基于分子信标策略的CRISPR/Cas12a荧光传感器用于循环肿瘤DNA的放大检测

引用本文: 张函笑, 代晓春, 周亚楠, 吕旭珍, 弓韬, 赵旭华, 于保锋. 基于分子信标策略的CRISPR/Cas12a荧光传感器用于循环肿瘤DNA的放大检测[J]. 分析化学, 2023, 51(2): 184-193. doi: 10.19756/j.issn.0253-3820.221203 shu

Citation: ZHANG Han-Xiao, DAI Xiao-Chun, ZHOU Ya-Nan, LYU Xu-Zhen, GONG Tao, ZHAO Xu-Hua, YU Bao-Feng. CRISPR/Cas12a Fluorescence Sensor Based on Molecular Beacon for Amplification Detection of Circular Tumor DNA[J]. Chinese Journal of Analytical Chemistry, 2023, 51(2): 184-193. doi: 10.19756/j.issn.0253-3820.221203 shu

基于分子信标策略的CRISPR/Cas12a荧光传感器用于循环肿瘤DNA的放大检测

山西医科大学基础医学院, 生物化学与分子生物学教研室, 太原 030001

通讯作者: 赵旭华,E-mail:zhaoxuhua1985@126.com; 于保锋,E-mail:shanxiyangcheng@126.com

基金项目:
山西省自然科学基金项目(Nos.202103021224240，201901D211317，201901D111190)、山西医科大学细胞生理学教育部重点实验室开放基金项目(No.KLMEC/SXMU-202011)和山西省“1331工程”重点学科建设计划项目(No.1331KSC)资助。

摘要: 构建了一种以分子信标（Molecular beacon，MB）为信号探针的CRISPR/Cas12a生物传感器，用于循环肿瘤DNA（Circular tumor DNA，ctDNA）的快速放大检测。MB具有良好的稳定性，其颈部末端分别标记有荧光素（FAM）和四甲基罗丹明（TAMRA）两种荧光基团。ctDNA不存在时，CRISPR/Cas12a体系无活性，无法切割MB，因此MB两端的荧光基团由于形成发夹结构的颈部相互靠近而发生荧光共振能量转移（Fluorescence resonance energy transfer，FRET），显示出TAMRA的荧光。当ctDNA存在时，ctDNA特异性识别Cas12a/crRNA二元复合物并激活Cas12a的反式切割活性。由于单链DNA是Cas12a最敏感的底物，因此MB的环部单链首先被切割，继而引起颈部双链的解离而导致两种荧光团彼此远离，无法发生FRET，最终显示出FAM的荧光信号。对MB环部的碱基数目、MB浓度以及crRNA与Cas12a的浓度比例等实验条件进行了优化。在最优条件下，1.7~500 pmol/L范围内，ctDNA浓度与传感器在518 nm处的荧光强度呈线性关系，检出限为0.6 pmol/L（3σ）。将此传感器用于血清样品中ctDNA的检测，回收率在93%~110%之间。

关键词:

English

CRISPR/Cas12a Fluorescence Sensor Based on Molecular Beacon for Amplification Detection of Circular Tumor DNA

Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China

Corresponding author: ZHAO Xu-Hua, ; YU Bao-Feng,

Received Date: 26 April 2022
Revised Date: 01 December 2022
Fund Project:
Supported by the Natural Science Foundation of Shanxi Province, China (Nos. 202103021224240, 201901D211317, 201901D111190), the Open Fund from Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, China (No. KLMEC/SXMU-202011) and the Shanxi “1331 Project” Key Subjects Construction (No. 1331KSC).

