Enhancing aptamer function and stability via in vitro selection using modified nucleic acids

Methods

Volumn 106, Issue , 2016, Pages 29-36

  Meek, Kirsten N ^a   Rangel, Alexandra E ^a   Heemstra, Jennifer M ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

Affinity reagent; Aptamer; In vitro selection; Nucleic acid; Polymerase engineering; Templated synthesis

Indexed keywords

APTAMER; MOLECULAR SCAFFOLD; NUCLEIC ACID; DNA DIRECTED DNA POLYMERASE;

BASE PAIRING; CHEMICAL MODIFICATION; HYDROGEN BOND; HYDROPHOBICITY; IN VITRO SELECTION; PRIORITY JOURNAL; REVIEW; SYNTHESIS; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE; CHEMISTRY; GENETIC ENGINEERING; GENETICS; PROCEDURES;

APTAMERS, NUCLEOTIDE; DNA-DIRECTED DNA POLYMERASE; GENETIC ENGINEERING; NUCLEIC ACIDS; SELEX APTAMER TECHNIQUE;

EID: 84962593020     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.03.008     Document Type: Review

References (46)

1. Ellington, A.D., Szostak, J.W., In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990), 818–822.
2. Robertson, D.L., Joyce, G.F., Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344 (1990), 467–468.
3. Tuerk, C., Gold, L., Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249 (1990), 505–510.
4. Stoltenburg, R., Reinemann, C., Strehlitz, B., SELEX—A (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 24 (2007), 381–403.
5. Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberadino, A., McConnell, E., Francis, T., DeRosa, M.C., Dumontier, M., Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database, 2012, bas006.
6. Green, L.S., Jellinek, D., Bell, C., Beebe, L.A., Feistner, B.D., Gill, S.C., Jucker, F.M., Janjić N., Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor. Chem. Biol. 2 (1994), 683–695.
7. Kimoto, M., Yamashige, R., Matsunaga, K.-I., Yokoyama, S., Hirao, I., Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat. Biotechnol. 31 (2013), 453–457.
8. Ng, E.W.M., Shima, D.T., Calias, P., Cunningham, E.T. Jr., Guyer, D.R., Adamis, A.P., Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov. 5 (2006), 123–132.
9. Jellinek, D., Green, L.S., Bell, C., Janjic, N., Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor. Biochemistry 33 (1994), 10450–10456.
10. Ruckman, J., Green, L.S., Beeson, J., Waugh, S., Gillette, W.L., Henninger, D.D., Claesson-Welsh, L., Janjic, N., 2′-Fluoropyrimidine RNA-based Aptamers to the 165-Amino Acid Form of Vascular Endothelial Growth Factor (VEGF165): inhibition of receptor binding and vegf-induced vascular permeability through interactions requiring the exon 7-encoded domain. J. Biol. Chem. 273 (1998), 20556–20567.
11. Griffin, L.C., Tidmarsh, G.F., Bock, L.C., Toole, J.J., Leung, L.L., In vivo anticoagulant properties of a novel nucleotide-based thrombin inhibitor and demonstration of regional anticoagulation in extracorporeal circuits. Blood 81 (1993), 3271–3276.
12. Kurreck, J., Antisense technologies. Eur. J. Biochem. 270 (2003), 1628–1644.
13. Sczepanski, J.T., Joyce, G.F., Binding of a structured D-RNA molecule by an L-RNA aptamer. J. Am. Chem. Soc. 135 (2013), 13290–13293.
14. Hoehlig, K., Maasch, C., Shushakova, N., Buchner, K., Huber-Lang, M., Purschke, W.G., Vater, A., Klussmann, S., A novel C5a-neutralizing mirror-image (L-)aptamer prevents organ failure and improves survival in experimental sepsis. Mol. Ther. 21 (2013), 2236–2246.
15. Yu, H., Zhang, S., Dunn, M.R., Chaput, J.C., An efficient and faithful in vitro replication system for threose nucleic acid. J. Am. Chem. Soc. 135 (2013), 3583–3591.
16. Yu, H., Zhang, S., Chaput, J.C., Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor. Nat. Chem. 4 (2012), 183–187.
17. Dunn, M.R., Chaput, J.C., An in vitro selection protocol for threose nucleic acid (TNA) using DNA display. Curr. Protoc. Nucleic Acid Chem. 57 (2014), 9.8.1–9.8.19.
18. Dunn, M.R., Larsen, A.C., Zahurancik, W.J., Fahmi, N.E., Meyers, M., Suo, Z., Chaput, J.C., DNA polymerase-mediated synthesis of unbiased threose nucleic acid (TNA) polymers requires 7-deazaguanine to suppress G: G mispairing during TNA transcription. J. Am. Chem. Soc. 137 (2015), 4014–4017.
19. Pinheiro, V.B., Arangundy-Franklin, S., Holliger, P., Compartmentalized self-tagging for in vitro-directed evolution of XNA polymerases. Curr. Protoc. Nucleic Acid Chem. 57 (2014), 9.9.1–9.9.18.
