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Aptamer-Based Affinity Chromatography for Protein Extraction and Purification

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Aptamers in Biotechnology

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 174))

Abstract

Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations.

Graphical Abstract Aptamer-protein complexes by X-ray crystallography

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References

  1. Fitzgerald J, Leonard P, Darcy E, Sharma S, O’Kennedy R (2017) Immunoaffinity chromatography: concepts and applications. Methods Mol Biol 1485:27–51

    CAS  PubMed  Google Scholar 

  2. Farmaki T (2016) Use of a phosphatidylinositol phosphate affinity chromatography (PIP chromatography) for the isolation of proteins involved in protein quality control and proteostasis mechanisms in plants. Methods Mol Biol 1450:223–232

    CAS  PubMed  Google Scholar 

  3. Licht P, Pavgi S (1992) Identification and purification of a high-affinity thyroxine binding protein that is distinct from albumin and prealbumin in the blood of a turtle, Trachemys scripta. Gen Comp Endocrinol 85:179–192

    CAS  PubMed  Google Scholar 

  4. Bansal V, Roychoudhury PK, Mattiasson B, Kumar A (2006) Recovery of urokinase from integrated mammalian cell culture cryogel bioreactor and purification of the enzyme using p-aminobenzamidine affinity chromatography. J Mol Recognit 19:332–339

    CAS  PubMed  Google Scholar 

  5. Wickerhauser M, Williams C (1984) A single-step method for the isolation of antithrombin III. Vox Sang 47:397–405

    CAS  PubMed  Google Scholar 

  6. Bayer EA, Wilchek M (1990) Application of avidin-biotin technology to affinity-based separations. J Chromatogr 510:3–11

    CAS  PubMed  Google Scholar 

  7. Roque AC, Gupta G, Lowe CR (2005) Design, synthesis, and screening of biomimetic ligands for affinity chromatography. Methods Mol Biol 310:43–62

    CAS  PubMed  Google Scholar 

  8. Chen C, Khoury GE, Lowe CR (2014) Affinity ligands for glycoprotein purification based on the multi-component Ugi reaction. J Chromatogr 969:171–180

    CAS  Google Scholar 

  9. Sun X, Weaver J, Wickramasinghe SR, Qian X (2018) Identification and characterization of novel Fc-binding heptapeptides from experiments and simulations. Polymers 10:778–800

    PubMed Central  Google Scholar 

  10. Trasatti JP, Woo J, Ladiwala A, Cramer S, Karande P (2018) Rational design of peptide affinity ligands for the purification of therapeutic enzymes. Biotechnol Prog 34:978–998

    Google Scholar 

  11. Kaufman DB, Hentsch ME, Baumbach GA, Buettner JA, Dadd CA, Huang PY, Hammond DJ, Carbonell RG (2002) Affinity purification of fibrinogen using a ligand from a peptide library. Biotechnol Bioeng 77:278–289

    CAS  PubMed  Google Scholar 

  12. Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM (2013) mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 110:857–870

    CAS  PubMed  Google Scholar 

  13. Perret G, Santambien P, Boschetti E (2015) The quest for affinity chromatography ligands: are the molecular libraries the right source? J Sep Sci 38:2559–2572

    CAS  PubMed  Google Scholar 

  14. Deisenhofer J (1981) Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Biochemistry 20:2361–2370

    CAS  PubMed  Google Scholar 

  15. Hober S, Nord K, Linhult M (2007) Protein A chromatography for antibody purification. J Chromatogr B 848:40–47

    CAS  Google Scholar 

  16. Bolton GR, Mehta KK (2016) The role of more than 40 years of improvement in protein A chromatography in the growth of the therapeutic antibody industry. Biotechnol Prog 32:1193–1202

    CAS  PubMed  Google Scholar 

  17. Goding JW (1978) Use of staphylococcal protein A as an immunological reagent. J Immunol Methods 20:241–253

    CAS  PubMed  Google Scholar 

  18. Grodzki AC, Berenstein E (2010) Antibody purification: affinity chromatography – protein A and protein G Sepharose. Methods Mol Biol 588:33–41

    CAS  PubMed  Google Scholar 

  19. Nilson BH, Lögdberg L, Kastern W, Björck L, Akerström B (1993) Purification of antibodies using protein L-binding framework structures in the light chain variable domain. J Immunol Methods 164:33–40

    CAS  PubMed  Google Scholar 

  20. Sheng S, Kong F (2012) Separation of antigens and antibodies by immunoaffinity chromatography. Pharm Biol 50:1038–1044

    CAS  PubMed  Google Scholar 

  21. Hirabayashi J, Hashidate T, Kasai K (2002) Glyco-catch method: a lectin affinity technique for glycoproteomics. J Biomol Tech 13:205–218

    PubMed  PubMed Central  Google Scholar 

  22. Mechref Y, Madera M, Novotny MV (2008) Glycoprotein enrichment through lectin affinity techniques. Methods Mol Biol 424:373–396

    CAS  PubMed  Google Scholar 

  23. Porath J, Carlsson J, Olsson I, Belfrage G (1975) Metal chelate affinity chromatography, a new approach to protein fractionation. Nature 258:598–599