Abstract: A CRISPR/Cas12a-based biosensor using molecular beacon (MB) as the reporter was constructed for amplification detection of circular tumor DNA (ctDNA). The molecular beacon with good stability was labeled with FAM and TAMRA at its ends, respectively. In the absence of ctDNA, the CRISPR/Cas12a system was inactive and MB could not be cleaved. Therefore, two fluorophores were in close proximity to each other, resulting in fluorescence resonance energy transfer (FRET). In the presence of ctDNA, it could recognize the Cas12a/crRNA complex and activate the trans-cleavage activity of Cas12a. Because ssDNA was the most susceptible substrate of Cas12a, the loop of MB was rapidly cleaved first. After cleavage, two fluorophores were far from each other, leading to the disappearance of FRET phenomenon and an obvious fluorescent enhancement of FAM. The experimental conditions such as the base numbers of the hairpin loop, the concentration of MB, and the concentration ratio of crRNA to Cas12a were optimized. Under the optimal conditions, a linear relationship ranging from 1.7 pmol/L to 500 pmol/L for ctDNA quantitative detection was observed and its detection limit was 600 fmol/L. In addition, this sensor could be used to detect ctDNA in serum samples and the recoveries were in the range of 93%-110%.

Key words:

CRISPR
/ Biosensor
/ Fluorescence resonance energy transfer
/ Circular tumor DNA

1. [1]
  BURRELL R A, MCGRANAHAN N, BARTEK J, SWANTON C. Nature, 2013, 501(7467):338-345.BURRELL R A, MCGRANAHAN N, BARTEK J, SWANTON C. Nature, 2013, 501(7467):338-345.
2. [2]
  MURTAZA M, DAWSON S J, TSUI D W Y, GALE D, FORSHEW T, PISKORZ A M, PARKINSON C, CHIN S F, KINGSBURY Z, WONG A S C, MARASS F, HUMPHRAY S, HADFIELD J, BENTLEY D, CHIN T M, BRENTON J D, CALDAS C, ROSENFELD N. Nature, 2013, 497(7447):108-112.MURTAZA M, DAWSON S J, TSUI D W Y, GALE D, FORSHEW T, PISKORZ A M, PARKINSON C, CHIN S F, KINGSBURY Z, WONG A S C, MARASS F, HUMPHRAY S, HADFIELD J, BENTLEY D, CHIN T M, BRENTON J D, CALDAS C, ROSENFELD N. Nature, 2013, 497(7447):108-112.
3. [3]
  YOUNG E, PHILPOTT H, SINGH R. World J. Gastroenterol., 2021, 27(31):5126-5151.YOUNG E, PHILPOTT H, SINGH R. World J. Gastroenterol., 2021, 27(31):5126-5151.
4. [4]
  GANDARA D R, PAUL S M, KOWANETZ M, SCHLEIFMAN E, ZOU W, LI Y, RITTMEYER A, FEHRENBACHER L, OTTO G, MALBOEUF C, LIEBER D S, LIPSON D, SILTERRA J, AMLER L, RIEHL T, CUMMINGS C A, HEGDE P S, SANDLER A, BALLINGER M, FABRIZIO D, MOK T, SHAMES D S. Nat. Med., 2018, 24(9):1441-1448.GANDARA D R, PAUL S M, KOWANETZ M, SCHLEIFMAN E, ZOU W, LI Y, RITTMEYER A, FEHRENBACHER L, OTTO G, MALBOEUF C, LIEBER D S, LIPSON D, SILTERRA J, AMLER L, RIEHL T, CUMMINGS C A, HEGDE P S, SANDLER A, BALLINGER M, FABRIZIO D, MOK T, SHAMES D S. Nat. Med., 2018, 24(9):1441-1448.
