A method for increasing the efficiency of selection of aptamers to cellular receptors

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Resumo

A method has been proposed to increase the efficiency of selection of aptamers to cellular receptors by the cell-Selex method, in particular to the receptor tyrosine kinase c-KIT. The use of Tween 20 in buffer solutions in concentrations not exceeding 0.01%, as well as trypsinolysis of surface proteins at the stage of elution of the combinatorial library of oligonucleotides bound to the cell surface, led to an increase in the specificity of aptamers and a decrease in nonspecific sorption according to the results of fluorescence microscopy, thermofluorimetric analysis and high-precision sequencing.

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Sobre autores

V. Kuznetsova

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Autor responsável pela correspondência
Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

T. Lebedev

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

V. Shershov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

G. Shtylev

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

I. Shishkin

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

R. Miftahov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

V. Butvilovskaya

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

I. Grechishnikova

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

О. Zasedateleva

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

А. Chudinov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: kuzneimb@gmail.com
Rússia, ul. Vavilova 32, Moscow, 119991

Bibliografia

  1. Liu H., Chen X., Focia P., He X. // EMBO J. 2007. V. 26. P. 891–901. https://doi.org/10.1038/sj.emboj.7601545
  2. Camorani S., Crescenzi E., Fedele M., Cerchia L. // Biochim. Biophys. Acta Rev. Cancer. 2018. V. 1869. P. 263–277. https://doi.org/10.1016/j.bbcan.2018.03.003
  3. Рулина А.В., Спирин П.В., Прасолов В.С. // Усп. биол. химии. 2010. T. 50. C. 349–386.
  4. Bibi S., Langenfeld F., Jeanningros S., Brenet F., Soucie E., Hermine O., Damaj G., Dubreuil P., Arock M. // Immunol. Allergy Clin. North Am. 2014. V. 34. P. 239–262. https://doi.org/10.1016/j.iac.2014.01.009
  5. Kövecsi A., Jung I., Szentirmay Z., Bara T., Bara T., Jr., Popa D., Gurzu S. // Oncotarget. 2017. V. 8. P. 55950– 55957. https://doi.org/10.18632/oncotarget.19116
  6. Sankhala K.K. // Expert Opin. Investig. Drugs. 2017. V. 26. P. 427–443. https://doi.org/10.1080/13543784.2017.1303045
  7. Hicke B.J., Marion C., Chang Y.-F., Gould T., Lynott C.K., Parma D., Schmidt P.G., Warren S. // J. Biol. Chem. 2001. V. 276. P. 48644–48654. https://doi.org/10.1074/jbc.m104651200
  8. Zhang Y., Chen Y., Han D., Ocsoy I., Tan W. // Bioanalysis. 2010. V. 2. P. 907–918. https://doi.org/10.4155/bio.10.46
  9. Wang C., Zhang M., Yang G., Zhang D., Ding H., Wang H., Fan M, Shen B., Shao N. // J. Biotechnol. 2003.V. 102. P. 15–22. https://doi.org/10.1016/s0168-1656(02)00360-7
  10. Cerhia L., Hamm J., Libri D., Tavitian B., Franciscis B. // FEBS Lett. 2002. V. 528. P. 12–16. https://doi.org/10.1016/s0014-5793(02)03275-1
  11. Blank M., Weinschenk T., Priemer M., Schluesener H. // J. Biol. Chem. 2001. V. 276. P. 16464–16468. https://doi.org/10.1074/jbc.m100347200
  12. Daniels D.A., Chen H., Hicke B.J., Swiderek K.M., Gold L. // Proc. Natl. Acad. Sci. USA. 2003. V. 100. P. 15416–15421. https://doi.org/10.1073/pnas.2136683100
  13. Laos R., Thomson J.M., Benner S.A. // Front. Microbiol. 2014. V. 5. P. 565. https://doi.org/10.3389/fmicb.2014.00565
  14. Tuerk C., Gold L. // Science. 1990. V. 249. P. 505–510. https://doi.org/10.1126/SCIENCE.2200121
  15. Ellington A.D., Szostak J.W. // Nature. 1990. V. 346. P. 818–822. https://doi.org/10.1038/346818a0