    CAS  PubMed  Google Scholar 

  24. Porath J (1992) Immobilized metal ion affinity chromatography. Protein Expr Purif 3:263–281

    CAS  PubMed  Google Scholar 

  25. Block H, Maertens B, Spriestersbach A, Brinker N, Kubicek J, Fabis R, Labahn J, Schäfer F (2009) Immobilized-metal affinity chromatography (IMAC): a review. Methods Enzymol 463:439–473

    CAS  PubMed  Google Scholar 

  26. Cheung RC, Wong JH, Ng TB (2012) Immobilized metal ion affinity chromatography: a review on its applications. Appl Microbiol Biotechnol 96:1411–1420

    CAS  PubMed  Google Scholar 

  27. Borregaard N, Esmann V (1980) Determination of phosphorylase kinase activity in crude homogenates by affinity chromatography on 5’-AMP Sepharose. Anal Biochem 105:53–57

    CAS  PubMed  Google Scholar 

  28. König G, Astancolle S, Piccinini G, Cennamo C (1977) Affinity chromatography of yeast nicotinamide-adenine dinucleotide-specific isocitrate dehydrogenase on immobilized nicotinamide-adenine dinucleotide. Effects of ligands. Ital J Biochem 26:486–496

    PubMed  Google Scholar 

  29. Holmberg L, Bladh B, Astedt B (1976) Purification of urokinase by affinity chromatography. Biochim Biophys Acta 445:215–222

    CAS  PubMed  Google Scholar 

  30. Masferrer J, Albertini R, Croxatto HR, García P, Pinto I (1985) Isolation and characterization of rat plasma glandular kallikrein. Biochem Pharmacol 34:51–56

    CAS  PubMed  Google Scholar 

  31. Dean PD, Watson DH (1979) Protein purification using immobilised triazine dyes. J Chromatogr 165:301–319

    CAS  PubMed  Google Scholar 

  32. Stellwagen E (1990) Chromatography on immobilized reactive dyes. Methods Enzymol 182:343–357

    CAS  PubMed  Google Scholar 

  33. Hongo S, Sato T (1981) Purification of rat liver asparagine synthetase by affinity chromatography on reactive blue 2-agarose. Anal Biochem 114:163–166

    CAS  PubMed  Google Scholar 

  34. Birkenmeier G, Usbeck E, Saro L, Kopperschläger G (1983) Triazine dye binding of human alpha-fetoprotein and albumin. J Chromatogr 265:27–35

    CAS  PubMed  Google Scholar 

  35. Naumann M, Reuter R, Metz P, Kopperschläger G (1989) Affinity chromatography of bovine heart lactate dehydrogenase using dye ligands linked directly or spacer-mediated to bead cellulose. J Chromatogr 466:319–329

    CAS  PubMed  Google Scholar 

  36. Lowe CR, Burton SJ, Burton NP, Alderton WK, Pitts JM, Thomas JA (1992) Designer dyes: ‘biomimetic’ ligands for the purification of pharmaceutical proteins by affinity chromatography. Trends Biotechnol 10:442–448

    CAS  PubMed  Google Scholar 

  37. El Khoury G, Wang Y, Wang D, Jacob SI, Lowe CR (2013) Design, synthesis, and assessment of a de novo affinity adsorbent for the purification of recombinant human erythropoietin. Biotechnol Bioeng 110:3063–3069

    PubMed  Google Scholar 

  38. Teng SF, Sproule K, Husain A, Lowe CR (2000) Affinity chromatography on immobilized “biomimetic” ligands. Synthesis, immobilization and chromatographic assessment of an immunoglobulin G-binding ligand. J Chromatogr B 740:1–15

    CAS  Google Scholar 

  39. Roque AC, Lowe CR (2006) Advances and applications of de novo designed affinity ligands in proteomics. Biotechnol Adv 24:17–26

    CAS  PubMed  Google Scholar 

  40. El Khoury G, Rowe LA, Lowe CR (2012) Biomimetic affinity ligands for immunoglobulins based on the multicomponent Ugi reaction. Methods Mol Biol 800:57–74

    PubMed  Google Scholar 

  41. Furka A, Sebestyen F, Asgedom M, Dibo G (1991) General method for rapid synthesis of multicomponent peptide mixtures. Int J Pept Protein Res 37:487–493

    CAS  PubMed  Google Scholar 

  42. Menegatti S, Naik AD, Gurgel PV, Carbonell RG (2012) Alkaline-stable peptide ligand affinity adsorbents for the purification of biomolecules. J Chromatogr A 1245:55–64

    CAS  PubMed  Google Scholar 

  43. Kish WS, Roach MK, Sachi H, Naik AD, Menegatti S, Carbonell RG (2018) Purification of human erythropoietin by affinity chromatography using cyclic peptide ligands. J Chromatogr B 1085:1–12

    CAS  Google Scholar 

  44. Fang Y-M, Lin D-Q, Yao S-J (2018) Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification. J Chromatogr A 1571:1–15

    CAS  PubMed  Google Scholar 

  45. Nord K, Gunneriusson E, Ringdahl J, Ståhl S, Uhlén M, Nygren PA (1997) Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat Biotechnol 15:772–777

