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The Toolbox for Modified Aptamers
- 作者:Sergey A. Lapa ; Alexander V. Chudinov ; Edward N. Timofeev
- 关键词:Aptamer ; Molecular evolution ; SELEX ; Nucleic acids ; Nucleotides ; Polymerases ; Modification ; Non ; natural nucleoside triphosphates ; PCR ; Primer extension
- 刊名:Molecular Biotechnology
- 出版年:2016
- 出版时间:February 2016
- 年:2016
- 卷:58
- 期:2
- 页码:79-92
- 全文大小:1,041 KB
- 参考文献:1.Pinheiro, V. B., & Holliger, P. (2014). Towards XNA nanotechnology: New materials from synthetic genetic polymers. Trends in Biotechnology, 32, 321–328.CrossRef
2.Faltin, B. (2013). Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clinical Chemistry, 59, 1567–1582.CrossRef 3.Deleavey, G. F., Damha, M. J., Zengerle, R., & von Stetten, F. (2012). Designing chemically modified oligonucleotides for targeted gene silencing. Chemistry & Biology, 19, 937–954.CrossRef 4.Sun, H., & Zu, Y. (2015). A highlight of recent advances in aptamer technology and its application. Molecules, 20, 11959–11980.CrossRef 5.Tuerk, C., & Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505–510.CrossRef 6.Ellington, A. D., & Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818–822.CrossRef 7.Darmostuk, M., Rimpelova, S., Gbelcova, H., & Ruml, T. (2015). Current approaches in SELEX: An update to aptamer selection technology. Biotechnology Advances, 33, 1141–1161.CrossRef 8.Ozer, A., Pagano, J. M., & Lis, J. T. (2014). New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization. Molecular Therapy Nucleic Acids, 3, e183.CrossRef 9.Rohloff, J. C., Gelinas, A. D., Jarvis, T. C., Ochsner, U. A., Schneider, D. J., Gold, L., & Janjic, N. (2014). Nucleic acid ligands with protein-like side chains: Modified aptamers and their use as diagnostic and therapeutic agents. Molecular Therapy Nucleic Acids, 3, e201.CrossRef 10.Tolle, F., & Mayer, G. (2013). Dressed for success—applying chemistry to modulate aptamer functionality. Chemical Science, 4, 60–67.CrossRef 11.Diafa, S., & Hollenstein, M. (2015). Generation of aptamers with an expanded chemical repertoire. Molecules, 20, 16643–16671.CrossRef 12.Zhu, B., Hernandez, A., Tan, M., Wollenhaupt, J., Tabor, S., & Richardson, C. C. (2015). Synthesis of 2′-Fluoro RNA by Syn5 RNA polymerase. Nucleic Acids Research, 43, e94.CrossRef 13.Meyer, A. J., Garry, D. J., Hall, B., Byrom, M. M., McDonald, H. G., Yang, X., et al. (2015). Transcription yield of fully 2′-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Research, 43, 7480–7488.CrossRef 14.Lauridsen, L. H., Rothnagel, J. A., & Veedu, R. N. (2012). Enzymatic recognition of 2′-modified ribonucleoside 5′-triphosphates: Towards the evolution of versatile aptamers. ChemBioChem, 13, 19–25.CrossRef 15.Chen, T., & Romesberg, F. E. (2014). Directed polymerase evolution. FEBS Letters, 588, 219–229.CrossRef 16.Kunkel, T. A. (1992). DNA replication fidelity. Journal of Biological Chemistry, 267, 18251–18254. 17.Keefe, A. D., & Cload, S. T. (2008). SELEX with modified nucleotides. Current Opinion in Chemical Biology, 12, 448–456.CrossRef 18.Eckstein, F. (2014). Phosphorothioates, essential components of therapeutic oligonucleotides. Nucleic Acid Therapeutics, 24, 374–387.CrossRef 19.Yang, X., & Gorenstein, D. G. (2004). Progress in thioaptamer development. Current Drug Targets, 5, 705–715.CrossRef 20.Jung, K. H., & Marx, A. (2005). Nucleotide analogues as probes for DNA polymerases. Cellular and Molecular Life Sciences, 62, 2080–2091.CrossRef 