Research Progress of Gene Mutation Detection Methods Based on Nanoparticles

doi:10.13560/j.cnki.biotech.bull.1985.2020-0812

Abstract

Abstract:

Gene mutation refers to a change in the composition or sequence of base pairs in the molecular structure. It is closely related to the occurrence of human diseases and has always attracted attention. The development of accurate and reliable detection methods,the further exploration of nucleic acid function regulation and the early detection and treatment of related diseases are the directions of researchers’ continuous efforts. In recent years,nanoparticles have been widely used in the field of biomedicine due to their excellent optical-,electrical- and bio-compatibility. It is the first work to systematically discuss the latest research progress in gene mutation detection based on the nanoparticle,to explain the main issues and challenges in this field,and to look forward to the future development trend,aiming to provide new options for gene mutation detection ideas.

Key words: nanoparticles, fluorescence method, single particle counting method, gene mutation

WANG Lei-lei, DONG Lian-hua, YANG Jing-ya, WANG Xia. Research Progress of Gene Mutation Detection Methods Based on Nanoparticles[J]. Biotechnology Bulletin, 2021, 37(3): 241-251.

Figures/Tables 8

References 59

[1]	姜涛. 有机靶向荧光纳米探针在肿瘤诊疗方面的研究[D]. 广州:南方医科大学, 2019.
	Jiang T. Research on organic targeted fluorescent nanoprobe in tumor diagnosis and treatment[D]. Guangzhou:Southern Medical University, 2019.
[2]	Xu JJ, Li LJ, Chen N, et al. Endonuclease IV based competitive DNA probe assay for differentiation of low-abundance point mutations by discriminating stable single-base mismatches[J]. Chemical Communications(Cambridge, England), 2017,53(68):9422-9425.
[3]	Lim SM, Kim EY, Kim HR, et al. Genomic profiling of lung adenocarcinoma patients reveals therapeutic targets and confers clinical benefit when standard molecular testing is negative[J]. Oncotarget, 2016,7(17):24172. doi: 10.18632/oncotarget.8138 URL pmid: 26992220
[4]	Kim TE, Jung ES, Jung CK, et al. DHPLC is a highly sensitive and rapid screening method to detect BRAFV600E mutation in papillary thyroid carcinoma[J]. Experimental and Molecular Pathology, 2013,94(1):203-209. doi: 10.1016/j.yexmp.2012.05.011 URL
[5]	Alvarez-Garcia V, Bartos C, Keraite I, et al. A simple and robust real-time qPCR method for the detection of PIK3CA mutations[J]. Scientific Report, 2018,8(1):4290.
[6]	Link-Lenczowska D, Pallisgaard N, Cordua S, et al. A comparison of qPCR and ddPCR used for quantification of the JAK2 V617F allele burden in Ph negative MPNs[J]. Annals of Hematology, 2018,97(12):2299-2308. doi: 10.1007/s00277-018-3451-1 pmid: 30056580
[7]	Hedenfalk I, Duggan D, Chen Y, et al. Gene-Expression profiles in hereditary breast cancer[J]. New England Journal of Medicine, 2001,344(8):539-548. pmid: 11207349
[8]	Kowalczyk A, Krajczewski J, Kowalik A, et al. New strategy for the gene mutation identification using surface enhanced Raman spectroscopy(SERS)[J]. Biosensors and Bioelectronics, 2019,132:326-332. doi: 10.1016/j.bios.2019.03.019 URL pmid: 30897539
[9]	彭梅花. 荧光金纳米颗粒的制备及其离子检测的应用研究[D]. 长沙:湖南大学, 2012.
	Peng MH. Preparation of fluorescent gold nanoparticles and its application in ion detection[D]. Changsha:Hunan University, 2012.
[10]	Tien DC, Tseng KH, Liao CY, et al. Discovery of Ionic silver in silver nanoparticle suspension fabricated by arc discharge method. journal of alloys and compounds[J]. Journal of Alloys and Compounds, 2008,463(1-2):408-411. doi: 10.1016/j.jallcom.2007.09.048 URL
[11]	曹祥威. 火花放电和高能球磨法可控制备纳米硅颗粒及性能表征[D]. 南京:南京航空航天大学, 2018.