    CAS  PubMed  Google Scholar 

  46. Wållberg H, Löfdahl PK, Tschapalda K, Uhlén M, Tolmachev V, Nygren PK, Ståhl S (2011) Affinity recovery of eight HER2-binding affibody variants using an anti-idiotypic affibody molecule as capture ligand. Protein Expr Purif 76:127–135

    PubMed  Google Scholar 

  47. Hamers-Casterman C, Atarhouch T, Muyldermans S, Robinson G, Hamers C, Songa EB, Bendahman N, Hamers R (1993) Naturally occurring antibodies devoid of light chains. Nature 363:446–448

    CAS  PubMed  Google Scholar 

  48. Georgiou G, Stathopoulos C, Daugherty PS, Nayak AR, Iverson BL, Curtiss 3rd R (1997) Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nat Biotechnol 15:29–34

    CAS  PubMed  Google Scholar 

  49. Lam KS, Lebl M, Krchnák V (1997) The “one-bead-one-compound” combinatorial library method. Chem Rev 97:411–448

    CAS  PubMed  Google Scholar 

  50. Wang Y, Li T (2002) Identification of affinity ligands for protein purification from synthetic chemical combinatorial libraries. Biotechnol Prog 18:524–529

    PubMed  Google Scholar 

  51. Lathrop JT, Fijalkowska I, Hammond D (2007) The Bead blot: a method for identifying ligand-protein and protein-protein interactions using combinatorial libraries of peptide ligands. Anal Biochem 361:65–76

    CAS  PubMed  Google Scholar 

  52. Pande J, Szewczyk MM, Grover AK (2010) Phage display: concept, innovations, applications and future. Biotechnol Adv 28:849–858

    CAS  PubMed  Google Scholar 

  53. Kabir S (2002) Immunoglobulin purification by affinity chromatography using protein A mimetic ligands prepared by combinatorial chemical synthesis. Immunol Invest 31:263–278

    CAS  PubMed  Google Scholar 

  54. Li R, Dowd V, Stewart DJ, Burton SJ, Lowe CR (1998) Design, synthesis, and application of a protein A mimetic. Nat Biotechnol 16:190–195

    CAS  PubMed  Google Scholar 

  55. Menegatti S, Bobay BG, Ward KL, Islam T, Kish WS, Naik AD, Carbonell RG (2016) Design of protease-resistant peptide ligands for the purification of antibodies from human plasma. J Chromatogr A 1445:93–104

    CAS  PubMed  Google Scholar 

  56. Tu Z, Xu Y, Fu J, Huang Z, Wang Y, Liu B, Tao Y (2015) Preparation and characterization of novel IgG affinity resin coupling anti-Fc camelid single-domain antibodies. J Chromatogr B 983–984:26–31

    Google Scholar 

  57. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822

    CAS  PubMed  Google Scholar 

  58. Ghosh G, Huang DB, Huxford T (2004) Molecular mimicry of the NF-kappaB DNA target site by a selected RNA aptamer. Curr Opin Struct Biol 14:21–27

    CAS  PubMed  Google Scholar 

  59. Blank M, Blind M (2005) Aptamers as tools for target validation. Curr Opin Chem Biol 9:336–342

    CAS  PubMed  Google Scholar 

  60. Romig TS, Bell C, Drolet DW (1999) Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. J Chromatogr B 731:275–284

    CAS  Google Scholar 

  61. Forier C, Boschetti E, Ouhammouch M, Cibiel A, Ducongé F, Nogré M, Tellier M, Bataille D, Bihoreau N, Santambien P, Chtourou S, Perret G (2017) DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources. J Chromatogr 1489:39–50

    CAS  Google Scholar 

  62. Beloborodov SS, Bao J, Krylova SM, Shala-Lawrence A, Johnson PE, Krylov SN (2018) Aptamer facilitated purification of functional proteins. J Chromatogr B 1073:201–206

    CAS  Google Scholar 

  63. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510

    CAS  PubMed  Google Scholar 

  64. Lorenz C, von Pelchrzim F, Schroeder R (2006) Genomic systematic evolution of ligands by exponential enrichment (Genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels. Nat Protoc 1:2204–2212

    CAS  PubMed  Google Scholar 

  65. Peselis A, Serganov A (2014) Structure and function of pseudoknots involved in gene expression control. Wiley Interdiscip Rev RNA 5:803–822

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Svoboda P, Di Cara A (2006) Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci 63:901–908

    CAS  PubMed  Google Scholar 

  67. Li W, Ma B, Shapiro B (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. J Biomol Struct Dyn 19:381–396

    CAS  PubMed  Google Scholar 

  68. Katahira M, Moriyama K, Kanagawa M, Saeki J, Kim MH, Nagaoka M, Ide M, Uesugi S, Kono T (1995) RNA quadruplex containing g and a. Nucleic Acids Symp Ser 34:197–198

    CAS  Google Scholar 

  69. Turner DH, Sugimoto N, Freier SM (1990) Thermodynamics and kinetics of base-pairing of DNA and RNA self-assembly and helix coil transition. Nucleic acids. Springer-Verlag, Berlin, pp 201–227

    Google Scholar 

  70. Gruenewald B, Nicola CU, Lusitg A, Schwarz G, Klump H (1979) Kinetics of the helix-coil transition of a polypeptide with non-ionic side groups, derived from ultrasonic relaxation measurements. Biophys Chem 9:137–147