21.Wolfe, J. L., Kawate, T., Belenky, A., & Stanton, V, Jr. (2002). Synthesis and polymerase incorporation of 50-amino-20,50-dideoxy-50-N-triphosphate nucleotides. Nucleic Acids Research, 30, 3739–3747.CrossRef 22.He, K., Porter, K. W., Hasan, A., Briley, J. D., & Shaw, B. R. (1999). Synthesis of 5-substituted 20-deoxycytidine 50-(a-P-borano)triphosphates, their incorporation into DNA and effects on exonuclease. Nucleic Acids Research, 27, 1788–1794.CrossRef 23.Darfeuille, F., Arzumanov, A., Gryaznov, S., Gait, M. J., Di Primo, C., & Toulmé, J. J. (2002). Loop-loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription. Proceedings of the National Academy of Sciences of the United States of America, 99, 9709–9714.CrossRef 24.Zaitseva, M., Kaluzhny, D., Shchyolkina, A., Borisova, O., Smirnov, I., & Pozmogova, G. (2010). Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions. Biophysical Chemistry, 146, 1–6.CrossRef 25.Kusser, W. (2000). Chemically modified nucleic acid aptamers for in vitro selections: Evolving evolution. Journal of Biotechnology, 74, 27–38. 26.Karlsen, K. K., & Wengel, J. (2012). Locked nucleic acid and aptamers. Nucleic Acid Therapeutics, 22, 366–370. 27.Veedu, R. N., Burri, H. V., Kumar, P., Sharma, P. K., Hrdlicka, P. J., Vester, B., & Wengel, J. (2010). Polymerase-directed synthesis of C5-ethynyl locked nucleic acids. Bioorganic & Medicinal Chemistry Letters, 20, 6565–6568.CrossRef 28.Perlíková, P., Eberlin, L., Ménová, P., Raindlová, V., Slavětínská, L., Tloušťová, E., et al. (2013). Synthesis and cytostatic and antiviral activities of 2′-deoxy-2′,2′-difluororibo- and 2′-deoxy-2′-fluororibonucleosides derived from 7-(Het)aryl-7-deazaadenines. ChemMedChem, 8, 832–846.CrossRef 29.Hollenstein, M., & Leumann, C. J. (2014). Synthesis and biochemical characterization of tricyclothymidine triphosphate (tc-TTP). ChemBioChem, 15, 1901–1904.CrossRef 30.Vastmans, K., Froeyen, M., Kerremans, L., Pochet, S., & Herdewijn, P. (2001). Reverse transcriptase incorporation of 1,5-anhydrohexitol nucleotides. Nucleic Acids Research, 29, 3154–3163.CrossRef 31.Bande, O., Abu El Asrar, R., Braddick, D., Dumbre, S., Pezo, V., Schepers, G., et al. (2015). Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry: A European Journal, 21, 5009–5022.CrossRef 32.Giller, G., Tasara, T., Angerer, B., Mühlegger, K., Amacker, M., & Winter, H. (2003). Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2′-deoxyribonucleoside-5′-triphosphates. Nucleic Acids Research, 31, 2630–2635.CrossRef 33.Bergen, K., Steck, A. L., Strütt, S., Baccaro, A., Welte, W., Diederichs, K., & Marx, A. (2012). Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates. Journal of the American Chemical Society, 134, 11840–11843.CrossRef 34.Obeid, S., Baccaro, A., Welte, W., Diederichs, K., & Marx, A. (2010). Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proceedings of the National Academy of Sciences of the United States of America, 107, 21327–21331.CrossRef 35.Lam, C., Hipolito, C., & Perrin, D. M. (2008). Synthesis and enzymatic incorporation of modified deoxyadenosine triphosphates. European Journal of Organic Chemistry, 29, 4915–4923.CrossRef 36.Lam, C. H., Hipolito, C. J., Hollenstein, M., & Perrin, D. M. (2011). A divalent metal-dependent self-cleaving DNAzyme with a tyrosine side chain. Organic & Biomolecular Chemistry, 9, 6949–6954.CrossRef 37.Kielkowski, P., Fanfrlík, J., & Hocek, M. (2014). 