	Cao XW. Spark discharge and high-energy ball milling can control the preparation of nano-silicon particles and their performance characterization[D]. Nanjing:Nanjing University of Aeronautics and Astronautics, 2018.
[12]	朱文壮, 刘轶群, 孟赓. 纳米金颗粒的晶种法制备及表征[J]. 中国兽医杂志, 2019,55(10):33-35, 130.
	Zhu WZ, Liu YQ, Meng G. Preparation and characterization of gold nanoparticles by seed method[J]. Chinese Journal of Veterinary Medicine, 2019,55(10):33-35, 130.
[13]	康永. 三种不同方式制备纳米磁性Fe3O4颗粒及光催化性[J]. 陶瓷, 2019(4):43-49.
	Kang Y. Three different ways to prepare nano-magnetic Fe3O4 particles and their photocatalytic properties[J]. Ceramics, 2019(4):43-49.
[14]	文凤, 宋晨, 熊伟荣, 等. 橙汁提取物生物制备银纳米颗粒及其生物相容性研究[J]. 中国临床解剖学杂志, 2020,38(3):270-276.
	Wen F, Song C, Xiong WR, et al. Study on bio-preparation of silver nanoparticles from orange juice extract and their biocompatibility[J]. Chinese Journal of Clinical Anatomy, 2020,38(3):270-276.
[15]	刘茜茜, 孙丽. 金纳米颗粒的绿色合成及光催化性能的研究[J]. 广州化学, 2019,44(4):56-60.
	Liu QQ, Sun L. Research on the green synjournal and photocatalytic properties of gold nanoparticles[J]. Guangzhou Chemistry, 2019,44(4):56-60.
[16]	Wei LY, Lu JG, Xu HZ, et al. Silver nanoparticles:synjournal, properties, and therapeutic applications[J]. Drug Discovery Today, 2015,20(5):595-601. doi: 10.1016/j.drudis.2014.11.014 URL pmid: 25543008
[17]	李新妮. 功能化的金和银纳米材料的制备及其分析应用研究[D]. 西安:陕西师范大学, 2019.
	Li XN. Research on the preparation and analytical application of functionalized gold and silver nanomaterials[D]. Xi’an:Shaanxi Normal University, 2019.
[18]	刘艳娥, 马思琪, 尹荔松. 纳米银粒子的制备及其表征[J]. 世界有色金属, 2019,21(21):256-258.
	Liu YE, Ma SQ, Yin LS. Preparation and characterization of nano silver particles[J]. World Nonferrous Metals, 2019,21(21):256-258.
[19]	展宗瑞, 张琪, 李倩, 等. 高分散粒径可控纳米金粒子制备及表征[J]. 山东化工, 2020,49(1):15-16, 19.
	Zhan ZR, Zhang Q, Li Q, et al. Preparation and characterization of highly dispersed gold nanoparticles with controllable particle size[J]. Shandong Chemical Industry, 2020,49(1):15-16, 19.
[20]	代昭, 韩阳. 小粒径金纳米粒子的制备及性能表征[J]. 天津工业大学学报, 2019,38(6):41-44, 51.
	Dai Z, Han Y. Preparation and performance characterization of small-size gold nanoparticles[J]. Journal of Tiangong University, 2019,38(6):41-44, 51.
[21]	Wang CQ, Yuan XQ, Liu XH, et al. Signal-on impedimetric electrochemical DNA sensor using dithiothreitol modified gold nanoparticle tag for highly sensitive DNA detection[J]. Analytica Chimica Acta, 2013,799:36-43. doi: 10.1016/j.aca.2013.09.024 URL pmid: 24091372
[22]	黄姣祺. 基于功能化纳米金的超灵敏核酸检测[D]. 重庆:中国人民解放军陆军军医大学, 2019.
	Huang JQ. Ultra-sensitive nucleic acid detection based on functionalized gold nanoparticles[D]. Chongqing:Third Military Medical University, 2019.
[23]	于长江. 磁纳米粒的表面改性及其生物医学应用研究[D]. 北京:中国协和医科大学, 2007.
	Yu CJ. Surface modification of magnetic nanoparticles and their biomedical applications[D]. Beijing:Peking Union Medical College, 2007.
[24]	Teng Y, Jia XF, Zhang S, et al. A nanocluster beacon based on the template transformation of DNA-templated silver nanoclusters[J]. Chemical Communications, 2016,52(8):1721-1724. doi: 10.1039/c5cc09138a URL pmid: 26666564
[25]	张秀梅. 金、铜纳米颗粒及其复合材料的制备与应用[D]. 济南:山东大学, 2019.
	Zhang XM. The preparation and application of gold and copper nanoparticles and their composite materials[D]. Ji’nan:Shandong University, 2019.
[26]	Qing ZH, Bai AL, Xing SH, et al. Progress in biosensor based on DNA-templated copper nanoparticles[J]. Biosensors and Bioelectronics, 2019,137:96-109. doi: 10.1016/j.bios.2019.05.014 URL pmid: 31085403
[27]	郭姣梅, 郝建华, 李晓涵, 等. 磁性纳米粒子的制备及环糊精葡萄糖基转移酶的固定化[J]. 功能材料, 2020,51(7):7190-7195.
	Guo JM, Hao JH, Li XH, et al. Preparation of magnetic nanoparticles and immobilization of cyclodextrin glucosyltransferase[J]. Functional Materials, 2020,51(7):7190-7195.
[28]	刘庆祖, 杨慧恺, 刘建恒, 等. 磁性纳米颗粒在肿瘤药物及肿瘤治疗中的研究进展[J]. 解放军医学院学报, 2020,41(4):409-412.