    CAS  PubMed  Google Scholar 

  71. Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM (2011) RNA and protein 3D structure modeling: similarities and differences. J Mol Model 17:2325–2336

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Laing C, Schlick T (2010) Computational approaches to 3D modeling of RNA. J Phys Condens Matter 22:283101

    PubMed  PubMed Central  Google Scholar 

  73. Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL (2016) Predicting RNA secondary structures from sequence and probing data. Methods 103:86–98

    CAS  PubMed  Google Scholar 

  74. Sun LZ, Zhang D, Chen SJ (2017) Theory and modeling of RNA structure and interactions with metal ions and small molecules. Annu Rev Biophys 46:227–246

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW (2016) Automated RNA 3D structure prediction with RNA composer. Methods Mol Biol 1490:199–215

    CAS  PubMed  Google Scholar 

  76. Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferr-D’Amar AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E (2015) RNA-puzzles round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21:1–19

    Google Scholar 

  77. Thirumalai D (1998) Native secondary structure formation in RNA may be a slave to tertiary folding. Proc Natl Acad Sci U S A 95:11506–11508

    CAS  PubMed  PubMed Central  Google Scholar 

  78. van Holde KE, Johnson WC, Ho PS (1998) Principles of physical biochemistry. Prentice Hall, Upper Saddle River, pp 9–11

    Google Scholar 

  79. Karshikoff A (2006) Non covalent interactions in proteins. Imperial College Press, London. ISBN: 978-1-86094-707-0

    Google Scholar 

  80. Blanco C, Bayas M, Yan F, Chen IA (2018) Analysis of evolutionarily independent protein-RNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios. Curr Biol 28:526–537

    CAS  PubMed  Google Scholar 

  81. Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS (2010) Origins of specificity in protein-DNA recognition. Annu Rev Biochem 79:233–269

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Privalov PL, Dragan AI, Crane-Robinson C (2011) Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components. Nucleic Acids Res 7:2483–2491

    Google Scholar 

  83. Wells RA, Kellie JL, Wetmore SD (2013) Significant strength of charged DNA-protein π-π interactions: a preliminary study of cytosine. J Phys Chem B 117:10462–10474

    CAS  PubMed  Google Scholar 

  84. Kim H, Jeong E, Lee SW, Han K (2003) Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Lett 552:231–239

    CAS  PubMed  Google Scholar 

  85. Nobeli I, Laskowski RA, Valdar WSJ, Thornton JM (2001) On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res 29:4294–4309

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Baldauf C, Gunther R, Hofmann HJ (2006) Theoretical prediction of the basic helix types in α, β-hybrid peptides. Biopolymers 84:408–413

    CAS  PubMed  Google Scholar 

  87. Tolstorukov MY, Jernigan RL, Zhurkin VB (2004) Protein–DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol 337:65–76

    CAS  PubMed  Google Scholar 

  88. Su Y, Yamashita MM, Greasley SE, Mullen CA, Shim JH, Jennings PA, Benkovic SJ, Wilson IA (1998) A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A. J Biol Mol 281:485–499

    CAS  Google Scholar 

  89. Gilson MK, Given GA, Bush BL, McCammon JA (1997) The statistical-thermodynamic basis for computation of binding affinities. Biophys J 72:1047–1069

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Nguyen QN, Perret G, Ducongé F (2016) Applications of high-throughput sequencing for in vitro selection and characterization of aptamers. Pharmaceuticals (Basel) 9:E76

    Google Scholar 

  91. Beck TF, Mullikin JC, Biesecker LG (2016) Systematic evaluation of Sanger validation of next-generation sequencing variants. Clin Chem 62:647–654

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Ouyang W, Yu Z, Zhao X, Lu S, Wang Z (2016) Aptamers in hematological malignancies and their potential therapeutic implications. Crit Rev Oncol Hematol 106:108–117

    PubMed  Google Scholar 

  93. Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T (2018) Aptamer therapeutics in cancer: current and future. Cancer 10:e80

    Google Scholar 

  94. Zhu Q, Liu G, Kai M (2015) DNA aptamers in the diagnosis and treatment of human diseases. Molecules 20:20979–20997

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP (2019) Molecular application of aptamers in the diagnosis and treatment of cancer and communicable diseases. Pharmaceuticals 11:e93

    Google Scholar 

  96. Zhou J, Rossi J (2017) Aptamers as targeted therapeutics: current potential and challenges. Nat Rev Drug Discov 16:181–202

    CAS  PubMed  Google Scholar 

  97. Modh H, Scheper T, Walter JG (2018) Aptamer-modified magnetic beads in biosensing. Sensors 18:e1041

    PubMed  Google Scholar 

  98. He F, Wen N, Xiao D, Yan J, Xiong H, Cai S, Liu Z, Liu Y (2019) Aptamer based targeted drug delivery systems: current potential and challenges. Curr Med Chem. https://doi.org/10.2174/0929867325666181008142831

  99. Wermuth PJ, Piera-Velazquez S, Jimenez SA (2018) Identification of novel systemic sclerosis biomarkers employing aptamer proteomic analysis. Rheumatology 57:1698–1706

    CAS  PubMed  Google Scholar 

  100. Xu L, Zhang Z, Zhang Q, Li P (2016) Mycotoxin determination in foods using advanced sensors based on antibodies or aptamers. Toxins 8:e239

