao, ZHU Peng-yu, WANG Yao, ZHU Shui-fang, FU Wei
Received:
2018-06-21
Published:
2018-09-26
Online:
2018-10-10
摘要: 数字 PCR 是近年来迅速发展起来的一种定量分析技术。该技术结果判定不依赖于扩增曲线的循环阈值(Ct),不受扩增效率的影响,具有很好的准确度和重现性,并且可以实现绝对定量分析。数字PCR已经在功能核酸检测、鉴定等研究领域显示出巨大的技术优势和应用前景。在对数字 PCR 技术的基本原理和定量方法介绍的基础上,对该技术在功能核酸检测的主要应用领域进行综述,并对数字PCR在功能核酸检测领域中的研究前景做出了展望。
刘晓, 朱鹏宇, 王垚, 朱水芳, 付伟. 数字PCR在功能核酸精准检测中的研究进展[J]. 生物技术通报, 2018, 34(9): 149-162.
LIU Xiao, ZHU Peng-yu, WANG Yao, ZHU Shui-fang, FU Wei. Development Progress of Digital PCR in the Precise Detection of Functional Nucleic Acid[J]. Biotechnology Bulletin, 2018, 34(9): 149-162.
[1] Lu Y.New Transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors[J]. Cheminform, 2010, 34(3):4589-4596. [2] Silverman SK.In vitro selection, characterization, and application of deoxyribozymes that cleave RNA[J]. Nucleic Acids Res, 2005, 33(19):6151-6163. [3] Navani NK, Li Y.Nucleic acid aptamers and enzymes as sensors[J]. Curr Opin Chem Biol, 2006, 10(3):272-281. [4] Torabi SF, Wu P, Mcghee CE, et al.In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing[J]. Proc Natl Acad Sci USA, 2015, 112(19):5903-5908. [5] Wu Y, Zhan S, Wang L, et al.Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles[J]. Analyst, 2014, 139(6):1550-1561. [6] Sun H, Li X, Li Y, et al.A novel colorimetric potassium sensor based on the substitution of lead from G-quadruplex[J]. Analyst, 2013, 138(3):856-862. [7] Sullenger BA, Gilboa E.Emerging clinical applications of RNA[J]. Nature, 2002, 418(6894):252-258. [8] Nimjee SM, Rusconi CP, Sullenger BA.Aptamers:An emerging class of therapeutics[J]. Annual Review of Medicine, 2005, 56 (1):555-583. [9] Vogelstein B, Kinzler KW.Digital PCR[J]. Proc Natl Acad Sci USA, 1999, 96(16):9236-9241. [10] Sykes PJ, Neoh SH, Brisco MJ, et al.Quantitation of targets for PCR by use of limiting dilution[J]. Biotechniques, 1992, 13:444-449. [11] Devin D, Hai Y, Giovanni T, et al.Transforming single DNA molecules into fluorescent magnetic patticles for dectection and enumeration of genetic variations[J]. PNAS, 2003, 100(15):8817-8822. [12] Pohl G, Shih IM.Principle and applications of digital PCR[J]. Expert Review of Molecular Diagnostics, 2004;4(1):41-47. [13] Hindson BJ, Ness KD, Masquelier D, et al.High-throughput droplet digital PCR system for absolute quantitation of DNA copy number[J]. Anal Chem, 2011;83(22):8604-8610. [14] Fu W, Zhu P, Wang C, et al.A highly sensitive and specific method for the screening detection of genetically modified organisms based on digital PCR without pretreatment[J]. Sci Rep, 2015, 5:12715. [15] Bustin S, Benes V, Garson J.The MIQE guidelines:minimum information for publication of quantitative real-time PCR experiments[J]. Clin Chem, 2009;55(4):611-622. [16] Ramakrishnan R, Qin J, Jones RC, Weaver LS.Integrated fluidic circuits(IFCs)for digital PCR[J]. Methods in Molecular Biology, 2013, 949:423-431. [17] Watanabe R, Soga N, Fujita D, et al.Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity[J]. Nat Commun, 2014, 5:4519-4531. [18] 王琦, 范颖. 微滴式数字 PCR技术进展[J]. 中国医学前沿. 