Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation

doi:10.1007/s40242-022-2124-8

Abstract

Abstract: Proteins play a central role in all domains of life, and precise regulation of their activity is essential for understanding the related biological processes and therapeutic functions. Nucleic acid aptamers, the molecular recognition components derived from systematic evolution of ligands by exponential enrichment(SELEX), can specifically identify proteins with antibody-like recognition characteristics and help to regulate their activity. This minireview covers the SELEX-based selection of protein-binding aptamers, membrane protein analytical techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins, including membrane receptors and non-membrane proteins(thrombin as a model), as well as the potential challenges and prospects regarding aptamer-mediated protein manipulation, aiming to supply some useful information for researchers in this field.

Key words: Aptamer, Protein activity regulation, Systematic evolution of ligands by exponential enrichment(SELEX), Membrane receptor, Thrombin

HU Lingling, LIU Ke, REN Guolan, LIANG Jiangong, WU Yuan. Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation[J]. Chemical Research in Chinese Universities, 2022, 38(4): 894-901.

References

[1] Qin X. F., Yu C. M., Wei J., Li L., Zhang C. W., Wu Q., Liu J. H., Yao S. Q., Huang W., Adv. Mater., 2019, 31, 1902791
[2] Kuenzi B. M., Remsing Rix L. L., Stewart P. A., Fang B., Kinose F., Bryant A. T., Boyle T. A., Koomen J. M., Haura E. B., Rix U.,Nat. Chem. Biol., 2017, 13, 1222
[3] Fan Y. F., Zhang W., Zeng L., Lei Z. N., Cai C. Y., Gupta P., Yang D. H., Cui Q., Qin Z. D., Chen Z. S., Trombetta L. D., Cancer Lett., 2018, 421, 186
[4] Cerchia C., Lavecchia A., Curr. Med. Chem., 2017, 24, 2312
[5] Hung M., C., Link W., J. Cell Sci., 2011, 124, 3381
[6] Gorostiza P., Isacoff E. Y., Science, 2008, 322, 395
[7] Kramer R. H., Mourot A., Adesnik H.,Nat. Neurosci., 2013, 16, 816
[8] Voss S., Klewer L., Wu Y. W.,Curr. Opin. Chem. Biol., 2015, 28, 194
[9] Liu Q., Tucker C. L., Curr. Opin. Chem. Biol., 2017, 40, 17
[10] Beyer H. M., Naumann S., Weber W., Radziwill G., Biotechnology Journal, 2015, 10, 273
[11] Kim K. S., Seeley R. J., Sandoval D. A., Nat. Rev. Neurosci., 2018, 19, 185
[12] Mogaki R., Okuro K., Ueki R., Sando S., Aida T.,J. Am. Chem. Soc., 2019, 141, 8035
[13] Cho M. H., Lee E. J., Son M., Lee J. H., Yoo D., Kim J. W., Park S. W., Shin J. S., Cheon J.,Nat. Mater., 2012, 11, 1038
[14] Qiao S. L., Wang Y., Lin Y. X., An H. W., Ma Y., Li L. L., Wang L., Wang H., ACS Appl.Mater. Interfaces, 2016, 8, 17016
[15] Schneider H., Yanakieva D., Macarrón A., Deweid L., Becker B., Englert S., Avrutina O., Kolmar H., ChemBioChem, 2019, 20, 3006