    PubMed  Google Scholar 

  101. Jin C, Zheng J, Li C, Qiu L, Zhang X, Tan W (2015) Aptamers selected by cell-SELEX for molecular imaging. J Mol Evol 81:162–171

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Flamm C, Fontana W, Hofacker IL, Schuster P (2000) RNA folding at elementary step resolution. RNA 6:325–338

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Tang X, Thomas S, Tapia L, Giedroc DP, Amato NM (2008) Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol 38:1055–1067

    Google Scholar 

  104. Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF (2017) Recent advances in RNA folding. J Biotechnol 261:97–104

    CAS  PubMed  Google Scholar 

  105. Li Y, Breaker RR (1999) Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2¢-hydroxyl group. J Am Chem Soc 121:5364–5372

    CAS  Google Scholar 

  106. Keefe AD, Cload ST (2008) SELEX with modified nucleotides. Curr Opin Chem Biol 12:448–456

    CAS  PubMed  Google Scholar 

  107. Burmeister PE, Lewis SD, Silva RF, Horwitz LR, Pendergrast PS, McCauley TG, Kurz JC, Epstein DM, Wilson C, Keefe AD (2005) Direct in vitro selection of a 2’-O-methyl aptamer to VEGF. Chem Biol 12:25–33

    CAS  PubMed  Google Scholar 

  108. Vaught JD, Bock C, Carter J, Fitzwater T, Otis M, Schneider D, Rolando J, Waugh S, Wilcox SK, Eaton BE (2010) Expanding the chemistry of DNA for in vitro selection. J Am Chem Soc 132:4141–4151

    CAS  PubMed  Google Scholar 

  109. Veedu RN, Vester B, Wengel J (2008) Polymerase chain reaction and transcription using locked nucleic acid nucleotide triphosphates. J Am Chem Soc 130:8124–8125

    CAS  PubMed  Google Scholar 

  110. Inomata E, Tashiro E, Miyakawa S, Nakamura Y, Akita K (2018) Alkaline-tolerant RNA aptamers useful to purify acid-sensitive antibodies in neutral conditions. Biochimie 145:113–124

    CAS  PubMed  Google Scholar 

  111. Tolle F, Brändle GM, Matzner D, Mayer G (2015) A versatile approach towards nucleobase-modified aptamers. Angew Chem Int Ed Engl 54:10971–10974

    CAS  PubMed  Google Scholar 

  112. Perret G, Boschetti E (2018) Aptamer affinity ligands in protein chromatography. Biochimie 145:98–112

    CAS  PubMed  Google Scholar 

  113. Urh M, Simpson D, Zhao K (2009) Affinity chromatography: general methods. Methods Enzymol 463:417–438

    CAS  PubMed  Google Scholar 

  114. Hage DS (2000) Periodate oxidation of antibodies for site-selective immobilization in immunoaffinity chromatography. Methods Mol Biol 147:69–82

    CAS  PubMed  Google Scholar 

  115. Balamurugan S, Obubuafo A, Soper SA, Spivak DA (2008) Surface immobilization methods for aptamer diagnostic applications. Anal Bioanal Chem 390:1009–1021

    CAS  PubMed  Google Scholar 

  116. Walter JG, Stahl F, Scheper T (2012) Aptamers as affinity ligands for downstream processing. Eng Life Sci 12:1–11

    Google Scholar 

  117. Labrou N, Clonis YD (1994) The affinity technology in downstream processing. J Biotechnol 36:95–119

    CAS  PubMed  Google Scholar 

  118. Deng Q, German I, Buchanan D, Kennedy RT (2001) Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal Chem 73:5415–5421

    CAS  PubMed  Google Scholar 

  119. Murphy MB, Fuller ST, Richardson PM, Doyle SA (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res 31:e110

    PubMed  PubMed Central  Google Scholar 

  120. Michaud M, Jourdan E, Villet A, Ravel A, Grosset C, Peyrin E (2003) A DNA aptamer as a new target-specific chiral selector for HPLC. J Am Chem Soc 125:8672–8679

    CAS  PubMed  Google Scholar 

  121. Zhao Q, Li XF, Le XC (2008) Aptamer-modified monolithic capillary chromatography for protein separation and detection. Anal Chem 80:3915–3920

    CAS  PubMed  Google Scholar 

  122. Kuehne C, Wedepohl S, Dernedde J (2017) Single-step purification of monomeric l-selectin via aptamer affinity chromatography. Sensors 17:226–232

    Google Scholar 

  123. Finlay TH, Troll V, Levy M, Johnson AJ, Hodgins LT (1978) New methods for the preparation of biospecific adsorbents and immobilized enzymes utilizing trichloro-s-triazine. Anal Biochem 87:77–90

    CAS  PubMed  Google Scholar 

  124. Walter JG, Kökpinar O, Friehs K, Stahl F, Scheper T (2008) Systematic investigation of optimal aptamer immobilization for protein-microarray applications. Anal Chem 80:7372–7378

    CAS  PubMed  Google Scholar 

  125. Kokpinar O, Walter JG, Shoham Y, Stahl F, Scheper T (2011) Aptamer-based downstream processing of his-tagged proteins utilizing magnetic beads. Biotechnol Bioeng 108:2371–2379