2016, 8(11):15-19. [19] Vargas DY, Kramer FR, Tyagi S, et al.Multiplex Real-Time PCR assays that measure the abundance of extremely rare mutations associated with cancer[J]. PLoS One, 2016, 11(5):e0156546. [20] Fu W, Zhu P, Wang C, et al.A highly sensitive and specific method for the screening detection of genetically modified organisms based on digital PCR without pretreatment[J]. Sci Rep, 2015, 5:12715. [21] Zhu P, Fu W, Wang C, et al.Development and application of absolute quantitative detection by duplex chamber-based digital PCR of genetically modified maize events without pretreatment steps[J]. Anal Chim Acta, 2016, 916(15):60-66. [22] Chen X, Zong K, Sun J, et al.Establishment of Droplet Digital PCR Quantitative Detection Method of Transgenic Rice Strain‘Bt Shanyou 63'[J]. Chinese Agricultural Science Bulletin, 2018, 34(6):131-136. [23] 吴潇, 吕贝贝, 等. QX200微滴式数字PCR方法检测转基因大豆GTS-40-3-2[J]. 上海农业学报, 2018, 34(1), 14-19. [24] Iwobi A, Gerdes L, et al.Droplet digital PCR for routine analysis of genetically modified foods(GMO)- A comparison with real-time quantitative PCR[J]. Food Control, 2016, 69:205-213. [25] Niu C, Xu Y, et al.Ultrasensitive single fluorescence-labeled probe-mediated single universal primer-multiplex-droplet digital polymerase chain reaction for high-throughput genetically modified organism screening[J]. Anal Chem, 2018, 90(9):55-86. [26] Ling L, Swain M, Conyers R, et al.A powerful new approach to measuring engraftment using copy number variations and droplet digital PCR, exemplified in a complex allogeneic bone marrow transplantation case[J]. Pathology, 2015, 47(S1):S87. [27] Zhang YN, Tang ET, Du ZQ. Detection of MET gene copy number in cancer samples using the droplet digital PCR method[J]. PLoS One, 2016, 11(1):e0 146784. [28] Vyrck M, Vandesompele J, Thas O.GLMMs for nucleic acid concentration estimation in digital droplet PCR[EB/OL]. [2016-06-12].https://biblio. ugent. be/publication/5992468. [29] D’Hont A, Ison D, Alix K, et al. Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes[J]. Genome, 1998, 41:221-225. [30] Sreenivasan TV, Ahloowalai BS, Cytogenetics. Sugarcane improvement through breeding[M]. Heinz DJ(ed). Amsterdam:Elsevier Science, 1987:211-253. [31] Sun Y, Joyce PA.Application of droplet digital PCR to determine copy number of endogenous genes and transgenes in sugarcane[J]. Plant Cell Rep, 2017, 36:1775-1783. [32] McCor PH. Using droplet digital PCR(ddPCR)to detect copy number variation in sugarcane, a high-level polyploid[J]. Euphytica, 2016, 209:439-448. [33] Félixurquídez D, Pérezurquiza M, et al.Development, optimization, and evaluation of a duplex droplet digital PCR assay to quantify the t-nos/hmg copy number ratio in genetically modified maize[J]. Anal Chem, 2016, 88(1):812-819. [34] Mali P, Yang L, et al.RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121):823-827. [35] Le CF, Ann R, David C, et al.Multiplex genome engineering using CRISPR/Cas systems[J]. Trends Genet, 2013, 32(12):815-820. [36] Jinek M, Chylinski K, Fonfara I, et al.A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821. [37] Yuichiro M, Berman JR, Cooper SB, et al.Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing[J]. Sci Rep, 2016, 6:23549. [38] Findlay SD, Vincent KM, Berman JR, et al.A digital PCR-based method for efficient and highly specific screening of genome edited cells[J]. PLoS One, 2016, 11(4):e0153901. [39] Mock U, Hauber I, Fehse B.Digital PCR to assess gene-editing frequencies(GEF-dPCR)mediated by designer nucleases[J]. Nature Protocols, 2016, 11(3):598-615. [40] Miyaoka Y, Chan AH, Judge LM, et al.Isolation of single-base genome-edited human iPS cells without antibiotic selection[J]. Nature Methods, 2014, 11(3):291-294. [41] Gevensleben H, Garcia-Murillas I, Graeser MK, et al.Noninvasive detection of HER2 amplification with plasma DNA digital PCR[J]. Clin Cancer Res, 2013, 19(12):3276-3284. [42] 赵钊, 陈盼盼, 张萍, 周永列. 