Fluorescence Signal Amplification Strategies Based on DNA Nanotechnology for miRNA Detection

Abstract

In this review, the most recent progresses in the field of fluorescence signal amplification strategies based on DNA nanotechnology for miRNA are summarized. The types of signal amplification are given and the principles of amplification strategies are explained, including rolling circle amplification(RCA), catalytic hairpin assembly (CHA), hybridization chain reaction(HCR) and DNA walker. Subsequently, the application of these signal amplification methods in biosensing and bioimaging are covered and described. Finally, the challenges and the outlook of fluorescence signal amplification methods for miRNA detection are briefly commented.

Keywords

Signal amplification / DNA nanotechnology / Fluorescence / miRNA detection / Biosensing and bioimaging

References

[1] Zhao Y X, Chen F, Li Q, Wang L H, Fan C H. Chem. Rev., 2015, 115: 12491.

[2] Newman A M, Bratman S V, To J, Wynne J F, Eclov N C W, Modlin L A, Liu C L, Neal J W, Wakelee H A, Merritt R E, Shrager J B, Loo W L Jr., Alizadeh A A, Diehn M. Nat. Med., 2014, 20: 548.

[3] Dai Y, Huang S, Tang M, Lv T Y, Hu C X, Tan Y H, Xu Z M, Yin Y B. Lupus, 2007, 16: 936.

[4] Thum T, Condorelli G. Circ. Res., 2015, 116: 751.

[5] Rodriguez M M, Linnes J C, Fan A, Ellenson C K, Pollock N R, Klapperich C M. Anal. Chem., 2015, 87: 7872.

[6] Sullenger B A, Gilboa E. Nature, 2002, 418: 252.

[7] Shi C, Shen X T, Niu S Y, Ma C P. J. Am. Chem. Soc., 2015, 137: 13804.

[8] Friedman R C, Farh K K H, Burge C B, Bartel D P. Genome Res., 2009, 19: 92.

[9] Yeung M L, Bennasser Y, Jeang K T. Curr. Med. Chem., 2007, 14: 191.

[10] Sawyers C L. Nature, 2008, 452: 548.

[11] Iorio M V, Croce C M. Mol. Med., 2012, 4: 143.

[12] Liu C Y, Wen J, Meng Y B, Zhang K L, Zhu J L, Ren Y, Qian X M, Yuan X B, Lu Y F, Kang C S. Adv. Mater., 2015, 27: 292.

[13] Huang F J, Xia F. Sci. Bull., 2017, 62: 312.

[14] Silahtaroglu A N, Nolting D, Dyrskjøt L, Berezikov E, Møller M, Tommerup N, Kauppinen S. Nat. Protoc., 2007, 2: 2520.

[15] Jin Z W, Geißler D, Qiu X, Wegner KD, Hildebrandt N. Angew. Chem. Int. Ed., 2015, 54: 10024.

[16] Causa F, Aliberti A, Cusano A M, Battista E, Netti P A. J. Am. Chem. Soc., 2015, 137: 1758.

[17] Oishi M, Sugiyama S. Small, 2016, 12: 5153.

[18] Dong J, Chen G Y, Wang W, Huang X, Peng H P, Pu Q L, Du F, Cui X, Deng Y, Tang Z. Anal. Chem., 2018, 90: 7107.

[19] Wu H, Liu Y L, Wang H Y, Wu J, Zhu F F, Zou P. Biosens. Bioelectron., 2016, 81: 303.

[20] Yu Y Y, Chen Z G, Shi L J, Yang F, Pan J B, Zhang B B, Sun D P. Anal. Chem., 2014, 86: 8200.

[21] Koo K M, Carrascosa L G, Shiddiky M J A, Trau M. Anal. Chem., 2016, 88: 2000.

[22] Huang F J, Lin M H, Duan R L, Lou X D, Xia F, Willner I. Nano Lett., 2018, 18: 5116.

[23] Miao P, Zhang T, Xu J H, Tang Y G. Anal. Chem., 2018, 90: 11154.

[24] Bi S, Zhang J L, Hao S Y, Ding C F, Zhang S S. Anal. Chem., 2011, 83: 3696.

[25] Wang Q, Yin B C, Ye B C. Biosens. Bioelectron, 2016, 80: 366.

[26] Pavlov V, Xiao Y, Gill R, Dishon A, Kotler M, Willner I. Anal. Chem., 2004, 76: 2152.

[27] Šípová H, Zhang S L, Dudley A M, Galas D, Wang K, Homola J. Anal. Chem., 2010, 82: 10110.