[16] Sun M., Liu S., Wei X. Y., Wan S., Huang M. J., Song T., Lu Y., Weng X. N., Lin Z., Chen H. L., Song Y. L., Yang C. Y., Angew. Chem. Int. Ed., 2021, 60, 10431
[17] Long S. B., Long M. B., White R. R., Sullenger B. A., RNA, 2008, 14, 2504
[18] Gelinas A. D., Davies D. R., Edwards T. E., Rohloff J. C., Carter J. D., Zhang C., Gupta S., Ishikawa Y., Hirota M., Nakaishi Y., Jarvis T. C., Janjic N.,J. Biol. Chem., 2014, 289, 8720
[19] Jarvis T. C., Davies D. R., Hisaminato A., Resnicow D. I., Gupta S., Waugh S. M., Nagabukuro A., Wadatsu T., Hishigaki H., Gawande B., Zhang C., Wolk S. K., Mayfield W. S., Nakaishi Y., Burgin A. B., Stewart L. J., Edwards T. E., Gelinas A. D., Schneider D. J., Janjic N., Structure, 2015, 23, 1293
[20] Kahsai A. W., Wisler J. W., Lee J., Ahn S., Cahill Iii T. J., Dennison S. M., Staus D. P., Thomsen A. R. B., Anasti K. M., Pani B., Wingler L. M., Desai H., Bompiani K. M., Strachan R. T., Qin X., Alam S. M., Sullenger B. A., Lefkowitz R. J.,Nat. Chem. Biol., 2016, 12, 709
[21] Lupu L. M., Wiegand P., Holdschick D., Mihoc D., Maeser S., Rawer S., Völklein F., Malek E., Barka F., Knauer S., Uth C., Hennermann J., Kleinekofort W., Hahn A., Barka G., Przybylski M.,Int. J. Mol. Sci., 2021, 22, 12832
[22] Wu J., Liang L., Zhang M., Zhu R., Wang Z., Yin Y., Yin B., Weng T., Fang S., Xie W., Wang L., Wang D., ACS Appl. Mater. Interfaces, 2022, 14, 12077
[23] Ni S. J., Zhuo Z. J., Pan Y. F., Yu Y. Y., Li F. F., Liu J., Wang L. Y., Wu X. Q., Li D. J., Wan Y. Y., Zhang L. H., Yang Z. J., Zhang B. T., Lu A. P., Zhang G., ACS Appl. Mater. Interfaces, 2021, 13, 9500
[24] Tran T. T. T., Delgado A., Jeong S., BioChip Journal, 2021, 15, 109
[25] Liu S., Xu Y.X., Jiang X., Tan H., Ying B.W., Biosens. Bioelectron., 2022, 208, 114168
[26] Tuerk C., Gold L., Science, 1990, 249, 505
[27] Ellington A. D., Szostak J. W., Nature, 1990, 346, 818
[28] Wu Y., Zhang L. Q., Cui C., Cansiz S., Liang H., Wu C. C., Teng Y. T., Chen W. J., Liu Y., Hou W. J., Zhang X. B., Tan W. H., J. Am. Chem. Soc., 2018, 140, 2
[29] Fan J., Wang H. H., Xie S., Wang M., Nie Z., ChemBioChem, 2020, 21, 282
[30] Zhang K. X., Gao H., Deng R. J., Li J. H.,Angew. Chem. Int. Ed., 2019, 58, 4790
[31] Bayat P., Nosrati R., Alibolandi M., Rafatpanah H., Abnous K., Khedri M., Ramezani M., Biochimie, 2018, 154, 132
[32] Huang C. J., Lin H. I., Shiesh S. C., Lee G. B., Biosens. Bioelectron., 2010, 25, 1761
[33] Liu Y., Peng C., Zhang H., Li J., Ou H., Sun Y., Wen C., Qi D., Hu X., Wu E., Tan W., Bioact. Mater., 2022, 12, 278
[34] Camorani S., Crescenzi E., Fedele M., Cerchia L., Biochim. Biophys. Acta, 2018, 1869, 263
[35] Kamatkar N., Levy M., Hébert J. M., Mol. Ther. Nucleic. Acids, 2019, 17, 530
[36] Zumrut H. E., Ara M. N., Maio G. E., Van N. A., Batool S., Mallikaratchy P. R., Anal. Biochem., 2016, 512, 1
[37] Hahn U.,Biochimie, 2018, 145, 84
[38] Hunter T.,Cell, 2000, 100, 113