    PubMed  Google Scholar 

  126. Ferguson JA, Boles TC, Adams CP, Walt DR (1996) A fiber-optic DNA biosensor microarray for the analysis of gene expression. Nat Biotechnol 14:1681–1684

    CAS  PubMed  Google Scholar 

  127. Weston PD, Avrameas S (1971) Proteins coupled to polyacrylamide beads using glutaraldehyde. Biochem Biophys Res Commun 45:1574–1580

    CAS  PubMed  Google Scholar 

  128. Cambiaso CL, Goffinet A, Vaerman JP, Heremans JF (1975) Glutaraldehyde-activated aminohexyl- derivative of Sepharose 4B as a new versatile immunoabsorbent. Immunochemistry 12:273–278

    CAS  PubMed  Google Scholar 

  129. Oktem HA, Bayramoglu G, Ozalp VC, Arica MY (2007) Single-step purification of recombinant Thermus aquaticus DNA polymerase using DNA-aptamer immobilized novel affinity magnetic beads. Biotechnol Prog 23:146–154

    CAS  PubMed  Google Scholar 

  130. Han B, Zhao C, Yin J, Wang H (2012) High performance aptamer affinity chromatography for single step selective extraction and screening of basic protein lysozyme. J Chromatogr B 903:112–117

    CAS  Google Scholar 

  131. Hemminki K, Suni R (1984) Sites of reaction of glutaraldehyde and acetaldehyde with nucleosides. Arch Toxicol 55:186–190

    CAS  PubMed  Google Scholar 

  132. Chockalingam PS, Gadgil H, Jarrett HW (2002) DNA-support coupling for transcription factor purification. Comparison of aldehyde, cyanogen bromide and N-hydroxysuccinimide chemistries. J Chromatogr A 942:167–175

    CAS  PubMed  Google Scholar 

  133. Stage DE, Mannik M (1974) Covalent binding of molecules to CNBr-activated agarose: parameters relevant to the activation and coupling reactions. Biochim Biophys Acta 343:382–391

    CAS  PubMed  Google Scholar 

  134. Kohn J, Wilchek M (1982) A new approach (cyano-transfer) for cyanogen bromide activation of Sepharose at neutral pH, which yields activated resins, free of interfering nitrogen derivatives. Biochem Biophys Res Commun 107:878–884

    CAS  PubMed  Google Scholar 

  135. Benes MJ, Adamkova K, Turkova J (1991) Activation of beaded cellulose with 2,4,6-trichlorotriazine. Bioact Compat Polym 6:406–413

    CAS  Google Scholar 

  136. Kawamura K, Okamoto F (2000) Condensation reaction of hexanucleotides containing guanine and cytosine with water soluble carbodiimide. Nucleic Acids Symp Ser 44:217–218

    Google Scholar 

  137. Miyakawa S, Nomura Y, Sakamoto T, Yamaguchi Y, Kato K, Yamazaki S, Nakamura Y (2008) Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G. RNA 14:1154–1163

    CAS  PubMed  PubMed Central  Google Scholar 

  138. Ahirwar R, Nahar P (2015) Development of an aptamer-affinity chromatography for efficient single step purification of Concanavalin A from Canavalia ensiformis. J Chromatogr B 997:105–109

    CAS  Google Scholar 

  139. Frost RG, Monthony JF, Engelhorn SC, Siebert CJ (1981) Covalent immobilization of proteins to N-hydroxysuccinimide ester derivatives of agarose. Effect of protein charge on immobilization. Biochim Biophys Acta 670:163–169

    CAS  PubMed  Google Scholar 

  140. Boschetti E, Perret G (2011) Patent Application WO/2012/090183

    Google Scholar 

  141. Sherbet GV, Lakshmi MS, Cajone F (1983) Isoelectric characteristics and the secondary structure of some nucleic acids. Biophys Struct Mech 10:121–128

    CAS  PubMed  Google Scholar 

  142. Steel AB, Levicky RL, Herne TM, Tarlov MJ (2000) Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly. Biophys J 79:975–981

    CAS  PubMed  PubMed Central  Google Scholar 

  143. Balamurugan S, Obubuafo A, McCarley RL, Soper SA, Spivak DA (2008) Effect of linker structure on surface density of aptamer monolayers and their corresponding protein binding efficiency. Anal Chem 80:9630–9634

    CAS  PubMed  PubMed Central  Google Scholar 

  144. Lowe CR (1977) The synthesis of several 8-substituted derivatives of adenosine 5′-monophosphate to study the effect of the nature of the spacer arm in affinity chromatography. Eur J Biochem 73:265–274

    CAS  PubMed  Google Scholar 

  145. Seifert A (2017) Method for obtaining aptamers. Patent Application Number EP2017/066940

    Google Scholar 

  146. Seifert A (2019) Anti-fibrinogen aptamers and uses thereof WO 2018/007530

    Google Scholar 

  147. Seifert A (2019) Anti-immunoglobulin G aptamers and uses thereof. WO 2018/019538

    Google Scholar 

  148. Perret G (2018) Aptamers directed against a kappa light chain-containing protein and uses thereof WO/2018/109213A1

    Google Scholar 

  149. Yan SB (1996) Review of conformation-specific affinity purification methods for plasma vitamin K-dependent proteins. J Mol Recognit 9:211–218