[28] Liu R J, Wang Q, Li Q, Yang X H, Wang K, Nie W Y. Biosens. Bioelectron., 2017, 87: 433.

[29] Wang Q, Li Q, Yang X H, Wang K M, Du S S, Zhang H, Nie Y J. Biosens. Bioelectron., 2016, 77: 1001.

[30] Zhao H Y, Wang L, Zhu J, Wei H P, Jiang W. Talanta, 2015, 138: 163.

[31] Yin B C, Liu Y Q, Ye B C. J. Am. Chem. Soc., 2012, 134: 5064.

[32] Qiu X, Hildebrandt N. ACS Nano, 2015, 9: 8449.

[33] Degliangeli F, Kshirsagar P, Brunetti V, Pompa P P, Fiammengo R. J. Am. Chem. Soc., 2014, 136: 2264.

[34] Dong H F, Jin S, Ju H X, Hao K H, Xu L P, Lu H T, Zhang X J. Anal. Chem., 2012, 84: 8670.

[35] Yang L, Liu C H, Ren W, Li Z P. ACS Appl. Mater. Interfaces., 2012, 4: 6450.

[36] Ou X W, Zhan S S, Sun C L, Cheng Y, Wang X D, Liu B F, Zhai T Y, Lou X D, Xia F. Biosens. Bioelectron., 2019, 124: 199.

[37] Min X H, Zhang M S, Huang F J, Lou X D, Xia F. ACS Appl. Mater. Interfaces., 2016, 8: 8998.

[38] Min X H, Zhuang Y, Zhang Z Y, Jia Y M, Hakeem A, Zheng F X, Cheng Y, Tang B Z, Lou X D, Xia F. ACS Appl. Mater. Interfaces., 2015, 7: 16813.

[39] Min X H, Xia L, Zhuang Y, Wang X D, Du J, Zhang X J, Lou X D, Xia F. Sci. Bull., 2017, 62: 997.

[40] Wang L D, Deng R J, Li J H. Chem. Sci., 2015, 6: 6777.

[41] Thomson J M, Parker J, Perou C M, Hammond S M. Nat. Methods., 2004, 1: 47.

[42] Válóczi A, Hornyik C, Varga N, Burgyán J, Kauppinen S, Havelda Z. Nucleic Acids Res., 2004, 32: e175.

[43] Gasic E V, Wu R M, Wood M, Walton E F, Hellens R P. Plant Methods, 2007, 3: 12.

[44] Chen C F, Ridzon D A, Broomer A J, Zhou Z H, Lee D H, Nguyen J T, Barbisin M, Xu N L, Mahuvakar V R, Andersen M R, Lao K Q, Livak K L, Guegler K J. Nucleic Acids Res., 2005, 33: e179.

[45] Liu N N, Huang F J, Lou X D, Xia F. Sci. China Chem., 2017, 60: 311.

[46] Song S P, Liang Z Q, Zhang J, Wang L H, Li G X, Fan C H. Angew. Chem. Int. Ed., 2009, 48: 8670.

[47] Ge Z L, Lin M H, Wang P, Pei H, Yan J, Shi J Y, Huang Q, He D N, Fan CH, Zuo X L. Anal. Chem., 2014, 86: 2124.

[48] Yin B C, Liu Y Q, Ye B C. J. Am. Chem. Soc., 2012, 134: 5064.

[49] Shi C, Liu Q, Ma C P, Zhong W W. Anal. Chem., 2014, 86: 336.

[50] Jiang Y, Li B L, Milligan J N, Bhadra S, Ellington A D. J. Am. Chem. Soc., 2013, 135: 7430.

[51] Xu Z Q, Liao L L, Chai Y Q, Wang H J, Yuan R. Anal. Chem., 2017, 89: 8282.

[52] Lizardi P M, Huang X H, Zhu Z R, Ward P B, Thomas D C, Ward D C. Nat. Genet., 1998, 19: 225.

[53] Schweitzer B, Roberts S, Grimwade B, Shao W P, Wang M M, Fu Q, Shu Q P, Laroche L, Zhou Z M, Tchernev V T, Christiansen J, Velleca M, Kingsmore S F. Nat. Biotechnol., 2002, 20: 359.

[54] Schweitzer B, Wiltshire S, Lambert J, O’Malley S, Kukanskis K, Zhu Z R, Kingsmore S F, Lizardi P M, Ward D C. PNAS, 2000, 97: 10113.

[55] Bi S, Zhang Z P, Zhu J J. Chem. Sci., 2013, 4: 1858.