[39] Lemmon M. A., Schlessinger J.,Cell, 2010, 141, 1117
[40] Christopoulos A.,Nat. Rev. Drug Discov., 2002, 1, 198
[41] Zhang Z. J., Liu J. W.,ACS Appl. Mater. Interfaces, 2016, 8, 6371
[42] Qu L., Qiao X. Y., Qi F., Nishida N., Hoshino T.,J. Chem. Inf. Model., 2021, 61, 2396
[43] Kang S., Hah S. S.,Bioconjug. Chem., 2014, 25, 1421
[44] Tang X. C., Feng C., Pan Q. H., Sun F. Y., Zhu X. L.,Trends Anal. Chem., 2021, 145, 116456
[45] Jia H. R., Zhang Z., Fang X. N., Jiang M., Chen M., Chen S. S., Gu K. D., Luo Z. F., Wu F. G., Tan W. H.,Mater. Today Nano, 2022, 100188
[46] Yang W., Nan H. X., Xu Z. X., Huang Z. X., Chen S., Li J. Y., Li J., Yang H. H., Anal. Chem., 2021, 93, 12265
[47] Wang L. P., Li W., Sun J., Zhang S.Y., Yang S., Li J. Y., Li J., Yang H. H., Anal. Chem., 2018, 90, 14433
[48] Chen X. G., Qiu L. P., Cai R., Cui C., Li L., Jiang J. H., Tan W. H., ACS Appl. Mater. Interfaces, 2020, 12, 37845
[49] Ambrosetti E., Bernardinelli G., Hoffecker I., Hartmanis L., Kiriako G., de Marco A., Sandberg R., Högberg B., Teixeira A. I.,Nat. Nanotechnol., 2021, 16, 85
[50] Maruyama I. N., Cells, 2014, 3, 304
[51] Cohen P., Nat. Rev. Drug Discov., 2002, 1, 309
[52] Trusolino L., Bertotti A., Comoglio P. M.,Nat. Rev. Mol. Cell Biol., 2010, 11, 834
[53] Wang L. P., Liang H., Sun J., Liu Y. C., Li J. Y., Li J. Y., Li J., Yang H. H., J. Am. Chem. Soc., 2019, 141, 12673
[54] Chen S., Xu Z., Li S., Liang H., Zhang C., Wang Z., Li J., Li J., Yang H., Angew. Chem. Int. Ed., 2022, 61, e202113795
[55] Zhang J. H., Qiu Z. Y., Fan J. H., He F., Kang W. Y., Yang S. H., Wang H. H., Huang J., Nie Z.,Angew. Chem. Int. Ed., 2021, 60, 6733
[56] Manandhar M., Chun E., Romesberg F. E.,J. Am. Chem. Soc., 2021, 143, 4859
[57] Padroni G., Withers J. M., TaladrizS. A., Reichenbach L. F., Parkinson J. A., Burley G. A.,J. Am. Chem. Soc., 2019, 141, 9555
[58] Zumrut H., Yang Z., Williams N., Arizala J., Batool S., Benner S. A., Mallikaratchy P., Biochemistry, 2020, 59, 552
[59] Sefah K., Yang Z., Bradley K. M., Hoshika S., Jiménez E., Zhang L., Zhu G., Shanker S., Yu F., Turek D., Tan W., Benner S. A.,Proc. Natl. Acad. Sci., 2014, 111, 1449
[60] Zhang L. Q., Yang Z. Y., Sefah K., Bradley K. M., Hoshika S., Kim M. J., Kim H. J., Zhu G., Jiménez E., Cansiz S., Teng I. T., Champanhac C., McLendon C., Liu C., Zhang W., Gerloff D. L., Huang Z., Tan W., Benner S. A.,J. Am. Chem. Soc., 2015, 137, 6734
[61] Gasse C., Zaarour M., Noppen S., Abramov M., Marlière P., Liekens S., De Strooper B., Herdewijn P., ChemBioChem, 2018, 19, 754
[62] Tan J., Zhao M. M., Wang J. M., Li Z. H., Liang L., Zhang L. Q., Yuan Q., Tan W. H.,Angew. Chem. Int. Ed., 2019, 58, 1621
[63] Chen G. C., Cao Y. H., Tang Y. X., Yang X., Liu Y. Y., Huang D. H., Zhang Y. J., Li C. Y., Wang Q. B.,Adv. Sci., 2020, 7, 1903783
[64] Chen S., Li J., Liang H., Lin X. H., Li J., Yang H. H., Chem. Eur. J., 2018, 24, 15988