  16. Zhu G., Zhang H., Jacobson O., Wang Z., Chen H., Yang X., Niu G., Chen X. // Bioconj. Chem. 2017. V. 28. P. 1068–1075. https://doi.org/10.1021/acs.bioconjchem.6b00746
  17. Wang D.L., Songc Y.L., Zhu Z., Li X.L., Zou Y., Yang H.T., Wang J.J., Yao P.S., Pan R.J., Yang C.J., Kang D.Z. // Biochem. Biophys. Res. Commun. 2014. V. 453. P. 681–685. https://doi.org/10.1016/j.bbrc.2014.09.023
  18. Hollenstein M. // Molecules. 2012. V. 17. P. 13569– 13591. https://doi.org/10.3390/molecules171113569
  19. Gold L., Ayers D., Bertino J, Bock C., Bock A., Brody E.N., Carter J., Dalby A.B., Eaton B.E., Fitzwater T., Flather D., Forbes A., Foreman T., Fowler C., Gawande B., Goss M., Gunn M., Gupta S., Halladay D., Heil J., Heilig J., Hicke B., Husar G., Janjic N., Jarvis T., Jennings S., Katilius E., Keeney T.R., Kim N., Koch T.H., Kraemer S., Kroiss L., Le N., Levine D., Lindsey W., Lollo B., Mayfield W., Mehan M., Mehler R., Nelson S.K., Nelson M., Nieuwlandt D., Nikrad M., Ochsner U., Ostroff R.M., Otis M., Parker T., Pietrasiewicz S., Resnicow D.I., Rohloff J., Sanders G., Sattin S., Schneider D., Singer B., Stanton M., Sterkel A., Stewart A., Stratford S., Vaught J.D., Vrkljan M., Walker J.J., Watrobka M., Waugh S., Weiss A., Wilcox S.K., Wolfson A., Wolk S.K., Zhang C., Zichi D. // PLoS One. 2010. V. 5. P. e15004. https://doi.org/10.1371/journal.pone.0015004
  20. Sefah K., Shangguan D., Xiong X., O’Donoghue M.B., Tan W. // Nat. Protoc. 2010. V. 5. P. 1169–1185. https://doi.org/10.1038/nprot.2010.66
  21. Вагапова Э.Р., Лебедев Т.Д., Попенко В.И., Леонова О.Г., Спирин П.В., Прасолов В.С. // Act. Nat. 2020. Т. 12. C. 51–55. https://doi.org/10.32607/actanaturae.10938
  22. Lebedev T.D., Vagapova E.R., Popenko V.I., Leonova O.G., Spirin P.V., Prassolov V.S. // Front. Oncol. 2019. V. 9. P. 1046. https://doi.org/10.3389/fonc.2019.01046
  23. Meyer S., Maufort J.P., Nie J., Stewart R., McIntosh B.E., Conti L.R., Ahmad K.M., Soh H.T., Thomson J.A. // PLoS One. 2013. V. 8. P. e71798. https://doi.org/10.1371/journal.pone.0071798
  24. Chudinov A.V., Shershov V.E., Pavlov A.S., Volkova O.S., Kuznetsova V.E., Zasedatelev A.S., Lapa S.A. // Russ. J. Bioorg. Chem. 2020. V. 46. P. 856–858. https://doi.org/10.1134/S1068162020050064
  25. Vasiliskov V.A., Lapa S.A., Kuznetsova V.E., Surzhikov S.A., Shershov V.E., Spitsyn M.A., Guseinov T.O., Miftahov R.A., Zasedateleva O.A., Lisitsa A.V., Radko S.P., Zasedatelev A.S., Timofeev E.N., Chudinov A.V. // Russ. J. Bioorg. Chem. 2019. V. 45. P. 221–223. https://doi.org/10.1134/s1068162019030063
  26. Chudinov A.V., Kiseleva Y.Y., Kuznetsova V.E., Shershov V.E., Spitsyn M.A., Guseinov T.O., Lapa S.A., Timofeev E.N., Archakov A.I., Lisitsa A.V., Radko S.P., Zasedatelevet A.S. // Mol Biol. 2017. V. 51. P. 474–482. https://doi.org/10.1134/S0026893317030025
  27. Lapa S.A., Pavlov A.S., Kuznetsova V.E., Shershov V.E., Spitsyn M.A., Guseinov T.O., Radko S.P., Zasedatelev A.S., Lisitsa A.V., Chudinov A.V. // Mol. Biol. 2019. V. 53. P. 460–469. https://doi.org/10.1134/S0026893319030099
  28. Lyu Y., Chen G., Shangguan D., Zhang L., Wan S., Wu Y., Zhang H., Duan L., Liu C., You M., Wang J., Tan W. // Theranostics. 2016. V. 6. P. 1440–1452. https://doi.org/10.7150/thno.15666
  29. Cerchia L., Duconge F., Pestourie C., Boulay J., Aissouni Y. // PLoS Biol. 2005. V. 3. P. e123. https://doi.org/10.1371/journal.pbio.0030123
  30. McKeague M., Derosa M.C. // J. Nucleic Acids. 2012. V. 2012. P. 748913. https://doi.org/10.1155/2012/748913
  31. Ouellet E., Foley J.H., Conway E.M., Haynes C. // Biotechnol. Bioeng. 2015. V. 112. P. 1506–1522. https://doi.org/10.1002/bit.25581