数字PCR法和探针扩增阻滞突变法检测非小细胞肺癌组织表皮生长因子受体突变的比较研究[J]. 中国卫生检验杂志, 2017, 27(12):1673-1675. [43] Feng WN, Gu WQ, Zhao N, et al.Comparison of the SuperARMS and Droplet Digital PCR for Detecting EGFR Mutation in ctDNA From NSCLC Patients[J]. Transl Oncol, 2018, 11(2):542-545. [44] Sedlak RH, Cook L, Huang ML, et al.Identification of chromosomally integrated human herpes virus 6 by Droplet Digital PCR[J]. Clinical Chemistry. 2014, 60(5):765772. [45] Beck J, Bierau S, Balzer S, et al.Digital. Droplet PCR for rapid quantification of donor DNA in the circulation of transplant recipients as a potential universal biomarker of graft injury[J]. Clin Chem, 2013, 59(12):1732-1741. [46] 郭瑛, 韩冰, 王丽, 等. 数字PCR技术在布鲁菌病疗效判定中的应用价值[J]. 河北医药, 2017, 39(15):2292-2295. [47] Deborah P, Hannah G, Carrie Z, et al.Absence of detectable HIV1 viremia after treatment cessation in an infant[J]. New England Journal of Medicine, 2013, 369(19):1828-1835. [48] Haydenrt G, Ingersolly, et al. Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus[J]. J Clin Microbiol, 2013, 51(2):540-546. [49] Kelley K, Cosman A, et al.Detection of methicillin-resistant Staphylococcus aureus by a duplex droplet digital PCR assay[J]. J Clin Microbiol, 2013, 51(7):2033-2039. [50] Devonshire AS, Honeyborne I, et al.Highly reproducible absolute quantification of Mycobacterium tuberculosis complex by digital PCR[J]. Anal Chem, 2015, 87(7):3706-3713. [51] Benjamin JH, Kevin DN, Donald AM, et al.High throughput droplet digital PCR system for absolute quantitation of DNA copy number[J]. Anal Chem, 2011, 83(22):8604-8610 [52] Cronn RC, Adams KL. Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP[J]. Biotechniques, 2003, 34:726-730, 732, 734. [53] Henrichsen CN, Chaignat E, Reymond A.Copy number variants, diseases, and gene expression[J]. Hum Mol Genet, 2009, 18:R1-R8. [54] De Jong WS, De Jong DM, Bodis M.A fluorogenic 5’ nuclease(TaqMan)assay to assess dosage of a marker tightly linked to red skin color in autotetraploid potato[J]. Theoretical & Applied Genetics, 2003, 107(8):1384-1390. [55] Mejía-Benítez MA, Bonnefond A, et al.Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children[J]. Diabetologia, 2015, 58(2):290-294. [56] Falchi M, El, Sayed Moustafa JS, Takousis P, et al. Low copy number of the salivary amylase gene predisposes to obesity[J]. Nature Genetics, 2014, 46(5):492-497. [57] Miotke L, Lau BT, Rumma RT, et al.High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR[J]. Anal Chem, 2014, 86(5):2618-2624. [58] Taly V, Pekin D, et al.Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients[J]. Clin Chem, 2013, 59(12):1722-1731. [59] 张永江, 黄洁芳, 王溪桥, 等. 微滴数字PCR(ddPCR)检测马铃薯S病毒(PVS)[J]. 农业生物技术学报, 2017, 25(10):1721-1728. [60] 陈嘉茵, 李晖, 方苓, 等. 一步法微滴数字PCR检测生菜中GII型诺如病毒[J]. 