7-Aryl-7-deazaadenine 2′-deoxyribonucleoside triphosphates (dNTPs): Better substrates for DNA polymerases than dATP in competitive incorporations. Angewandte Chemie Int Ed, 53, 7552–7555.CrossRef 38.Hocek, M., & Fojta, M. (2008). Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Organic & Biomolecular Chemistry, 6, 2233–22341.CrossRef 39.Hocek, M. (2014). Synthesis of base-modified 2′-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified dna for applications in bioanalysis and chemical biology. Journal of Organic Chemistry, 79, 9914–9921.CrossRef 40.Hollenstein, M. (2012). Nucleoside triphosphates: Building blocks for the modification of nucleic acids. Molecules, 17, 13569–13591.CrossRef 41.Baccaro, A., Steck, A., & Marx, A. (2012). Barcoded nucleotides. Angewandte Chemie Int Ed, 51, 254–257.CrossRef 42.Zhu, Z., & Waggoner, A. S. (1997). Molecular mechanism controlling the incorporation of fluorescent nucleotides into DNA by PCR. Cytometry, 28, 206–211.CrossRef 43.Ramanathan, A., Pape, L., & Schwartz, D. C. (2005). High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Analytical Biochemistry, 337, 1–11.CrossRef 44.Brakmann, S., & Löbermann, S. (2001). High-density labeling of dna: Preparation and characterization of the target material for single-molecule sequencing. Angewandte Chemie Int Ed, 40, 1427–1429.CrossRef 45.Anderson, J. P., Angerer, B., & Loeb, L. A. (2005). Incorporation of reporter-labeled nucleotides by DNA polymerases. Biotechniques, 38, 257–264.CrossRef 46.Yu, H., Chao, J., Patek, D., Mujumdar, R., Mujumdar, S., & Waggoner, A. S. (1994). Cyanine dye dUTP analogs for enzymatic labeling of DNA probes. Nucleic Acids Research, 22, 3226–3232.CrossRef 47.Zhu, Z., Chao, J., Yu, H., & Waggoner, A. S. (1994). Directly labeled DNA probes using fluorescent nucleotides with different length linkers. Nucleic Acids Research, 22, 3418–3422.CrossRef 48.Tasara, T., Angerer, B., Damond, M., Winter, H., Dörhöfer, S., Hübscher, U., & Amacker, M. (2003). Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. II. High-density labeling of natural DNA. Nucleic Acids Research, 31, 2636–2646.CrossRef 49.Lacenere, C., Garg, M. K., Stoltz, B. M., & Quake, S. R. (2006). Effects of a modified dye-labeled nucleotide spacer arm on incorporation by thermophilic DNA polymerases. Nucleosides, Nucleotides & Nucleic Acids, 25, 9–15.CrossRef 50.Dziuba, D., Pohl, R., & Hocek, M. (2014). Bodipy-labeled nucleoside triphosphates for polymerase synthesis of fluorescent DNA. Bioconjugate Chemistry, 25, 1984–1995.CrossRef 51.Riedl, J., Ménová, P., Pohl, R., Orság, P., Fojta, M., & Hocek, M. (2012). GFP-like fluorophores as DNA labels for studying DNA-protein interactions. Journal of Organic Chemistry, 77, 8287–8293.CrossRef 52.Riedl, J., Pohl, R., Ernsting, N. P., Orság, P., Fojta, M., & Hocek, M. (2012). Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions. Chemical Science, 3, 2797–2806.CrossRef 53.Dziuba, D., Pohl, R., & Hocek, M. (2015). Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: Fluorescent light-up probes for DNA-binding proteins. Chemical Communications, 51, 4880–4882.CrossRef 54.Jäger, S., Rasched, G., Kornreich-Leshem, H., Engeser, M., Thum, O., & Famulok, M. (2005). A versatile toolbox for variable DNA functionalization at high density. Journal of the American Chemical Society, 127, 15071–15082.CrossRef 55.Kuwahara, M., Nagashima, J., Hasegawa, M., Tamura, T., Kitagata, R., Hanawa, K., et al. (2006). Systematic characterization of 2′-deoxynucleoside-5′-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Research, 34, 5383–5394.CrossRef 56.Kuwahara, M., Obika, S., Nagashima, J., Ohta, Y., Suto, Y., Ozaki, H., et al. (2008). Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides. Nucleic Acids Research, 36, 4257–4265.CrossRef 57.Kuwahara, M., & Sugimoto, N. (2010). Molecular evolution of functional nucleic acids with chemical modifications. Molecules, 15, 5423–5444.CrossRef 58.Brudno, Y., & Liu, D. R. (2009). Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers. Chemistry & Biology, 16, 265–276.CrossRef 59.Ono, T., Scalf, M., & Smith, L. M. (1997). 2′-Fluoro modified nucleic acids: Polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Research, 25, 4581–4588.CrossRef 60.Renders, M., Miller, E., Hollenstein, M., & Perrin, D. (2015). A method for selecting modified DNAzymes without the use of modified DNA as a template in PCR. Chemical Communications, 51, 1360–1362.CrossRef 61.Tolle, F., Brändle, G. M., Matzner, D., & Mayer, G. A. (2015). Versatile approach towards nucleobase-modified aptamers. Angewandte Chemie Int Ed, 54, 10971–10974.CrossRef 62.Horiya, S., MacPherson, I. S., & Krauss, I. J. (2014). Recent strategies targeting HIV glycans in vaccine design. Nature Chemical Biology, 10, 990–999.CrossRef 63.Temme, J. S., MacPherson, I. S., DeCourcey, J. F., & Krauss, I. J. (2014). High temperature SELMA: Evolution of DNA-supported oligomannose clusters which are tightly recognized by HIV bnAb 2G12. Journal of the American Chemical Society, 136, 1726–1729.CrossRef 64.Lee, I., & Berdis, A. J. (2010). Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases. Biochimica et Biophysica Acta, 1804, 1064–1080.CrossRef 65.Betz, K., Malyshev, D. A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T. J., et al. (2012). KlenTaq polymerase replicates unnatural base pairs by inducing a Watson–Crick geometry. Nature Chemical Biology, 8, 612–614.CrossRef 66.Ahle, J. D., Barr, S., Chin, A. M., & Battersby, T. R. (2005). Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: Identification and insight into polymerase replication of the non-natural nucleobases. Nucleic Acids Research, 33, 3176–3184.CrossRef 67.Yang, Z., Sismour, A. M., Sheng, P., Puskar, N. L., & Benner, S. A. (2007). Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Research, 35, 4238–4249.CrossRef 68.Kimoto, M., Kawai, R., Mitsui, T., Yokoyama, S., & Hirao, I. (2009). An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. Nucleic Acids Research, 37, e14.CrossRef 69.Morihiro, K., Hoshino, H., Hasegawa, O., Kasahara, Y., Nakajima, K., Kuwahara, M., et al. (2015). Polymerase incorporation of a 2′-deoxynucleoside-5′-triphosphate bearing a 4-hydroxy-2-mercaptobenzimidazole nucleobase analogue. Bioorganic & Medicinal Chemistry Letters, 25, 2888–2891.CrossRef 70.Hsu, G. W., Ober, M., Carell, T., & Beese, L. S. (2004). Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature, 431, 217–221.CrossRef 71.Reineks, E. Z., & Berdis, A. J. (2004). Evaluating the contribution of base stacking during translesion DNA replication. Biochemistry, 43, 393–404.CrossRef 72.Zhang, X., Motea, E., Lee, I., & Berdis, A. J. (2010). Replication of a universal nucleobase provides unique insight into the role of entropy during DNA polymerization and pyrophosphorolysis. Biochemistry, 49, 3009–3023.CrossRef 73.Lavergne, T., Degardin, M., Malyshev, D. A., Quach, H. T., Dhami, K., Ordoukhanian, P., & Romesberg, F. E. (2013). Expanding the scope of replicable unnatural DNA: Stepwise optimization of a predominantly hydrophobic base pair. Journal of the American Chemical