	Liu QZ, Yang HK, Liu JH, et al. Research progress of magnetic nanoparticles in tumor medicine and tumor therapy[J]. Journal of PLA Medical College, 2020,41(4):409-412.
[29]	李万万, 沈梦飞, 刘心怡. 纳米材料在体外诊断技术中的应用研究进展[J]. 科技导报, 2018,36(22):74-86.
	Li WW, Shen MF, Liu XY. Research progress in the application of nanomaterials in vitro diagnostic technology[J]. Science and Technology Review, 2018,36(22):74-86.
[30]	谢春娟. 复合荧光二氧化硅纳米颗粒的制备及其在生物分析和光催化降解中的应用[D]. 上海:上海大学, 2010.
	Xie CJ. Preparation of composite fluorescent silica nanoparticles and their applications in bioanalysis and photocatalytic degradation[D]. Shanghai:Shanghai University, 2010.
[31]	陈锦文. 量子点的制备及其在药物分析中的应用研究进展[J]. 西北药学杂志, 2020,35(4):630-633.
	Chen JW. Preparation of quantum dots and its application in pharmaceutical analysis[J]. Northwest Pharmaceutical Journal, 2020,35(4):630-633.
[32]	Mirkin CA, Letsinger RL, Mucic RC, et al. A DNA-based method for rationally assembling nanoparticles into macroscopic materials[J]. Nature, 1996,382(6592):607-609. doi: 10.1038/382607a0 URL pmid: 8757129
	Cao YW, Jin R, Mirkin CA. DNA-modified core- shell Ag/Au nanoparticles[[J]. Journal of the American Chemical Society, 2001,123(32):7961-7962.
[33]	Park C, Song Y, Jang K, et al. Target switching catalytic hairpin assembly and gold nanoparticle colorimetric for EGFR mutant detection[J]. Sensors and Actuators B:Chemical, 2018,261:497-504. doi: 10.1016/j.snb.2018.01.183 URL
[34]	Li X, Song J, Chen BL, et al. A label-free colorimetric assay for detection of c-Myc mRNA based on peptide nucleic acid and silver nanoparticles[J]. Science Bulletin, 2016,61(4):276-281. doi: 10.1007/s11434-016-1004-3 URL
[35]	Wang Y, Meng WW, Chen X, et al. DNA-templated Copper nanoparticles as signalling probe for electrochemical determination of microRNA-222[J]. Microchimica ACTA, 2020,187(1):4. doi: 10.1007/s00604-019-4011-7 URL pmid: 31797053
[36]	Sun HB, Kong JM, Wang QW, et al. Dual signal amplification by eatrp and DNA-Templated Silver nanoparticles for ultrasensitive electrochemical detection of nucleic acids[J]. ACS Applied Materials & Interfaces, 2019,11(31):22757-27568.
[37]	Liu M, Hu P, Zhang G, et al. Copy number variation analysis by ligation-dependent PCR based on magnetic nanoparticles and chemiluminescence[J]. Theranostics, 2015,5(1):71. doi: 10.7150/thno.10117 URL pmid: 25553099
[38]	Wang LY, Yao MW, Fang XY, et al. Novel competitive chemiluminescence DNA assay based on Fe₃O₄@SiO₂@Au-Functionalized magnetic nanoparticles for sensitive detection of p53 tumor suppressor gene[J]. Appl Biochem Biotechnol, 2019,187(1):152-162. doi: 10.1007/s12010-018-2808-1 URL pmid: 29911263
[39]	邓立. 核酸功能化银纳米颗粒探针的设计及传感应用[D]. 长沙:湖南大学, 2017.
	Deng L. Design and sensing application of nucleic acid functionalized silver nanoparticle probe[D]. Changsha:Hunan University, 2017.
[40]	Wang H, Jiang X, Wang X, et al. Hairpin DNA-assisted silicon/silver-based surface-enhanced Raman scattering sensing platform for ultrahighly sensitive and specific discrimination of deafness mutations in a real system[J]. Analytical Chemistry, 2014,86(15):7368-7376. doi: 10.1021/ac501675d pmid: 25001041
[41]	Gao JX, Ma L, Lei Z, et al. Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes[J]. Analyst, 2016,141(5):1772-1778. doi: 10.1039/c5an02510a URL pmid: 26899365
[42]	Wang S, Zhang F, Chen CY, et al. Ultrasensitive graphene quantum dots-based catalytic hairpin assembly amplification resonance light scattering assay for p53 mutant DNA detection[J]. Sensors and Actuators B:Chemical, 2019,291:42-47. doi: 10.1016/j.snb.2019.04.015 URL
[43]	Lv SV, Chen F, Chen CY, et al. A novel CdTe quantum dots probe amplified resonance light scattering signals to detect microRNA-122[J]. Talanta, 2017,165:659-663. doi: 10.1016/j.talanta.2017.01.020 URL pmid: 28153313