  32. Kissmann A.K., Bolotnikov G., Li R., Müller F., Xing H., Krämer M., Gottschalk K.E., Andersson J., Weil T., Rosenau F. // Appl. Microbiol. Biotechnol. 2024. V. 108. P. 284. https://doi.org/10.1007/s00253-024-13085-7
  33. Zhang H.L., Lv C., Li Z.H., Jiang S., Cai D., Liu S.S., Wang T., Zhang K.H. // Front. Chem. 2023. V. 11. P. 1144347. https://doi.org/10.3389/fchem.2023.1144347
  34. Ouellet E, Lagally E.T., Cheung K.C., Haynes C.A. // Biotechnology. 2014. V. 111. P. 2265–2279. https://doi.org/10.1002/bit.25294
  35. Schutze T., Arndt P., Menger M., Wochner A., Vingron M., Erdmann V., Lehrach H., Kaps Ch., Glokler J. // Nucleic Acids Res. 2009. V. 38. P. e23. https://doi.org/10.1371/journal.pone.0029604
  36. Pearson K., Doherty C., Zhang D., Becker N.A., Maher L.J. // Anal. Biochem. 2022. V. 650. P. 114712. https://doi.org/10.1016/j.ab.2022.114712
  37. Raber H.F., Kubiczek D.H., Bodenberger N., Kissmann A.K., D’souza D., Xing H., Mayer D., Xu P., Knippschild U., Spellerberg B., Weil T., Rosenau F. // Int. J. Mol. Sci. 2021. V. 22. P. 10425. https://doi.org/10.3390/ijms221910425
  38. Catuogno S., Esposito C.L. // Biomedicines. 2017. V. 5. P. 49. https://doi.org/10.3390/biomedicines5030049
  39. Flanagan Sh.P., Fogel R., Edkins A.L., Ho L., Limson J. // Anal. Methods. 2021. V. 13. P. 1191–1203. https://doi.org/10.1039/d0ay01878c
  40. Shangguan D., Meng L., Cao Z.C., Xiao Z., Fang X., Li Y., Cardona D., Witek R.P., Liu C., Tan W. // Anal. Chem. 2008. V. 80. P. 721–728. https://doi.org/10.1021/ac701962v
  41. Cherney L.T., Obrecht N.M., Krylov S.N. // Anal. Chem. 2013. V. 85. P. 4157–4164. https://doi.org/10.1021/ac400385v
  42. Mayer G., Ahmed M.S., Dolf A. // Nat. Protoc. 2010. V. 5. P. 1993–2004. https://doi.org/10.1038/nprot.2010.163
  43. Xiong L., Xia M., Wang Q., Meng Z., Zhang J., Yu G., Dong Z., Lu Y., Sun Y. // Biotechnol. Lett. 2022. V. 44. P. 777–786. https://doi.org/10.1007/s10529-022-03252-z
  44. Hua T., Zhang X., Tang B., Chang Ch., Liu G., Feng L., Yu Y., Zhang D., Hou J. // BMC Vet. Res. 2018. V. 14. P. 138. https://doi.org/10.1186/s12917-018-1457-5
  45. Zhang Y., Wu Y., Zheng H., Xi H., Ye T., Chan C.Y., Kwok C.K. // Anal. Chem. 2021. V. 93. P. 5744–5753. https://doi.org/10.1021/acs.analchem.0c04862
  46. Замай А.С., Замай Г.С., Коловская О.С., Замай Т.Н., Березовский М.В. // Патент RU2518368С1, 2012.
  47. Zhang K., Sefah K., Tang L., Zhao Z., Zhu G., Ye M., Sun W., Goodison S., Tan W. // ChemMedChem. 2012. V. 7. P. 79–84. https://doi.org/10.1002/cmdc.201100457
  48. Gu L., Yan W., Liu S., Ren W., Lyu M., Wang S. // Anal. Biochem. 2018. V. 561–562. P. 89–95. https://doi.org/10.1016/j.ab.2018.09.004

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2. Fig. 1. Electrophoretic separation of primer extension reaction products in a reaction with Kod XL DNA polymerase. Denaturing 15% PAAG (acrylamide-bisacrylamide ratio 19:1), 50°C, registration in the fluorescence range of the Cy3 dye.

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3. Fig. 2. Melting temperature curves of the amplification product after each selection cycle.

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4. Fig. 3. Non-specific sorption using the example of one round of selection (a) and using Tween 20 as part of buffer solutions (b).

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5. Fig. 4. Evaluation of the effect of Tween 20 on the viability of FDC-P1 cells using fluorescence microscopy (DAPI dye).

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6. Fig. 5. Images of non-specific sorption of a fluorescently labeled DNA library during heat treatment of cells in a buffer solution (a) and trypsinolysis of aptamers bound to the cell surface (b), obtained using fluorescence microscopy, using the example of one round of selection.

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