5. [5]
  SIRAVEGNA G, MARSONI S, SIENA S, BARDELLI A. Nat. Rev. Clin. Oncol, 2017, 14(9):531-548.SIRAVEGNA G, MARSONI S, SIENA S, BARDELLI A. Nat. Rev. Clin. Oncol, 2017, 14(9):531-548.
6. [6]
  BEDARD P L, HANSEN A R, RATAIN M J, SIU L L. Nature, 2013, 501(7467):355-364.BEDARD P L, HANSEN A R, RATAIN M J, SIU L L. Nature, 2013, 501(7467):355-364.
7. [7]
  WAN J C M, MASSIE C, GARCIA-CORBACHO J, MOULIERE F, BRENTON J D, CALDAS C, PACEY S, BAIRD R, ROSENFELD N. Nat. Rev. Cancer, 2017, 17(4):223-238.WAN J C M, MASSIE C, GARCIA-CORBACHO J, MOULIERE F, BRENTON J D, CALDAS C, PACEY S, BAIRD R, ROSENFELD N. Nat. Rev. Cancer, 2017, 17(4):223-238.
8. [8]
  DIEHL F, SCHMIDT K, CHOTI M A, ROMANS K, GOODMAN S, LI M, THORNTON K, AGRAWAL N, SOKOLL L, SZABO S A, KINZLER K W, VOGELSTEIN B, DIAZ JR L A. Nat. Med., 2008, 14(9):985-990.DIEHL F, SCHMIDT K, CHOTI M A, ROMANS K, GOODMAN S, LI M, THORNTON K, AGRAWAL N, SOKOLL L, SZABO S A, KINZLER K W, VOGELSTEIN B, DIAZ JR L A. Nat. Med., 2008, 14(9):985-990.
9. [9]
  FREIDIN M B, FREYDINA D V, LEUNG M, MONTERO FERNANDEZ A, NICHOLSON A G, LIM E. Clin. Chem., 2015, 61(10):1299-1304.FREIDIN M B, FREYDINA D V, LEUNG M, MONTERO FERNANDEZ A, NICHOLSON A G, LIM E. Clin. Chem., 2015, 61(10):1299-1304.
10. [10]
  STAHLBERG A, KRZYZANOWSKI P M, JACKSON J B, EGYUD M, STEIN L, GODFREY T E. Nucleic Acids Res., 2016, 44:e105.STAHLBERG A, KRZYZANOWSKI P M, JACKSON J B, EGYUD M, STEIN L, GODFREY T E. Nucleic Acids Res., 2016, 44:e105.
11. [11]
  DAS J, IVANOV I, MONTERMINI L, RAK J, SARGENT E H, KELLEY S O. Nat. Chem., 2015, 7(7):569-575.DAS J, IVANOV I, MONTERMINI L, RAK J, SARGENT E H, KELLEY S O. Nat. Chem., 2015, 7(7):569-575.
12. [12]
  TEENGAM P, SIANGPROH W, TUANTRANONT A, VILAIVAN T, CHAILAPAKUL O, HENRY C S. Anal. Chem., 2017, 89(10):5428-5435.TEENGAM P, SIANGPROH W, TUANTRANONT A, VILAIVAN T, CHAILAPAKUL O, HENRY C S. Anal. Chem., 2017, 89(10):5428-5435.
13. [13]
  NOH S, HA D T, YANG H, KIM M S. Analyst, 2015, 140(12):3947-3952.NOH S, HA D T, YANG H, KIM M S. Analyst, 2015, 140(12):3947-3952.
14. [14]
  FAURE G, SHMAKOV S A, YAN W X, CHENG D R, SCOTT D A, PETERS J E, MAKAROVA K S, KOONIN E V. Nat. Rev. Microbiol., 2019, 17(8):513-525.FAURE G, SHMAKOV S A, YAN W X, CHENG D R, SCOTT D A, PETERS J E, MAKAROVA K S, KOONIN E V. Nat. Rev. Microbiol., 2019, 17(8):513-525.