Society, 135, 5408–5419.CrossRef 74.Walsh, J. M., & Beuning, P. J. (2012). Synthetic nucleotides as probes of DNA polymerase specificity. Journal of Nucleic Acids, 2012, 530963.CrossRef 75.Washington, M. T., Helquist, S. A., Kool, E. T., Prakash, L., & Prakash, S. (2003). Requirement of Watson–Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta. Molecular and Cellular Biology, 23, 5107–5112.CrossRef 76.Wolfle, W. T., Washington, M. T., Kool, E. T., Spratt, T. E., Helquist, S. A., Prakash, L., & Prakash, S. (2005). Evidence for a Watson–Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa. Molecular and Cellular Biology, 25, 7137–7143.CrossRef 77.Ong, J. L., Loakes, D., Jaroslawski, S., Too, K., & Holliger, P. (2006). Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. Journal of Molecular Biology, 361, 537–550.CrossRef 78.Hendrickson, C. L., Devine, K. G., & Benner, S. A. (2004). Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2′-deoxyadenosine. Nucleic Acids Research, 32, 2241–2250.CrossRef 79.Morales, J. C., & Kool, E. T. (2000). Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry, 39, 12979–12988.CrossRef 80.Obeid, S., Busskamp, H., Welte, W., Diederichs, K., & Marx, A. (2012). Interactions of non-polar and “Click-able” nucleotides in the confines of a DNA polymerase active site. Chemical Communications, 48, 8320–8322.CrossRef 81.Obeid, S., Bußkamp, H., Welte, W., Diederichs, K., & Marx, A. (2013). Snapshot of a DNA polymerase while incorporating two consecutive C5-modified nucleotides. Journal of the American Chemical Society, 135, 15667–15669.CrossRef 82.Poongavanam, V., Madala, P. K., Højland, T., & Veedu, R. N. (2014). Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations. PLoS One, 9, e102126.CrossRef 83.Wynne, S. A., Pinheiro, V. B., Holliger, P., & Leslie, A. G. (2013). Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly Cy-dye labelled DNA. PLoS One, 8, e70892.CrossRef 84.Ramsay, N., Jemth, A. S., Brown, A., Crampton, N., Dear, P., & Holliger, P. (2010). CyDNA: Synthesis and replication of highly cy-dye substituted DNA by an evolved polymerase. Journal of the American Chemical Society, 132, 5096–5104.CrossRef 85.Laos, R., Thomson, J. M., & Benner, S. A. (2014). DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Frontiers in Microbiology, 5, 565.CrossRef 86.Ishino, S., & Ishino, Y. (2014). DNA polymerases as useful reagents for biotechnology—The history of developmental research in the field. Frontiers in Microbiology, 5, 465.CrossRef 87.Kranaster, R., & Marx, A. (2010). Engineered DNA polymerases in biotechnology. ChemBioChem, 11, 2077–2084.CrossRef 88.Hansen, C. J., Wu, L., Fox, J. D., Arezi, B., & Hogrefe, H. H. (2011). Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide gamma-phosphate derivative. Nucleic Acids Research, 39, 1801–1810.CrossRef 89.Padilla, R., & Sousa, R. (1999). Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2′-groups using a mutantT7 RNA polymerase (RNAP). Nucleic Acids Research, 27, 1561–1563.CrossRef 90.Padilla, R., & Sousa, R. (2002). A Y639F/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs. Nucleic Acids Research, 30, e138.CrossRef 91.Meyer, A.J., Ellefson, J.W. & Ellington, A.D. (2014) Library generation by gene shuffling. Current Protocols in Molecular Biology, 105, Unit 15.12. doi:10.1002/0471142727.mb1512s105 . 92.Cole, M. F., & Gaucher, E. A. (2011). Exploiting models of molecular evolution to efficiently direct protein engineering. Journal of Molecular Evolution, 72, 193–203.CrossRef 93.Chen, F., Gaucher, E. A., Leal, N. A., Hutter, D., Havemann, S. A., Govindarajan, S., et al. (2010). Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proceedings of the National Academy of Sciences of the United States of America, 107, 1948–1953.CrossRef 94.Matsuura, T., & Yomo, T. (2006). In vitro evolution of proteins. Journal of Bioscience and Bioengineering, 101, 449–456.CrossRef 95.Henry, K. A., Arbabi-Ghahroudi, M., & Scott, J. K. (2015). Beyond phage display: Non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold. Frontiers in Microbiology, 6, 755. 96.Pande, J., Szewczyk, M. M., & Grover, A. K. (2010). Phage display: Concept, innovations, applications and future. Biotechnology Advances, 28, 849–858.CrossRef 97.Tawfik, D. S., & Griffiths, A. D. (1998). Man-made cell-like compartments for molecular evolution. Nature Biotechnology, 16, 652–656.CrossRef 98.Loakes, D., & Holliger, P. (2009). Polymerase engineering: Towards the encoded synthesis of unnatural biopolymers. Chemical Communications, 31, 4619–4631.CrossRef 99.Pinheiro, V. B., Taylor, A. I., Cozens, C., Abramov, M., Renders, M., Zhang, S., et al. (2012). Synthetic genetic polymers capable of heredity and evolution. Science, 336, 341–344.CrossRef 100.Taylor, A. I., Pinheiro, V. B., Smola, M. J., Morgunov, A. S., Peak-Chew, S., Cozens, C., et al. (2015). Catalysts from synthetic genetic polymers. Nature, 518, 427–430.CrossRef 101.Avino, A., Fabrega, C., Tintore, M., & Eritja, R. (2012). Thrombin binding aptamer, more than a simple aptamer: Chemically modified derivatives and biomedical applications. Current Pharmaceutical Design, 18, 2036–2047.CrossRef 102.Peng, C. G., & Damha, M. J. (2007). G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d -arabinonucleic acids (2′F-ANA). Nucleic Acids Research, 35, 4977–4988.CrossRef 103.Kolganova, N. A., Varizhuk, A. M., Novikov, R. A., Florentiev, V. L., Pozmogova, G. E., Borisova, O. F., et al. (2014). Anomeric DNA quadruplexes. Artificial DNA PNA XNA, 5, e28422.CrossRef 104.Davies, D. R., Gelinas, A. D., Zhang, C., Rohloff, J. C., Carter, J. D., O’Connell, D., et al. (2012). Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proceedings of the National Academy of Sciences of the United States of America, 109, 19971–19976.CrossRef 105.Gupta, S., Hirota, M., Waugh, S. M., Murakami, I., Suzuki, T., Muraguchi, M., et al. (2014). Chemically modified DNA aptamers bind interleukin-6 with high affinity and inhibit signaling by blocking its interaction with interleukin-6 receptor. Journal of Biological Chemistry, 289, 8706–8719.CrossRef 106.Scuotto, M., Rivieccio, E., Varone, A., Corda, D., Bucci, M., Vellecco, V., et al. (2015). Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Research, 43, 7702–7716.CrossRef 107.Rohloff, J. C., Fowler, C., Ream, B., Carter, J. D., Wardle, G., & Fitzwater, T. (2015). Practical synthesis of cytidine-5-carboxamide-modified nucleotide reagents. Nucleosides, Nucleotides & Nucleic Acids, 34, 180–198.CrossRef 108.Vaught, J. D., Bock, C., Carter, J., Fitzwater, T., Otis, M., Schneider, D., et al. (2010). Expanding the chemistry of DNA for in vitro selection. Journal of the American Chemical Society, 132, 4141–4151.CrossRef 109.Hollenstein, M. (2013). Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues—synthesis and biochemical characterization. Organic & Biomolecular Chemistry, 11, 5162–5172.CrossRef 110.Hollenstein, M. (2012). Synthesis of deoxynucleoside triphosphates that include proline, urea, or sulfonamide groups and their polymerase incorporation into DNA. Chemistry, 18, 13320–13330.CrossRef 111.Shoji, A., Kuwahara, M., Ozaki, H., & Sawai, H. (2007). Modified DNA aptamer that binds the (R)-isomer of a thalidomide derivative with high enantioselectivity. Journal of the American Chemical Society, 129, 1456–1464.CrossRef 112.Battersby, T. R., Ang, D. N., Burgstaller, P., Jurczyk, S. C., Bowser, M. T., Buchanan, D. D., et al. (1999). Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog. Journal of the American Chemical Society, 121, 9781–9789.CrossRef 113.Hollenstein, M., Hipolito, C. J., Lam, C. H., & Perrin, D. M. (2013). Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS Combinatorial Science, 15, 174–182.CrossRef 114.Imaizumi, Y., Kasahara, Y., Fujita, H., Kitadume, S., Ozaki, H., Endoh, T., et al. (2013). Efficacy of base-modification on target binding of small molecule DNA aptamers. Journal of the American Chemical Society, 135, 9412–9419.CrossRef 115.Latham, J. A., Johnson, R., & Toole, J. J. (1994). The application of a modified nucleotide in aptamer selection: Novel thrombin aptamers containing 5-(1-pentynyl)-2′-deoxyuridine. Nucleic Acids Research, 22, 2817–2822.CrossRef 116.Holzberger, B., & Marx, A. (2009). Enzymatic synthesis of perfluoroalkylated DNA. Bioorganic & Medicinal Chemistry, 17, 3653–3658.CrossRef 117.Kuwahara, M., Suto, Y., Minezaki, S., Kitagata, R., Nagashima, J., & Sawai, H. (2006). Substrate property and incorporation accuracy of various dATP analogs during enzymatic polymerization using thermostable DNA polymerases. Nucleic Acids Symposium Series, 50, 31–32.CrossRef 118.Dadová, J., Orság, P., Pohl, R., Brázdová, M., Fojta, M., & Hocek, M. (2013). Vinylsulfonamide and acrylamide modification of DNA for cross-linking with proteins. Angewandte Chemie Int Ed, 52, 10515–10518.CrossRef 119.Raindlová, V., Pohl, R., & Hocek, M. (2012). Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination. Chemistry: A European Journal, 18, 4080–4087.CrossRef
- 作者单位:Sergey A. Lapa (1)
Alexander V. Chudinov (1) Edward N. Timofeev (1)
1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- 刊物主题:Biotechnology; Biochemistry, general; Cell Biology; Protein Science; Biological Techniques; Human Genetics;
- 出版者:Springer US
- ISSN:1559-0305
文摘
Aptamers are nucleic acid-based scaffolds that can bind with high affinity to a variety of biological targets. Aptamers are identified from large DNA or RNA libraries through a process of directed molecular evolution (SELEX). Chemical modification of nucleic acids considerably increases the functional and structural diversity of aptamer libraries and substantially increases the affinity of the aptamers. Additionally, modified aptamers exhibit much greater resistance to biodegradation. The evolutionary selection of modified aptamers is conditioned by the possibility of the enzymatic synthesis and replication of non-natural nucleic acids. Wild-type or mutant polymerases and their non-natural nucleotide substrates that can support SELEX are highlighted in the present review. A focus is made on the efforts to find the most suitable type of nucleotide modifications and the engineering of new polymerases. Post-SELEX modification as a complementary method will be briefly considered as well. Keywords Aptamer Molecular evolution SELEX Nucleic acids Nucleotides Polymerases Modification Non-natural nucleoside triphosphates PCR Primer extension
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