食品科学:1-8[2018-03-22]. [61] Rothrock MJ, Hiett KL, Kiepper BH, et al.Quantification of zoonotic bacterial pathogens within commercial poultry processing water samples using droplet digital PCR[J]. Advances in Microbiology, 2013, 3(5):403-411. [62] Bian X, Jing F, et al.A microfluidic droplet digital PCR for simultaneous detection of pathogenic Escherichia coli, O157 and Listeria monocytogenes[J]. Biosens Bioelectron, 2015, 74:770-777. [63] Coker PR, Smith KL, Fellows PF, et al.Bacillus anthracis virulence in Guinea pigs vaccinated with anthrax vaccine adsorbed is linked to plasmid quantities and clonality[J]. J Clin Microbiol, 2003, 41(3):1212-1218. [64] Pilo P, Rossano A, Bamamga H, et al.Bovine Bacillus anthracis in cameroon[J]. Appl Environ Microbiol. 2011, 77:5818-5821. [65] Straub T, Baird C, Bartholomew RA, et al.Estimated copy number of Bacillus anthracis plasmids pXO1 and pXO2 using digital PCR[J]. J Microbiol Methods, 2013, 92(1):9-10. [66] Ottesen EA, Hong JW, Quake SR, et al.Microfluidic digital PCR enables multigene analysis of individual environmental bacteria[J]. Science, 2006, 314(5804):1464-1467. [67] Hua SST, Palumbo JD, Dan EP, et al.Development of a droplet digital PCR assay for population analysis of aflatoxigenic and atoxigenic Aspergillus flavus, mixtures in soil[J]. Mycotoxin Research, 2018(8):1-8. [68] Zhu P, Ying S, Tian W, et al.Ultra-sensitive and absolute quantitative detection of Cu2+, based on DNAzyme and digital PCR in water and drink samples[J]. Food Chemistry, 2017, 221:1770-1777. [69] Zhu P, Tian W, Cheng N, et al.Ultra-sensitive “turn-on” detection method for Hg(2+)based on mispairing biosensor and emulsion PCR.[J]. Talanta, 2016, 155:168-174. [70] Cheng N, Zhu P, Xu Y, et al.High-sensitivity assay for Hg(II)and Ag(I)ion detection:A new class of droplet digital PCR logic gates for an intelligent DNA calculator[J]. Biosensors & Bioelectronics, 2016, 84(15):1-6. [71] Dingle TC, Sedlak RH, Cook L, et al.Tolerance of droplet-digital PCR vs real-time quantitative PCR to inhibitory substances.[J]. Clin Chem, 2013, 59(11):1670-1672. |
[1] | 李天顺, 李宸葳, 王佳, 朱龙佼, 许文涛. 功能核酸筛选过程中次级文库的有效制备[J]. 生物技术通报, 2023, 39(3): 116-122. |
[2] | 李会杰, 董莲华, 陈桂芳, 刘思渊, 杨佳怡, 杨靖亚. 食品中椰毒假单胞菌微滴式数字PCR定量检测方法的建立[J]. 生物技术通报, 2023, 39(1): 127-136. |
[3] | 胡雪莹, 张越, 郭雅杰, 仇天雷, 高敏, 孙兴滨, 王旭明. 不同施肥处理农田土壤中噬菌体与细菌携带抗生素抗性基因的比较[J]. 生物技术通报, 2022, 38(9): 116-126. |
[4] | 程深伟, 张克强, 梁军锋, 刘福元, 郜兴亮, 杜连柱. 畜禽养殖粪污中典型致病菌的三重微滴式数字PCR定量检测方法的建立[J]. 生物技术通报, 2022, 38(9): 271-280. |
[5] | 周子琦, 张洋子, 兰欣悦, 刘洋儿, 朱龙佼, 许文涛. 发光核酸适配体的筛选及应用[J]. 生物技术通报, 2022, 38(5): 240-247. |
[6] | 刘宁宁, 王鑫昕, 兰欣悦, 褚华硕, 陈旭, 常世敏, 李腾飞, 许文涛. G-三链体可视化核酸传感器用于四环素的检测[J]. 生物技术通报, 2022, 38(10): 106-114. |
[7] | 杨敏, 李舒婷, 杨文平, 李相阳, 许文涛. DNA/银纳米簇介导的功能核酸生物传感器研究进展[J]. 生物技术通报, 2020, 36(6): 245-254. |
[8] | 杨镇州, 刘刚, 许丽. 基于RNAi技术的转基因玉米逆转录数字PCR检测方法[J]. 生物技术通报, 2020, 36(5): 56-63. |
[9] | 杨镇州, 刘刚, 梁文. 转基因大豆MON89788芯片式数字PCR定量方法的建立[J]. 生物技术通报, 2020, 36(5): 68-73. |
[10] | 纪艺, 徐晓丽, 姜媛媛, 汪小福, 徐俊锋, 李玥莹, 陈笑芸. 基于数字PCR的不同品种鸭组织中线粒体与核DNA拷贝数差异研究[J]. 生物技术通报, 2020, 36(5): 86-91. |
[11] | 肖冰, 罗云波, 黄昆仑, 张园, 许文涛. 功能核酸荧光标记型定量统一化检测技术的研究进展[J]. 生物技术通报, 2019, 35(7): 213-221. |
[12] | 谢银侠, 王蔚然, 程楠, 许文涛. 电信号分子在电化学功能核酸生物传感器中的研究进展[J]. 生物技术通报, 2019, 35(5): 157-169. |
[13] | 苏秋菊, 周翔, 李光鹏, 白春玲, 许文涛, 刘榜. MSTN基因编辑牛的鉴定及基因分型新方法[J]. 生物技术通报, 2019, 35(4): 208-212. |
[14] | 肖冰, 刘榜, 罗云波, 黄昆仑, 张园, 李夏莹, 张秀杰, 许文涛, 周翔. 功能核酸荧光免标记型定量统一化检测技术的研究进展[J]. 生物技术通报, 2019, 35(3): 194-202. |
[15] | 李宸葳, 杜再慧, 林少华, 罗云波, 许文涛. Pb2+功能核酸生物传感器的研究进展[J]. 生物技术通报, 2019, 35(1): 131-139. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||