[44]	Zhang YW, Li HL, Sun XP. Silver nanoparticles as a fluorescent sensing platform for nucleic acid detection[J]. Chinese Journal of Analytical Chemistry, 2011,39(7):998-1002. doi: 10.3724/SP.J.1096.2011.00998 URL
[45]	Ma HY, Li ZB, Xue N, et al. A Gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA[J]. Microchimica ACTA, 2018,185(2):93. doi: 10.1007/s00604-017-2633-1 URL pmid: 29594738
[46]	Park KW, Lee CY, Batule BS, et al. Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles[J]. RSC Advances, 2018,8(4):1958-1962. doi: 10.1039/C7RA11071E URL
[47]	Yang SJ, Liu MY, Deng FJ, et al. Biomimetic modification of silica nanoparticles for highly sensitive and ultrafast detection of DNA and AgAg⁺ions[J]. Applied Surface Science, 2020,510:145421. doi: 10.1016/j.apsusc.2020.145421 URL
[48]	Yew YT, Sofer Z, Mayorga-Martinez CC, et al. Black phosphorus nanoparticles as a novel fluorescent sensing platform for nucleic acid detection[J]. Materials Chemistry Frontiers, 2017,1(6):1130-1136. doi: 10.1039/C6QM00341A URL
[49]	Li T, Xu X, Zhang GQ, et al. Nonamplification sandwich assay platform for sensitive nucleic acid detection based on aunps enumeration with the dark-field microscope[J]. Analytical Chemistry, 2016,88(8):4188-4191. doi: 10.1021/acs.analchem.6b00535 URL pmid: 27023372
[50]	Pei XJ, Yin HY, Lai TC, et al. Multiplexed detection of attomoles of nucleic acids using fluorescent nanoparticle counting platform[J]. Analytical Chemistry, 2018,90(2):1376-1383. doi: 10.1021/acs.analchem.7b04551 URL pmid: 29226673
[51]	Pei XJ, Lai TC, Tao GY, et al. Ultraspecific multiplexed detection of low-abundance single-nucleotide variants by combining a masking tactic with fluorescent nanoparticle counting[J]. Analytical Chemistry, 2018,90(6):4226-4233. doi: 10.1021/acs.analchem.8b00685 URL pmid: 29504392
[52]	Fan ZJ, Yu J, Lin JY, et al. Exosome-specific tumor diagnosis via biomedical analysis of exosome-containing microRNA biomarkers[J]. Analyst, 2019,144(19):5856-5865. doi: 10.1039/c9an00777f URL pmid: 31482867
[53]	Gao JB, Sann EE, Wang XY, et al. Visual detection of the prostate specific antigen via a sandwich immunoassay and by using a superwettable chip coated with pH-responsive silica nanoparticles[J]. Microchimica ACTA, 2019,186(8):550. doi: 10.1007/s00604-019-3662-8 URL pmid: 31325059
[54]	Agans RT, Gordon A, Hussain S, et al. Titanium dioxide nanoparticles elicit lower direct inhibitory effect on human gut microbiota than silver nanoparticles[J]. Toxicological Sciences, 2019,172(2):411-441. doi: 10.1093/toxsci/kfz183 URL pmid: 31550005
[55]	蒲源, 王丹, 钱骏, 等. 荧光纳米材料及其生物成像应用[J]. 中国材料进展, 2017(2):103-111.
	Pu Y, Wang D, Qian J, et al. Fluorescent nanomaterials and their Bioimaging applications[J]. Progress in Chinese Materials, 2017(2):103-111.
[56]	Díaz-González M, de la Escosura-Muñiz A, Fernandez-Argüelles MT, et al. Quantum dot bioconjugates for diagnostic applications[J]. Topics in Current Chemistry, 2020,378(2):1-44. doi: 10.1007/s41061-019-0261-4 URL
[57]	Sun FF, You Y, Liu J, et al. DNA Three-way junction for differentiation of single nucleotide polymorphisms with fluorescent copper nanoparticles[J]. Chemistry-A European Journal, 2017,23(29):6979-6982. doi: 10.1002/chem.201701361 URL
[58]	Park C, Kang J, Baek I, et al. Highly sensitive and selective detection of single-nucleotide polymorphisms using gold nanoparticle MutS enzymes and a micro cantilever resonator[J]. Talanta, 2019,205:120154. doi: 10.1016/j.talanta.2019.120154 URL pmid: 31450442
[59]	Yu Z, Grasso MF, Cui X, et al. Sensitive and label-free SERS detection of single-stranded DNA assisted by silver nanoparticles and gold-coated magnetic nanoparticles[J]. ACS Applied Bio Materials, 2020,3(5):2626-2632. doi: 10.1021/acsabm.9b01218 URL