[56] Zhao Y X, Qi L, Chen F, Dong Y H, Kong Y, Wu Y Y, Fan C H. Chem. Commun., 2012, 48: 3354.

[57] Yin P, Choi H M T, Calvert C R, Pierce N A. Nature, 2008, 451: 318.

[58] Zheng A X, Wang J R, Li J, Song X R, Chen G R, Yang H H. Biosens. Bioelectron., 2012, 36: 217.

[59] Hou T, Wang X Z, Liu X J, Lu T T, Liu S F, Li F. Anal. Chem., 2014, 86: 884.

[60] Dirks R M, Pierce N A. Proc. Natl. Acad. Sci. USA, 2004, 101: 15275.

[61] Huang R C, Chiu W J, Li Y J, Huang C C. ACS Appl. Mater. Interfaces, 2014, 6: 21780.

[62] Sherman W B, Seeman N C. Nano Lett., 2004, 4: 1203.

[63] Shin J S, Pierce N A. J. Am. Chem. Soc., 2004, 126: 10834.

[64] Jung C, Allen P B, Ellington A D. ACS Nano, 2017, 11: 8047.

[65] Bath J, Green S J, Turberfield A J. Angew. Chem. Int. Ed., 2005, 44: 4358.

[66] Tian Y, He Y, Chen Y, Yin P, Mao C. Angew. Chem. Int. Ed., 2005, 117: 4429.

[67] O’Donovan P, Perrett C M, Zhang X H, Montaner B, Xu Y Z, Harwood C A, McGregor J M, Walker S L, Hanaoka F, Karran P. Science, 2005, 309: 1871.

[68] You M X, Chen Y, Zhang X B, Liu H P, Wang R W, Wang K L, Williams K R, Tan W H. Angew. Chem. Int. Ed., 2012, 124: 2507.

[69] Wang L D, Deng R J, Li J H. Chem. Sci., 2015, 6: 6777.

[70] Cai S X, Chen M, Liu M M, He W H, Liu Z J, Wu D Z, Xia Y K, Yang H H, Chen J H. Biosens. Bioelectron., 2016, 85: 184.

[71] Shlyahovsky B, Li Y, Lioubashevski O, Elbaz J, Willner I. ACS Nano, 2009, 3: 1831.

[72] He Y, Liu D R. Nature Nanotech., 2010, 5: 778.

[73] Shin J S, Pierce N A. J. Am. Chem. Soc., 2004, 126: 10834.

[74] Thubagere A J, Li W, Johnson R F, Chen Z, Doroudi S, Lee Y L, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L. Science, 2017, 357: eaan6558.

[75] Ge J, Zhang L L, Liu S J, Yu R Q, Chu X. Anal. Chem., 2014, 86: 1808.

[76] Deng R J, Tang L H, Tian Q Q, Wang Y, Lin L, Li J H. Angew. Chem. Int. Ed., 2014, 53: 2389.

[77] Zhang Z, Wang Y Y, Zhang N B, Zhang S S. Chem. Sci., 2016, 7: 4184.

[78] Tian W M, Li P J, He W L, Liu C H, Li Z P. Biosens. Bioelectron., 2019, 128: 17.

[79] Wei Q M, Huang J, Li J, Wang J L, Yang X H, Liu JB, Wang K M. Chem. Sci., 2018, 9: 7802.

[80] Yue S Z, Song X Y, Song W L, Bi S. Chem. Sci., 2019, 10: 1651.

[81] Li D X, Wu Y L, Gan C F, Yuan R, Xiang Y. Nanoscale, 2018, 10: 17623.

[82] Liu H Y, Tian T, Zhang Y H, Ding L H, Yu J H, Yan M. Biosens. Bioelectron., 2017, 89: 710.

[83] Zhang Y, Chen Z W, Tao Y, Wang Z Z, Ren J S, Qu X G. Chem. Commun., 2015, 51: 11496.

[84] Li L, Feng J, Liu H Y, Li Q L, Tong L L, Tang B. Chem. Sci., 2016, 7: 1940.

[85] Li S Y, Zhang F, Chen X M, Cai C Q. Sensor Actuat B: Chem., 2018, 263: 87.

[86] Qu X M, Xiao M S, Li F, Lai W, Li L, Zhou Y, Lin C L, Li Q, Ge ZL, Wen Y L, Pei H, Liu G. ACS Appl. Bio. Mater., 2018, 1: 859.

[87] Liang C P, Ma C Q, Liu H, Guo X G, Yin B C, Ye B C. Angew. Chem. Int. Ed., 2017, 56: 9077.