Abstract
Aptamers are DNA or RNA molecules that specifically bind certain targets with high affinity due to the formation of unique spatial structures. Aptamers with specified properties could be obtained from combinatorial libraries of nucleic acids by in vitro selection procedure. Here, we optimized conditions of chemical synthesis of DNA library on the automated ASM-800 DNA/RNA synthesizer. Enzymatic hydrolysis and high-throughput sequencing methods were used to analyze compositions of synthesized combinatorial libraries. The DNA library generated under the chosen conditions is characterized by the sufficiently uniform randomization and can be applied for the in vitro selection.
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REFERENCES
Vorobyeva, M., Vorobjev, P., and Venyaminova, A., Molecules, 2016, vol. 21, p. 1613.
Cowperthwaite, M.C. and Ellington, A.D., J. Mol. Evol., 2008, vol. 67, pp. 95–102.
Blind, M. and Blank, M., Mol. Ther. Nucleic Acids, 2015, vol. 4. e223.
Takahashi, M., Wu, X., Ho, M., Chomchan, P., Rossi, J.J., Burnett, J.C., and Zhou, J., Sci. Rep., vol. 6, p. 33 697.
Hall, B., Micheletti, J.M., Satya, P., Ogle, K., Pollard, J., and Ellington, A.D., Curr. Protoc. Nucleic Acid Chem., 2009, chapter 9, unit 9.2.
Fitzwater, T. and Polisky, B., Methods Enzymol., 1996, vol. 267, pp. 275–301.
Dawson, R., Elliott, D., Elliott, W., and Jones, K., Data for Biochemical Research, 3rd ed., Oxford: Clarendon, 1986.
Aird, D., Ross, M.G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D.B., Nusbaum, C., and Gnirke, A., Genome Biol., 2011, vol. 12, p. R18.
Thiel, W.H., Bair, T., Wyatt, ThielK., Dassie, J.P., Rockey, W.M., Howell, C.A., Liu, X.Y., Dupuy, A.J., Huang, L., Owczarzy, R., Behlke, M.A., McNamara, J.O., and Giangrande, P.H., Nucleic Acid Ther., 2011, vol. 21, pp. 253–263.
Takahashi, M., Wu, X., Ho, M., Chomchan, P., Rossi, J.J., Burnett, J.C., and Zhou, J., Sci. Rep., 2016, vol. 6, p. 33 697.
Davydova, A.S., Vorob’eva, M.A., Krasitskaya, V.V., Tupikin, A.E., Vorob’ev, P.E., Kabilov, M.R., Frank, L.A., and Ven’yaminova, A.G., Acta Naturae, 2017, vol. 9, p. 15.
Davydova, A., Vorobyeva, M., Bashmakova, E., Vorobjev, P., Krasheninina, O., Tupikin, A., Kabilov, M., Krasitskaya, V., Frank, L., and Venyaminova, A., Anal. Biochem., 2019, vol. 570, pp. 43–50.
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Funding
The work was supported by the Russian Scientific Foundation, project no. 16-14-10296 and by Russian State funded budget project No. АААА-А17-117020210021-7 to ICBFM SB RAS.
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Davydova, A.S., Krasheninina, O.A., Tupikin, A.E. et al. Synthesis of Random DNA Libraries for In Vitro Selection and Analysis of Their Nucleotide Composition. Russ J Bioorg Chem 45, 656–661 (2019). https://doi.org/10.1134/S1068162019060141
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DOI: https://doi.org/10.1134/S1068162019060141