    CAS  PubMed  Google Scholar 

  150. Morfini M (2014) Innovative approach for improved rFVIII concentrate. Eur J Haematol 93:361–368

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Macdougall AJ, Brown JR, Plumbridge TW (1980) Immobilization of DNA for affinity chromatography and drug-binding studies. Biochem J 191:855–858

    CAS  PubMed  PubMed Central  Google Scholar 

  152. Denizli A, Pişkin E (1995) DNA-immobilized polyhydroxyethylmethacrylate microbeads for affinity sorption of human immunoglobulin G and anti-DNA antibodies. J Chromatogr B 666:215–222

    CAS  Google Scholar 

  153. Bartnicki F, Kowalska E, Pels K, Strzalka W (2015) Imidazole-free purification of His3-tagged recombinant proteins using ssDNA aptamer-based affinity chromatography. J Chromatogr A 1418:130–139

    CAS  PubMed  Google Scholar 

  154. Teng IT, Li X, Yadikar HA, Yang Z, Li L, Lyu Y, Pan X, Wang KK, Tan W (2018) Identification and characterization of DNA aptamers specific for phosphorylation epitopes of Tau protein. J Am Chem Soc 14:14314–14323

    Google Scholar 

  155. Cho S, Lee BR, Cho BK, Kim JH, Kim BG (2013) In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars. Biotechnol Bioeng 110:905–913

    CAS  PubMed  Google Scholar 

  156. Tang XL, Hua Y, Guan Q, Yuan CH (2016) Improved detection of deeply invasive candidiasis with DNA aptamers specific binding to (1→3)-β-D-glucans from Candida albicans. Eur J Clin Microbiol Infect Dis 35:587–595

    CAS  PubMed  Google Scholar 

  157. Gonçalves GRF, Gandolfi ORR, Santos LS, Bonomo RCF, Veloso CM, Veríssimo LAA, Fontan RDCI (2017) Immobilization of sugars in supermacroporous cryogels for the purification of lectins by affinity chromatography. J Chromatogr B 1068–1069:71–77

    Google Scholar 

  158. Javaherian S, Musheev MU, Kanoatov M, Berezovski MV, Krylov SN (2009) Selection of aptamers for a protein target in cell lysate and their application to protein purification. Nucleic Acids Res 37:e62

    PubMed  PubMed Central  Google Scholar 

  159. Sinitsyn VV, Mamontova AG, Konovalov GA, Kukharchuk VV (1990) Apheresis of low density lipoproteins using a heparin-based sorbent with low antithrombin III binding capacity. Atherosclerosis 84:55–59

    CAS  PubMed  Google Scholar 

  160. Levashov PA, Afanas’eva OI, Dmitrieva OA, Klesareva EV, Adamova II, Afanas’eva MI, Bespalova ZD, Sidorova MV, Pokrovskiĭ SN (2010) Preparation of affinity sorbents with immobilized synthetic ligands for therapeutic apheresis. Biomed Khim 56:739–746

    CAS  PubMed  Google Scholar 

  161. Wallukat G, Haberland A, Berg S, Schulz A, Freyse EJ, Dahmen C, Kage A, Dandel M, Vetter R, Salzsieder E, Kreutz R, Schimke I (2012) The first aptamer-apheresis column specifically for clearing blood of β1-receptor autoantibodies. Circ J 76:2449–2455

    CAS  PubMed  Google Scholar 

  162. Wallukat G, Müller J, Haberland A, Berg S, Schulz A, Freyse EJ, Vetter R, Salzsieder E, Kreutz R, Schimke I (2016) Aptamer BC007 for neutralization of pathogenic autoantibodies directed against G-protein coupled receptors: a vision of future treatment of patients with cardiomyopathies and positivity for those autoantibodies. Atherosclerosis 244:44–47

    CAS  PubMed  Google Scholar 

  163. Huang S, Gan N, Liu H, Zhou Y, Chen Y, Cao Y (2017) Simultaneous and specific enrichment of several amphenicol antibiotics residues in food based on novel aptamer functionalized magnetic adsorbents using HPLC-DAD. J Chromatogr B 1060:247–254

    CAS  Google Scholar 

  164. Pichon V, Combès A (2016) Selective tools for the solid-phase extraction of Ochratoxin A from various complex samples: immunosorbents, oligosorbents, and molecularly imprinted polymers. Anal Bioanal Chem 408:6983–6999

    CAS  PubMed  Google Scholar 

  165. Michaud M, Jourdan E, Ravelet C, Villet A, Ravel A, Grosset C, Peyrin E (2004) Immobilized DNA aptamers as target-specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomers. Anal Chem 76:1015–1020

    CAS  PubMed  Google Scholar 

  166. Ruta J, Grosset C, Ravelet C, Fize J, Villet A, Ravel A, Peyrin E (2007) Chiral resolution of histidine using an anti-D-histidine L-RNA aptamer microbore column. J Chromatogr B 845:186–190

    CAS  Google Scholar 

  167. Martin JA, Phillips JA, Parekh P, Sefah K, Tan W (2011) Capturing cancer cells using aptamer immobilized square capillary channels. Mol Biosyst 7:1720–1727

    CAS  PubMed  Google Scholar 

  168. Zamay AS, Zamay GS, Kolovskaya OS, Zamay TN, Berezovski MV (2017) Aptamer-based methods for detection of circulating tumor cells and their potential for personalized diagnostics. Adv Exp Med Biol 994:67–81

    CAS  PubMed  Google Scholar 

  169. Chen B, Ye Q, Zhou K, Wang Y (2016) Adsorption and separation of HCV particles by novel affinity aptamer-functionalized adsorbents. J Chromatogr B 1017–1018:174–181

    Google Scholar 

  170. Jayasena SD (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45:1628–1650

    CAS  PubMed  Google Scholar 

  171. Chaou T, Vialet B, Azéma L (2016) DNA aptamer selection in methanolic media: adenine-aptamer as proof-of-concept. Methods 97:11–19

    CAS  PubMed  Google Scholar 

  172. Cho SY, Kang SY, Kong Y (1990) Purification of antigenic protein of sparganum by immunoaffinity chromatography using a monoclonal antibody. Kisaengchunghak Chapchi 28:135–142

    CAS  PubMed  Google Scholar 

  173. Regnault V, Rivat C, Pfister M, Stoltz JF (1991) Monoclonal antibodies against human plasma protein C and their uses for immunoaffinity chromatography. Thromb Res 63:629–640

    CAS  PubMed  Google Scholar 

  174. Song KM, Lee S, Ban C (2012) Aptamers and their biological applications. Sensors 12:612–631

    PubMed  Google Scholar 

  175. Ferreira CS, Missailidis S (2007) Aptamer-based therapeutics and their potential in radiopharmaceutical design. Braz Arch Biol Technol 50:63–76

    Google Scholar 

  176. Kim HC, McMillan CW, White GC, Bergman GE, Horton MW, Saidi P (1992) Purified factor IX using monoclonal immunoaffinity technique: clinical trials in hemophilia B and comparison to prothrombin complex concentrates. Blood 79:568–575

    CAS  PubMed  Google Scholar 

  177. Pålsson E, Smeds AL, Petersson A, Larsson PO (1999) Faster isolation of recombinant factor VIII SQ, with a superporous agarose matrix. J Chromatogr A 840:39–50

    PubMed  Google Scholar 

  178. Tiede A, Klamroth R, Oldenburg J (2015) Turoctocog alfa (recombinant factor VIII). Manufacturing, characteristics and clinical trial results. Hamostaseologie 35:364–371

    CAS  PubMed  Google Scholar 

  179. Reinhart D, Weik R, Kunert R (2012) Recombinant IgA production: single step affinity purification using camelid ligands and product characterization. J Immunol Methods 378:95–101

    CAS  PubMed  Google Scholar 

  180. Fleminger G, Hadas E, Wolf T, Solomon B (1990) Oriented immobilization of periodate-oxidized monoclonal antibodies on amino and hydrazide derivatives of Eupergit C. Appl Biochem Biotechnol 23:123–137

    CAS  PubMed  Google Scholar 

  181. Wang H, Liu Y, Yang Y, Deng T, Shen G, Yu R (2004) A protein A-based orientation-controlled immobilization strategy for antibodies using nanometer-sized gold particles and plasma-polymerized film. Anal Biochem 324:219–226

    CAS  PubMed  Google Scholar 

  182. Ikeda T, Hata Y, Ninomiya K, Ikura Y, Takeguchi K, Aoyagi S, Hirota R, Kuroda A (2009) Oriented immobilization of antibodies on a silicon wafer using Si-tagged protein A. Anal Biochem 385:132–137

    CAS  PubMed  Google Scholar 

  183. Tajima N, Takai M, Ishihara K (2011) Significance of antibody orientation unraveled: well-oriented antibodies recorded high binding affinity. Anal Chem 83:1969–1976

    CAS  PubMed  Google Scholar 

  184. Kuwahara M, Obika S (2013) In vitro selection of BNA (LNA) aptamers. Artif DNA PNA XNA 4:39–48

    PubMed  PubMed Central  Google Scholar 

  185. Hagiwara K, Fujita H, Kasahara Y, Irisawa Y, Obika S, Kuwahara M (2015) In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids. Mol Biosyst 11:71–76

    CAS  PubMed  Google Scholar 

  186. Gold L, Walker JJ, Wilcox SK, Williams S (2012) Advances in human proteomics at high scale with the SOMAscan proteomics platform. Nat Biotechnol 29:543–549

    CAS  Google Scholar 

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Authors and Affiliations

  1. LFB Biotech, Les Ulis, France

    G. Perret

  2. JAM Conseil, Neuilly-sur-Seine, France

    E. Boschetti

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  1. G. Perret
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  1. Basel, Switzerland

    Katharina Urmann

  2. University Hannover, Gottfried-Wilhelm Leibniz, Hannover, Niedersachsen, Germany

    Johanna-Gabriela Walter

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Perret, G., Boschetti, E. (2019). Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. In: Urmann, K., Walter, JG. (eds) Aptamers in Biotechnology. Advances in Biochemical Engineering/Biotechnology, vol 174. Springer, Cham. https://doi.org/10.1007/10_2019_106

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