[65] Ueki R., Hayashi S., Tsunoda M., Akiyama M., Liu H., Ueno T., Urano Y., Sando S.,Chem. Commun., 2021, 57, 5969
[66] Wang M., He F., Li H., Yang S., Zhang J., Ghosh P., Wang H. H., Nie Z., Nano Lett., 2019, 19, 2603
[67] Hong G. S., Antaris A. L., Dai H. J.,Nat. Biomed. Eng., 2017, 1, 0010
[68] Yuan Q., Wu Y., Wang J., Lu D. Q., Zhao Z. L., Liu T., Zhang X. B., Tan W. H., Angew. Chem., 2013, 125, 14215
[69] Lei Z. H., Sun C. X., Pei P. P., Wang S. F., Li D. D., Zhang X., Zhang F., Angew. Chem. Int. Ed., 2019, 58, 8166
[70] Zhong Y. T., Ma Z. R., Wang F. F., Wang X., Yang Y. J., Liu Y. L., Zhao X., Li J. C., Du H. T., Zhang M. X., Cui Q. H., Zhu S. J., Sun Q. C., Wan H., Tian Y., Liu Q., Wang W. Z., Garcia K. C., Dai H. J.,Nat. Biotechnol., 2019, 37, 1322
[71] Lino M. M., Simões S., Vilaça A., Antunes H., Zonari A., Ferreira L., ACS Nano, 2018,12, 5207
[72] Dai W. H., Dong H. F., Guo K. K., Zhang X. J., Chem. Sci., 2018, 9, 1753
[73] Scott J. D., Pawson T., Science, 2009, 326, 1220
[74] Tang W., Hu J. H., Liu D. R., Nat. Commun., 2017, 8, 15939
[75] Amero P., Lokesh G. L. R., Chaudhari R. R., Cardenas Z. R., Schubert T., Attia Y. M., Montalvo G. E., Elsayed A. M., Ivan C., Wang Z., Cristini V., Franciscis V. D., Zhang S., Volk D. E., Mitra R., Rodriguez A. C., Sood A. K., Lopez B. G.,J. Am. Chem. Soc., 2021, 143, 7655
[76] Riccardi C., Napolitano E., Platella C., Musumeci D., Montesarchio D., Pharmacol. Ther., 2021, 217, 107649
[77] Griffin L. C., Tidmarsh G. F., Bock L. C., Toole J. J., Leung L. L., Blood, 1993, 81, 3271
[78] Musumeci D., Montesarchio D.,Pharmacol. Ther., 2012, 136, 202
[79] Huo S. D., Zhao P. K., Shi Z. Y., Zou M. C., Yang X. T., Warszawik E., Loznik M., Göstl R., Herrmann A.,Nat.Chem., 2021, 13, 131
[80] Chen Y. J., Mellot G., van Luijk D., Creton C., Sijbesma R. P., Chem. Soc. Rev., 2021, 50, 6659
[81] Zhao P. K., Huo S. D., Fan J. L., Chen J. L., Kiessling F., Boersma A. J., Göstl R., Herrmann A., Angew. Chem. Int. Ed., 2021, 60, 14707
[82] Kuai H. L., Zhao Z. L., Mo L. T., Liu H., Hu X. X., Fu T., Zhang X. B., Tan W. H.,J. Am. Chem. Soc., 2017, 139, 9128
[83] Mao Y., Gu J., Chang D. R., Wang L., Yao L. L., Ma Q. H., Luo Z. F., Qu H., Li Y. F., Zheng L.,Nucleic Acids Res., 2020, 48, 10680
[84] Shiang Y. C., Huang C. C., Wang T. H., Chien C. W., Chang H. T., Adv. Funct. Mater., 2010, 20, 3175
[85] Shiang Y. C., Hsu C. L., Huang C. C., Chang H. T.,Angew. Chem. Int. Ed., 2011, 50, 7660
[86] Wang J., Wei Y. R., Hu X. X., Fang Y. Y., Li X. Y., Liu J., Wang S. F., Yuan Q.,J. Am. Chem. Soc., 2015, 137, 10576
[87] Riccardi C., Russo K. I., Musumeci D., Morvan F., Meyer A., Vasseur J. J., Paduano L., Montesarchio D.,ACS Appl. Mater. Interfaces, 2017, 9, 35574
[88] Liu K., Jin Y., Liang J. G., Wu Y., Chem. J. Chinese Universities, 2021, 42(11), 3477