分类		成本	耗时	优点	缺点
测序法	第一代测序	高	长	读长长,适用于所有的突变类型	通量低,操作繁琐,自动化程度低,无法大规模使用
	第二代测序	低	长	通量高,灵敏度高,准确性高,自动化程度高	读长短,依赖于PCR扩增,不适用于序列已知的单基因突变检测,无法在单细胞、单分子水平检测
	第三代测序	高	短	读长长,通量高,不需要PCR扩增	出错率高,要多次重复检测
高效液相色谱法		低	短	通量高,自动化程度高,操作简便,重复性好,准确性高	只能检测有无突变,不能检测出突变类型,结果判断容易出错
PCR法	实时荧光定量PCR	高	短	通量高,特异性好,自动化程度高,灵敏度高	需要外标,依赖于标准曲线,准确性易受操作中因素影响
	数字PCR	高	短	灵敏度高,特异性好,重复性好,可实现绝对定量	试剂盒研发难度较大,费用高昂
微阵列法		高	短	灵敏度高,通量高,样品用量少	效率低,过程繁琐,缺乏标准化,不适于低丰度检测

分类		成本	耗时	优点	缺点
测序法	第一代测序	高	长	读长长,适用于所有的突变类型	通量低,操作繁琐,自动化程度低,无法大规模使用
	第二代测序	低	长	通量高,灵敏度高,准确性高,自动化程度高	读长短,依赖于PCR扩增,不适用于序列已知的单基因突变检测,无法在单细胞、单分子水平检测
	第三代测序	高	短	读长长,通量高,不需要PCR扩增	出错率高,要多次重复检测
高效液相色谱法		低	短	通量高,自动化程度高,操作简便,重复性好,准确性高	只能检测有无突变,不能检测出突变类型,结果判断容易出错
PCR法	实时荧光定量PCR	高	短	通量高,特异性好,自动化程度高,灵敏度高	需要外标,依赖于标准曲线,准确性易受操作中因素影响
	数字PCR	高	短	灵敏度高,特异性好,重复性好,可实现绝对定量	试剂盒研发难度较大,费用高昂
微阵列法		高	短	灵敏度高,通量高,样品用量少	效率低,过程繁琐,缺乏标准化,不适于低丰度检测