15. [15]
  YAN W X, HUNNEWELL P, ALFONSE L E, CARTE J M, KESTON-SMITH E, SOTHISELVAM S, GARRITY A J, CHONG S, MAKAROVA K S, KOONIN E V, CHENG D R, SCOTT D A. Science, 2019, 363(6422):88-91.YAN W X, HUNNEWELL P, ALFONSE L E, CARTE J M, KESTON-SMITH E, SOTHISELVAM S, GARRITY A J, CHONG S, MAKAROVA K S, KOONIN E V, CHENG D R, SCOTT D A. Science, 2019, 363(6422):88-91.
16. [16]
  QIAO J, LIN S, SUN W, MA L, LIU Y. Chem. Commun., 2020, 56(83):12616-12619.QIAO J, LIN S, SUN W, MA L, LIU Y. Chem. Commun., 2020, 56(83):12616-12619.
17. [17]
  KLEINSTIVER B P, SOUSA A A, WALTON R T, TAK Y E, HSU J Y, CLEMENT K, WELCH M M, HORNG J E, MALAGON-LOPEZ J, SCARFÒ I, MAUS M V, PINELLO L, ARYEE M J, JOUNG J K. Nat. Biotechnol., 2019, 37(3):276-282.KLEINSTIVER B P, SOUSA A A, WALTON R T, TAK Y E, HSU J Y, CLEMENT K, WELCH M M, HORNG J E, MALAGON-LOPEZ J, SCARFÒ I, MAUS M V, PINELLO L, ARYEE M J, JOUNG J K. Nat. Biotechnol., 2019, 37(3):276-282.
18. [18]
  STELLA S, MESA P, THOMSEN J, PAUL B, ALCÓN P, JENSEN S B, SALIGRAM B, MOSES M E, HATZAKIS N S, MONTOYA G. Cell, 2018, 175(7):1856-1871.e21.STELLA S, MESA P, THOMSEN J, PAUL B, ALCÓN P, JENSEN S B, SALIGRAM B, MOSES M E, HATZAKIS N S, MONTOYA G. Cell, 2018, 175(7):1856-1871.e21.
19. [19]
  CHEN J S, MA E, HARRINGTON L B, DA COSTA M, TIAN X, PALEFSKY J M, DOUDNA J A. Science, 2018, 360(6387):436-439.CHEN J S, MA E, HARRINGTON L B, DA COSTA M, TIAN X, PALEFSKY J M, DOUDNA J A. Science, 2018, 360(6387):436-439.
20. [20]
  ZHANG G, ZHANG L, TONG J, ZHAO X, REN J. Microchem. J., 2020, 158:105239.ZHANG G, ZHANG L, TONG J, ZHAO X, REN J. Microchem. J., 2020, 158:105239.
21. [21]
  XIONG Y, ZHANG J, YANG Z, MOU Q, MA Y, XIONG Y, LU Y. J. Am. Chem. Soc., 2020, 142(1):207-213.XIONG Y, ZHANG J, YANG Z, MOU Q, MA Y, XIONG Y, LU Y. J. Am. Chem. Soc., 2020, 142(1):207-213.
22. [22]
  ZHANG H, ZHOU Y, LUO D, LIU J, YANG E, YANG G, FENG G, CHEN Q, WU L. RSC Adv., 2021, 11(9):4983-4990.ZHANG H, ZHOU Y, LUO D, LIU J, YANG E, YANG G, FENG G, CHEN Q, WU L. RSC Adv., 2021, 11(9):4983-4990.
23. [23]
  YING Z M, WU Z, TU B, TAN W, JIANG J H. J. Am. Chem. Soc., 2017, 139(29):9779-9782.YING Z M, WU Z, TU B, TAN W, JIANG J H. J. Am. Chem. Soc., 2017, 139(29):9779-9782.
24. [24]
  PENG L, ZHOU J, YIN L, MAN S, MA L. Anal. Chim. Acta, 2020, 1125:162-168.PENG L, ZHOU J, YIN L, MAN S, MA L. Anal. Chim. Acta, 2020, 1125:162-168.
25. [25]