20. Pinheiro, V.B., Taylor, A.I., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J.C., Wengel, J., Peak-Chew, S.Y., McLaughlin, S.H., Herdewijn, P., Holliger, P., Synthetic genetic polymers capable of heredity and evolution. Science 336 (2012), 341–344.
21. Alves Ferreira-Bravo, I., Cozens, C., Holliger, P., DeStefano, J.J., Selection of 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res. 43 (2015), 9587–9599.
22. Kasahara, Y., Irisawa, Y., Fujita, H., Yahara, A., Ozaki, H., Obika, S., Kuwahara, M., Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2′-O,4′-C-methylene-bridged/locked nucleic acid primer. Anal. Chem. 85 (2013), 4961–4967.
23. Kasahara, Y., Irisawa, Y., Ozaki, H., Obika, S., Kuwahara, M., 2′,4′-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2′-O,4′-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorg. Med. Chem. Lett. 23 (2013), 1288–1292.
24. Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S.M., Driver, D.A., Berg, R.H., Kim, S.K., Norden, B., Nielsen, P.E., PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365 (1993), 566–568.
25. Brudno, Y., Birnbaum, M.E., Kleiner, R.E., Liu, D.R., An in vitro translation, selection and amplification system for peptide nucleic acids. Nat. Chem. Biol. 6 (2010), 148–155.
26. Niu, J., Hili, R., Liu, D.R., Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids. Nat. Chem. 5 (2013), 282–292.
27. Latham, J.A., Johnson, R., Toole, J.J., The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2′-deoxyuridine. Nucleic Acids Res. 22 (1994), 2817–2822.
28. 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., Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE, 5, 2010, e15004.
29. Rich, A., Horizons in Biochemistry. 1962, Academic Press, New York.
30. Sismour, A.M., Benner, S.A., The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res. 33 (2005), 5640–5646.
31. Morales, J.C., Kool, E.T., Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat. Struct. Mol. Biol. 5 (1998), 950–954.
32. McMinn, D.L., Ogawa, A.K., Wu, Y., Liu, J., Schultz, P.G., Romesberg, F.E., Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base. J. Am. Chem. Soc. 121 (1999), 11585–11586.
33. Hirao, I., Kimoto, M., Mitsui, T., Fujiwara, T., Kawai, R., Sato, A., Harada, Y., Yokoyama, S., An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nat. Methods 3 (2006), 729–735.
34. Yang, Z., Hutter, D., Sheng, P., Sismour, A.M., Benner, S.A., Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res. 34 (2006), 6095–6101.
35. Georgiadis, M.M., Singh, I., Kellett, W.F., Hoshika, S., Benner, S.A., Richards, N.G.J., Structural basis for a six nucleotide genetic alphabet. J. Am. Chem. Soc. 137 (2015), 6947–6955.
36. 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., In vitro selection with artificial expanded genetic information systems. Proc. Natl. Acad. Sci. 111 (2014), 1449–1454.
37. Hirao, I., Mitsui, T., Kimoto, M., Yokoyama, S., An efficient unnatural base pair for PCR amplification. J. Am. Chem. Soc. 129 (2007), 15549–15555.
38. Kimoto, M., Kawai, R., Mitsui, T., Yokoyama, S., Hirao, I., An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. Nucleic Acids Res., 37, 2009 e14–e14.
39. Hollenstein, M., Hipolito, C.J., Lam, C.H., Perrin, D.M., A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M(2+)). Nucleic Acids Res. 37 (2009), 1638–1649.
40. Perrin, D.M., Garestier, T., Hélène, C., Bridging the gap between proteins and nucleic acids: a metal-independent RNaseA mimic with two protein-like functionalities. J. Am. Chem. Soc. 123 (2001), 1556–1563.
41. Thum, O., Jäger, S., Famulok, M., Functionalized DNA: a new replicable biopolymer. Angew. Chem. Int. Ed. 40 (2001), 3990–3993.
42. Vaught, J.D., Bock, C., Carter, J., Fitzwater, T., Otis, M., Schneider, D., Rolando, J., Waugh, S., Wilcox, S.K., Eaton, B.E., Expanding the chemistry of DNA for in vitro selection. J. Am. Chem. Soc. 132 (2010), 4141–4151.
43. Renders, M., Miller, E., Hollenstein, M., Perrin, D., A method for selecting modified DNAzymes without the use of modified DNA as a template in PCR. Chem. Commun. 51 (2015), 1360–1362.
44. Hili, R., Niu, J., Liu, D.R., DNA ligase-mediated translation of DNA into densely functionalized nucleic acid polymers. J. Am. Chem. Soc. 135 (2013), 98–101.
45. Guo, C., Watkins, C.P., Hili, R., Sequence-defined scaffolding of peptides on nucleic acid polymers. J. Am. Chem. Soc. 137 (2015), 11191–11196.
46. Tolle, F., Brandle, G.M., Matzner, D., Mayer, G., A versatile approach towards nucleobase-modified aptamers. Angew. Chem. Int. Ed. 54 (2015), 10971–10974.