分类	优点	局限性	参考文献
银纳米颗粒（AgNP）	导电性、抗菌性好,制备简单,选择性高	化学稳定性差,极易氧化,毒性作用	[24]
金纳米颗粒（AuNP）	易修饰,重现性好,良好的光学和电学特性,操作简便,环境污染小	灵敏度有限,制备粒径均匀可控大小可行性受限	[25]
铜纳米颗粒（CuNP）	尺寸小,经济效益高,安全性高,可降低复杂样品的背景信号	在水溶液中不稳定,容易氧化,长期检测面临困难,光稳定性脆弱	[25-26]
磁纳米颗粒（MNP）	表面积大,表面活性位点多,传质能力强,具有超顺磁性,还原性好,易于合成、生产,低毒性,分离速度快	在空气中易氧化,亲水性差,易聚合纳米团块导致其分散性与生物相容性变差	[27-28]
高分子荧光纳米颗粒	灵敏度高,特异性强,容易制得,成本低,可实现多目标的检测	难以离心沉淀,分离困难,内部染料存在泄露的可能,潜在的生物毒性	[29]
复合二氧化硅荧光纳米颗粒	发光强度大,光稳定性好,良好的水溶性和表面化学活性,合成条件简单,无毒	容易团聚,大规模生产面临挑战	[30]
量子点	亮度高,光稳定性好,吸收光谱宽,斯托克斯位移大,光电化学活性强,摩尔消光系数大,量子产率高,荧光寿命长	合成条件苛刻,毒性作用与环境污染,易黏合聚集,长期稳定性不高,固有闪烁,生产成本高	[31]

分类	优点	局限性	参考文献
银纳米颗粒（AgNP）	导电性、抗菌性好,制备简单,选择性高	化学稳定性差,极易氧化,毒性作用	[24]
金纳米颗粒（AuNP）	易修饰,重现性好,良好的光学和电学特性,操作简便,环境污染小	灵敏度有限,制备粒径均匀可控大小可行性受限	[25]
铜纳米颗粒（CuNP）	尺寸小,经济效益高,安全性高,可降低复杂样品的背景信号	在水溶液中不稳定,容易氧化,长期检测面临困难,光稳定性脆弱	[25-26]
磁纳米颗粒（MNP）	表面积大,表面活性位点多,传质能力强,具有超顺磁性,还原性好,易于合成、生产,低毒性,分离速度快	在空气中易氧化,亲水性差,易聚合纳米团块导致其分散性与生物相容性变差	[27-28]
高分子荧光纳米颗粒	灵敏度高,特异性强,容易制得,成本低,可实现多目标的检测	难以离心沉淀,分离困难,内部染料存在泄露的可能,潜在的生物毒性	[29]
复合二氧化硅荧光纳米颗粒	发光强度大,光稳定性好,良好的水溶性和表面化学活性,合成条件简单,无毒	容易团聚,大规模生产面临挑战	[30]
量子点	亮度高,光稳定性好,吸收光谱宽,斯托克斯位移大,光电化学活性强,摩尔消光系数大,量子产率高,荧光寿命长	合成条件苛刻,毒性作用与环境污染,易黏合聚集,长期稳定性不高,固有闪烁,生产成本高	[31]