  LI S Y, CHENG Q X, LIU J K, NIE X Q, ZHAO G P, WANG J. Cell Res., 2018, 28(4):491-493.LI S Y, CHENG Q X, LIU J K, NIE X Q, ZHAO G P, WANG J. Cell Res., 2018, 28(4):491-493.
26. [26]
  LI X, ZHANG D, GAN X, LIU P, ZHENG Q, YANG T, TIAN G, DING S, YAN Y. ACS Synth. Biol., 2021, 10(6):1481-1489.LI X, ZHANG D, GAN X, LIU P, ZHENG Q, YANG T, TIAN G, DING S, YAN Y. ACS Synth. Biol., 2021, 10(6):1481-1489.
27. [27]
  LOO A H, SOFER Z, BOUSA D, ULBRICH P, BONANNI A, PUMERA M. ACS Appl. Mater. Interfaces, 2016, 8(3):1951-1957.LOO A H, SOFER Z, BOUSA D, ULBRICH P, BONANNI A, PUMERA M. ACS Appl. Mater. Interfaces, 2016, 8(3):1951-1957.
28. [28]
  UYGUN Z O, YENIAY L, GIRGIN SAĞIN F. Anal. Chim. Acta, 2020, 1121:35-41.UYGUN Z O, YENIAY L, GIRGIN SAĞIN F. Anal. Chim. Acta, 2020, 1121:35-41.
29. [29]
  SOARES J C, SOARES A C, RODRIGUES V C, MELENDEZ M E, SANTOS A C, FARIA E F, REIS R M, CARVALHO A L, OLIVEIRA O N. ACS Appl. Mater. Interfaces, 2019, 11(50):46645-46650.SOARES J C, SOARES A C, RODRIGUES V C, MELENDEZ M E, SANTOS A C, FARIA E F, REIS R M, CARVALHO A L, OLIVEIRA O N. ACS Appl. Mater. Interfaces, 2019, 11(50):46645-46650.
30. [30]
  CHANG H, ZHANG Y, YANG F, WANG C, DONG H. Front. Chem., 2018, 6:530.CHANG H, ZHANG Y, YANG F, WANG C, DONG H. Front. Chem., 2018, 6:530.
31. [31]
  WANG J, HUA G, LI L, LI D, WANG F, WU J, YE Z, ZHOU X, YE S, YANG J, ZHANG X, REN L. Analyst, 2020, 145(16):5553-5562.WANG J, HUA G, LI L, LI D, WANG F, WU J, YE Z, ZHOU X, YE S, YANG J, ZHANG X, REN L. Analyst, 2020, 145(16):5553-5562.
32. [32]
  WANG Y, KONG S L, SU X D. RSC Adv., 2020, 10(3):1476-1483.WANG Y, KONG S L, SU X D. RSC Adv., 2020, 10(3):1476-1483.
33. [33]
  LIU G, MA X, TANG Y, MIAO P. Analyst, 2020, 145(4):1174-1178.LIU G, MA X, TANG Y, MIAO P. Analyst, 2020, 145(4):1174-1178.

扫一扫看文章

计量

PDF下载量: 26
文章访问数: 1204
HTML全文浏览量: 115

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

基于分子信标策略的CRISPR/Cas12a荧光传感器用于循环肿瘤DNA的放大检测

通讯作者: 赵旭华,E-mail:zhaoxuhua1985@126.com; 于保锋,E-mail:shanxiyangcheng@126.com

English

CRISPR/Cas12a Fluorescence Sensor Based on Molecular Beacon for Amplification Detection of Circular Tumor DNA

Corresponding author: ZHAO Xu-Hua, ; YU Bao-Feng,

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

基于分子信标策略的CRISPR/Cas12a荧光传感器用于循环肿瘤DNA的放大检测

通讯作者: 赵旭华,E-mail:zhaoxuhua1985@126.com; 于保锋,E-mail:shanxiyangcheng@126.com

English

CRISPR/Cas12a Fluorescence Sensor Based on Molecular Beacon for Amplification Detection of Circular Tumor DNA

Corresponding author: ZHAO Xu-Hua, ; YU Bao-Feng,

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs