Affinity approaches in RNAi-based therapeutics purification

Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences

Volumn 1021, Issue , 2016, Pages 45-56

  Pereira, Patrícia ^a   Queiroz, João A ^a   Figueiras, Ana ^a,b   Sousa, Fani ^a  

^a UNIVERSITY OF BEIRA INTERIOR   (Portugal)

^b UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

Affinity chromatography; Non coding RNAs; Review; RNA purification

Indexed keywords

AFFINITY CHROMATOGRAPHY; BIOACTIVITY; CHROMATOGRAPHY; GENE EXPRESSION; PURIFICATION; REVIEWS; RNA;

CLINICAL APPLICATION; HIGH PURITY; HIGH SPECIFICITY; HUMAN DISEASE; MICRORNAS; NON-CODING RNAS; RNA INTERFERENCE; SHORT INTERFERING RNA;

NUCLEIC ACIDS;

AMINO ACID DERIVATIVE; BORONIC ACID DERIVATIVE; LONG UNTRANSLATED RNA; MICRORNA; PIWI INTERACTING RNA; SMALL INTERFERING RNA; UNTRANSLATED RNA;

AFFINITY CHROMATOGRAPHY; BIOGENESIS; CLINICAL TRIAL (TOPIC); DRUG PURIFICATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNAI THERAPEUTICS; SIGNAL TRANSDUCTION; ISOLATION AND PURIFICATION;

CHROMATOGRAPHY, AFFINITY; HUMANS; RNA, UNTRANSLATED; RNAI THERAPEUTICS;

EID: 84979462515     PISSN: 15700232     EISSN: 1873376X     Source Type: Journal    
DOI: 10.1016/j.jchromb.2016.01.022     Document Type: Review

References (105)

1. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
2. Lehman N. RNA in evolution. Wiley Interdiscip. Rev. RNA 2010, 1:202-213.
3. Ramachandran P.V., Ignacimuthu S. RNA interference-a silent but an efficient therapeutic tool. Appl. Biochem. Biotechnol. 2013, 169:1774-1789.
4. Dogini D.B., Pascoal V.D., Avansini S.H., Vieira A.S., Pereira T.C., Lopes-Cendes I. The new world of RNAs. Genet. Mol. Biol. 2014, 37:285-293.
5. Gomes A.Q., Nolasco S., Soares H. Non-coding RNAs: multi-tasking molecules in the cell. Int. J. Mol. Sci. 2013, 14:16010-16039.
6. Shi X., Sun M., Liu H., Yao Y., Song Y. Long non-coding RNAs: a new frontier in the study of human diseases. Cancer Lett. 2013, 339:159-166.
7. Harries L.W. Long non-coding RNAs and human disease. Biochem. Soc. Trans. 2012, 40:902-906.
8. Sullenger B.A., Gilboa E. Emerging clinical applications of RNA. Nature 2002, 418:252-258.
9. Kreiter S., Diken M., Selmi A., Tureci O., Sahin U. Tumor vaccination using messenger RNA: prospects of a future therapy. Curr. Opin. Immunol. 2011, 23:399-406.
10. Pascolo S. Vaccination with messenger RNA. Methods Mol. Med. 2006, 127:23-40.
11. Scott L.G., Hennig M. RNA structure determination by NMR. Methods Mol. Biol. 2008, 452:29-61.
12. Doudna J.A. Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol. Biol. 1997, 74:365-370.
13. Wittmann A., Suess B. Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett. 2012, 586:2076-2083.
14. Ponchon L., Dardel F. Large scale expression and purification of recombinant RNA in Escherichia coli. Methods 2011, 54:267-273.
15. Sherlin L.D., Bullock T.L., Nissan T.A., Perona J.J., Lariviere F.J., Uhlenbeck O.C., Scaringe S.A. Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. RNA 2001, 7:1671-1678.
16. Pereira P., Sousa A., Queiroz J., Correia I., Figueiras A., Sousa F. Purification of pre-miR-29 by arginine-affinity chromatography. J. Chromatogr. B 2014, 951-952:16-23.
17. Martins R., Queiroz J.A., Sousa F. A new affinity approach to isolate Escherichia coli 6S RNA with histidine-chromatography. J. Mol. Recognit. 2010, 23:519-524.
18. Huang L., Lieberman J. Production of highly potent recombinant siRNAs in Escherichia coli. Nat. Protoc. 2013, 8:2325-2336.
19. Li M.M., Wang W.P., Wu W.J., Huang M., Yu A.M. Rapid production of novel pre-microRNA agent hsa-mir-27b in Escherichia coli using recombinant RNA technology for functional studies in mammalian cells. Drug Metab. Dispos. 2014, 42:1791-1795.
20. Nagao N., Suzuki H., Numano R., Umekage S., Kikuchi Y. Short hairpin RNAs of designed sequences can be extracellularly produced by the marine bacterium Rhodovulum sulfidophilum. J. Gen. Appl. Microbiol. 2014, 60:222-226.
21. Dunin-Horkawicz S., Czerwoniec A., Gajda M.J., Feder M., Grosjean H., Bujnicki J.M. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 2006, 34:D145-149.
22. Martins R., Queiroz J.A., Sousa F. Ribonucleic acid purification. J. Chromatogr. A 2014, 1355:1-14.
23. Easton L.E., Shibata Y., Lukavsky P.J. Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA 2010, 16:647-653.
24. McCarthy S.M., Gilar M., Gebler J. Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA. Anal. Biochem. 2009, 390:181-188.
25. Noll B., Seiffert S., Hertel F., Debelak H., Hadwiger P., Vornlocher H.P., Roehl I. Purification of small interfering RNA using nondenaturing anion-exchange chromatography. Nucleic Acid Ther. 2011, 21:383-393.
26. Koubek J., Lin K.F., Chen Y.R., Cheng R.P., Huang J.J. Strong anion-exchange fast performance liquid chromatography as a versatile tool for preparation and purification of RNA produced by in vitro transcription. RNA 2013, 19:1449-1459.
27. Hagen F.S., Young E.T. Preparative polyacrylamide gel electrophoresis of ribonucleic acid. Identification of multiple molecular species of bacteriophage T7 lysozyme messenger ribonucleic acid. Biochemistry 1974, 13:3394-3400.
28. Kim I., McKenna S.A., Viani Puglisi E., Puglisi J.D. Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA 2007, 13:289-294.
29. Gallas A., Alexander C., Davies M.C., Puri S., Allen S. Chemistry and formulations for siRNA therapeutics. Chem. Soc. Rev. 2013, 42:7983-7997.
30. Kim V.N. Small RNAs: classification, biogenesis, and function. Mol. Cells 2005, 19:1-15.
31. Gavrilov K., Saltzman W.M. Therapeutic siRNA: principles, challenges, and strategies. Yale J. Biol. Med. 2012, 85:187-200.
32. Huang Y., Zhang J.L., Yu X.L., Xu T.S., Wang Z.B., Cheng X.C. Molecular functions of small regulatory noncoding RNA. Biochemistry (Mosc) 2013, 78:221-230.
33. Guzman-Villanueva D., El-Sherbiny I.M., Herrera-Ruiz D., Vlassov A.V., Smyth H.D. Formulation approaches to short interfering RNA and MicroRNA: challenges and implications. J. Pharm. Sci. 2012, 101:4046-4066.
34. Qurashi A., Jin P. Small RNA-mediated gene regulation in neurodevelopmental disorders. Curr. Psychiatr. Rep. 2010, 12:154-161.
35. Nilsen T.W. Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet. 2007, 23:243-249.
36. Zhang Y., Wang Z., Gemeinhart R.A. Progress in microRNA delivery. J. Controlled Release 2013, 172:962-974.
37. Broderick J.A., Zamore P.D. MicroRNA therapeutics. Gene Ther. 2011, 18:1104-1110.
38. Zhu J., Fu H., Wu Y., Zheng X. Function of lncRNAs and approaches to lncRNA-protein interactions. Sci. China Life Sci. 2013, 56:876-885.
39. Memczak S., Jens M., Elefsinioti A., Torti F., Krueger J., Rybak A., Maier L., Mackowiak S.D., Gregersen L.H., Munschauer M., Loewer A., Ziebold U., Landthaler M., Kocks C., le Noble F., Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495:333-338.
40. Burnett J.C., Rossi J.J. RNA-based therapeutics: current progress and future prospects. Chem. Biol. 2012, 19:60-71.
41. Ferrel R.E. RNA Methodologies-Laboratory Guide for Isolation and Characterization 2005, Academic Press, York, USA.
42. Uhlen M. Affinity as a tool in life science. Biotechniques 2008, 44:649-654.
43. Roque A.C., Lowe C.R. Affinity chromatography: history, perspectives, limitations and prospects. Methods Mol. Biol. 2008, 421:1-21.
44. Labrou N.E. Design and selection of ligands for affinity chromatography. J. Chromatogr. B 2003, 790:67-78.
45. Sousa F., Prazeres D.M., Queiroz J.A. Affinity chromatography approaches to overcome the challenges of purifying plasmid DNA. Trends Biotechnol. 2008, 26:518-525.
46. Lowe C.R., Lowe A.R., Gupta G. New developments in affinity chromatography with potential application in the production of biopharmaceuticals. J. Biochem. Biophys. Methods 2001, 49:561-574.
47. Yarus M., Widmann J.J., Knight R. RNA-amino acid binding: a stereochemical era for the genetic code. J. Mol. Evol. 2009, 69:406-429.
48. Mallik R., Hage D.S. Affinity monolith chromatography. J. Sep. Sci. 2006, 29:1686-1704.
49. Pereira P., Sousa A., Queiroz J.A., Figueiras A., Sousa F. Pharmaceutical-grade pre-miR-29 purification using an agmatine monolithic support. J. Chromatogr. A 2014, 1368:173-182.
50. Sousa A., Sousa F., Queiroz J.A. Advances in chromatographic supports for pharmaceutical-grade plasmid DNA purification. J. Sep. Sci. 2012, 35:3046-3058.
51. Ayyar B.V., Arora S., Murphy C., O'Kennedy R. Affinity chromatography as a tool for antibody purification. Methods 2012, 56:116-129.
52. Moore P.B. Structural motifs in RNA. Annu. Rev. Biochem. 1999, 68:287-300.
53. Weith H.L., Wiebers J.L., Gilham P.T. Synthesis of cellulose derivatives containing the dihydroxyboryl group and a study of their capacity to form specific complexes with sugars and nucleic acid components. Biochemistry 1970, 9:4396-4401.
54. Singh N., Willson R.C. Boronate affinity adsorption of RNA: possible role of conformational changes. J. Chromatogr. A 1999, 840:205-213.
55. Schott H., Rudloff E., Schmidt P., Roychoudhury R., Koessel H. A dihydroxyborylsubstituted methacrylic polymer for the column chromatographic separation of mononucleotides, oligonucleotides, and transfer ribonucleic acid. Biochemistry 1973, 12:932-938.
56. Ackerman S., Cool B., Furth J. Removal of DNA from RNA by chromatography on acetylated N-[N'-(m-dihydroxylborylphenyl) succinamyl]aminoethyl cellulose. Anal. Biochem. 1979, 100:174-178.
57. Rosenberg M., Gilham P.T. The isolation of 3'-terminal polynucleotides from RNA molecules. Biochim. Biophys. Acta 1971, 246:337-340.
58. Liu X., Scouten W.H. Part 1: Boronic Acids as Selective Ligands for Affinity Chromatography, Miscellaneous Methods in Affinity Chromatography 2002, Taylor and Francis Group, Florida.
59. Yurkevich A., Kolodkina I., Ivanova E., Pichuzhkina E. Study of the interaction of polyols with polymers containing N-substituted [(4-boronophenyl) methylammonio] groups. Carbohydr. Res. 1975, 43:215-224.
60. Elmas B., Onur M.A., Senel S., Tuncel A. Thermosensitive N-isopropylacrylamidevinylphenylboronic acid copolymer latex particles for nucleotide isolation. Colloids Surf. A 2004, 232:253-259.
61. Clcek H. Nucleotide isolation by boronic acid functionalized hydrogel beads. J. Bioact. Compat. Polym. 2005, 20:245-257.
62. Tanaka N., Kobayashi H., Ishizuka H., Minakuchi H., Nakanishi K., Hosoya K., Ikegami T. Monolithic silica columns for high efficiency chromatographic separations. J. Chromatogr. A 2002, 965:35-49.
63. Srivastava A., Shakya A.K., Kumar A. Boronate affinity chromatography of cells and biomacromolecules using cryogel matrices. Enzyme Microb. Technol. 2012, 51:373-381.
64. Srisawat C., Engelke D.R. RNA affinity tags for purification of RNAs and ribonucleoprotein complexes. Methods 2002, 26:156-161.
65. Pestourie C., Tavitian B., Duconge F. Aptamers against extracellular targets for in vivo applications. Biochimie 2005, 87:921-930.
66. Porath J. Immobilized metal ion affinity chromatography. Protein Expression Purif. 1992, 3:263-281.
67. Evan G.I., Lewis G.K., Ramsay G., Bishop J.M. Isolation of monoclonal antibodies specific for human cmyc proto-oncogene product. Mol. Cell Biol. 1985, 5:3610-3616.
68. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Séraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1999, 17:1030-1032.
69. Uhlen M., Nilsson B., Guss B.M., Lindberg M., Gatenbeck S., Philipson L. Gene fusion vectors based on the gene for staphylococcal protein A. Gene 1983, 23:369-378.
70. Yoon J.H., Srikantan S., Gorospe M. MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs. Methods 2012, 58:81-87.
71. Simons P.C., Vander Jagt D.L. Purification of glutathione S-transferases by glutathione-affinity chromatography. Methods Enzymol. 1981, 77:235-237.
72. Schmidt T.G., Koepke J., Frank R., Skerra A. Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin. J. Mol. Biol. 1996, 255:753-766.
73. Leppek K., Stoecklin G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res. 2014, 42:e13.
74. Prickett K.S., Amberg D.C., Hopp T.P. A calcium-dependent antibody for identification and purification of recombinant proteins. Biotechniques 1989, 7:580-589.
75. Srisawat C., Engelke D.R. Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 2001, 7:632-641.
76. Srisawat C., Goldstein I.J., Engelke D.R. Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res. 2001, 29:E4.
77. Wei K., Yan F., Xiao H., Yang X., Xie G., Xiao Y., Wang T., Xun Y., Huang Z., Han M., Zhang J., Xiang S. Affinity purification of binding miRNAs for messenger RNA fused with a common tag. Int. J. Mol. Sci. 2014, 15:14753-14765.
78. Orom U.A., Lund A.H. Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods 2007, 43:162-165.
79. Gong C., Popp M.W., Maquat L.E. Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes. Methods 2012, 58:88-93.
80. Flores-Jasso C.F., Salomon W.E., Zamore P.D. Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates. RNA 2013, 19:271-279.
81. Batey R.T., Kieft J.S. Improved native affinity purification of RNA. RNA 2007, 13:1384-1389.
82. Di Tomasso G., Lampron P., Dagenais P., Omichinski J.G., Legault P. The ARiBo tag: a reliable tool for affinity purification of RNAs under native conditions. Nucleic Acids Res. 2011, 39:e18.
83. Di Tomasso G., Dagenais P., Desjardins A., Rompre-Brodeur A., Delfosse V., Legault P. Affinity purification of RNA using an ARiBo tag. Methods Mol. Biol. 2012, 941:137-155.
84. Di Tomasso G., Salvail-Lacoste A., Bouvette J., Omichinski J.G., Legault P. Affinity purification of in vitro transcribed RNA with homogeneous ends using a 3'-ARiBo tag. Methods Enzymol. 2014, 549:49-84.
85. Salvail-Lacoste A., Di Tomasso G., Piette B.L., Legault P. Affinity purification of T7 RNA transcripts with homogeneous ends using ARiBo and CRISPR tags. RNA 2013, 19:1003-1014.
86. Walker S.C., Scott F.H., Srisawat C., Engelke D.R. RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol. Biol. 2008, 488:23-40.
87. Afonso A., Pereira P., Queiroz J.A., Sousa A., Sousa F. Purification of pre-miR-29 by a new O-phospho-l-tyrosine affinity chromatographic strategy optimized using design of experiments. J. Chromatogr. A 2014, 1343:119-127.
88. Pereira P., Sousa A., Queiroz J., Figueiras A., Sousa F. New approach for purification of pre-miR-29 using lysine-affinity chromatography. J. Chromatogr. A. 2014, 1331:129-132.
89. Martins R., Maia C.J., Queiroz J.A., Sousa F. A new strategy for RNA isolation from eukaryotic cells using arginine affinity chromatography. J. Sep. Sci. 2012, 35:3217-3226.
90. Martins R., Queiroz J.A., Sousa F. Histidine affinity chromatography-based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA. Biomed. Chromatogr. 2011, 26(7):781-788.
91. Jones D.S., Lundgren H.K., Jay F.T. The separation of ribonucleic acids from Escherichia coli on lysin-agarose. Nucleic Acids Res. 1976, 3:1569-1576.
92. Sousa F., Cruz C., Queiroz J.A. Amino acids-nucleotides biomolecular recognition: from biological occurrence to affinity chromatography. J. Mol. Recognit. 2010, 23:505-518.
93. Calnan B.J., Tidor B., Biancalana S., Hudson D., Frankel A.D. Arginine-mediated RNA recognition: the arginine fork. Science 1991, 252:1167-1171.
94. Pereira P., Cruz C., Queiroz J.A., Figueiras A., Sousa F. Analysis of pre-miR-29b binding conditions to amino acids by using a surface plasmon resonance biosensor. Anal. Methods 2016, 8:205.
95. Ellis J.J., Broom M., Jones S. Protein-RNA interactions: structural analysis and functional classes. Proteins 2007, 66:903-911.
96. Treger M., Westhof E. Statistical analysis of atomic contacts at RNA-protein interfaces. J. Mol. Recognit. 2001, 14:199-214.
97. Hoffman M.M., Khrapov M.A., Cox J.C., Yao J., Tong L., Ellington A.D. AANT: the amino acid-nucleotide interaction database. Nucleic Acids Res. 2004, 32:D174-181.
98. Luscombe N.M., Laskowski R.A., Thornton J.M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 2001, 29:2860-2874.
99. Puglisi J.D., Wyatt J.R., Tinoco I. Solution conformation of an RNA hairpin loop. Biochemistry 1990, 29:4215-4226.
100. Janas T., Widmann J.J., Knight R., Yarus M. Simple, recurring RNA binding sites for l-arginine. RNA 2010, 16:805-816.
101. Pfaunmiller E.L., Paulemond M.L., Dupper C.M., Hage D.S. Affinity monolith chromatography: a review of principles and recent analytical applications. Anal. Bioanal. Chem. 2013, 405:2133-2145.
102. Arrua R.D., Alvarez Igarzabal C.I. Macroporous monolithic supports for affinity chromatography. J. Sep. Sci. 2011, 34:1974-1987.
103. Ponchon L., Catala M., Seijo B., El Khouri M., Dardel F., Nonin-Lecomte S., Tisne C. Co-expression of RNA-protein complexes in Escherichia coli and applications to RNA biology. Nucleic Acids Res. 2013, 41:e150.
104. Ponchon L., Dardel F. Recombinant RNA technology: the tRNA scaffold. Nat. Methods 2007, 4:571-576.
105. Jin J., Cid M., Poole C.B., McReynolds L.A. Protein mediated miRNA detection and siRNA enrichment using p19. Biotechniques 2010, 48:xvii-xxiii.