Abstract
This review will summarize recent progress of liquid-phase oligonucleotide synthesis and also briefly introduce the challenge to develop a process that applies our original liquid-phase synthesis technology for practical use.
Recent progress in various types of oligonucleotide therapeutics, such as antisense, aptamer, siRNA and miRNA, has led to growing demand for economical and/or large scale production. Conventionally-known solid-phase synthesis which has been only a method of choice over the past few decades rapidly supplies oligonucleotides in high quality but in a limited quantity. Major issues of solid-phase synthesis that need to be addressed are scale-up and manufacturing cost. The former is attributable to the dedicated synthesizer’s capacity and the latter associate with heterogeneous reactions: use of expensive resins and excess amidite reagents.
Liquid-phase approaches may overcome these limitations. Behind the progress of solid-phase synthesis, researchers have investigated unique liquid-phase approaches. Among them, several methods utilizing soluble supports instead of solid resins are combining the advantage of solid-phase synthesis and liquid-phase synthesis, and expected to have possibility of industry applicable methods.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Freier SM, Watt AT (2001) Basic principles of antisense drug discovery. In: Crooke ST (ed) Antisense drug technology: principles, strategies, and applications, 2nd edn. Marcel Dekker, New York
a) Sharma VK, Sharma RK, Singh SK (2014) Antisense oligonucleotides: modifications and clinical trials. Med Chem Commun 5:1454–1471; b) Sharma VK, Rungta P, Prasad AK (2014) Nucleic acid therapeutics: basic concepts and recent developments. RCS Adv 4:16618–16631
Geary RS, Khatsenko O, Bunker K et al (2001) Absolute bioavailability of 2′-O-(2-methoxyethyl)-modified antisense oligonucleotides following intraduodenal instillation in rats. J Pharmacol Exp Ther 296:898–904
a) Campbell MA, Wengel J (2011) Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 40:5680–5689; b) Kaur H, Babu BR, Maiti S (2007) Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA) Chem Rev 107:4672–4697; c) Obika S (2004) Development of bridged nucleic acid analogues for antigene technology. Chem Pharm Bull 52:1399–1404
Summerton J, Weller D (1997) Morpholino antisense oligomers: design, preparation, and properties. Antisense Nucleic Acid Drug Dev 7:187–195
a) Geary RS, Baker BF, Crooke ST (2015) Clinical and preclinical pharmacokinetics and pharmacodynamics of mipomersen (Kynamro®): a second-generation antisense oligonucleotide inhibitor of apolipoprotein B. Clin Pharmacokinet 54:133–146; b) Hair P, Cameron F, McKeage K (2013) Mipomersen sodium: first global approval. Drugs 73:487–493
Sanghvi YS, Schulte M (2004) Therapeutic oligonucleotides: the state-of-the-art in purification technologies. Curr Opin Drug Discov Devel 6:765–776
Reese CB (1978) The chemical synthesis of oligo- and poly-nucleotides by the phosphotriester approach. Tetrahedron 34:3143–3179
a) Reese CB, Song Q (1997) A new approach to the synthesis of oligonucleotides and their phosphorothioate analogues in solution. Bioorg Med Chem Lett 7:2787–2792; b) Reese CB, Song Q (1999) The H-phosphonate approach to the solution phase synthesis of linear and cyclic oligoribonucleotides. Nucl Acids Res 27:963–971; c) Reese CB, Song Q (1999) The H-phosphonate approach to the synthesis of oligonucleotides and their phosphorothioate analogues in solution. J Chem Soc Perkin Trans 1 1477–1486; d) Reese CB, Yan H (2002) Solution phase synthesis of ISIS 2922 (Vitravene) by the modified H-phosphonate approach. J Chem Soc Perkin Trans 1:2619–2633
Bayer E, Mutter M (1972) Liquid phase synthesis of peptide. Nature 237:512–513
Kamaike K, Hasegawa Y, Masuda I et al (1990) Oligonucleotide synthesis in terms of a novel type of polymer-support: a cellulose acetate functionalized with 4-(2-hydroxyethylsulfonyl)dihydrocinnamoyl substituent. Tetrahedron 46:163–184
Gimenez A, Kungurtsev V, Virta P et al (2012) Acetylated and methylated β-cyclodextrins as viable soluble supports for the synthesis of short 2′-oligodeoxyribo-nucleotides in solution. Molecules 17:12012–12120
a) Bonora GM (1987) Gazzetta Chim Ital 117:379–380; b) Bonora GM (1995) Polyethylene glycol. Appl Biochem Biotechnol 54:3–17
a) Bonora GM, Scremin CL, Colonna FP et al (1990) Nucleic Acids Res 18:3155–3159; b) Colonna FP, Scremin CL, Bonora GM (1991) Large scale H.E.L.P. synthesis of oligodeoxynucleotides by the hydroxybenzotriazole phosphotriester approach. Tetrahedron Lett 32:3251–3254; c) Bonora GM, Scremin CL, Colonna FP et al (1991) Nucleosides Nucleotides 10:269–273
Bonora GM, Biancotto G, Maffini M et al (1993) Large scale, liquid phase synthesis of oligonucleotides by the phosphoramidite approach. Nucleic Acids Res 21:1213–1217
Zaramella S, Bonora GM (1995) The application of H-phosphonate chemistry in the HELP synthesis of oligonucleotides. Nucleosides Nucleotides 14:809–813
a) Scremin CL, Bonora GM (1993) Liquid phase synthesis of phosphorothioate oligonucleotides on polyethylene glycol support. Tetrahedron Lett 34:4663–4666; b) Bonora GM, Zaramella S, Ravikumar V (2001) Large-scale solution synthesis of phosphorothioate oligonucleotides: a comparison of the phosphoroamidite and phosphotriester dimeric approaches. Croat Chim Acta 74:779–786
Bonora GM, Rossin R, Zaramella S et al (2000) A liquid-phase process suitable for large-scale synthesis of phosphorothioate opligonucleotides. Org Proc Res Dev 4:225–231
a) Donga RA, Khaliq-Uz-Zaman SM, Chan TH et al (2006) A novel approach to oligonucleotide synthesis using an imidazolium ion tag as a soluble support. J Org Chem 71:7907–7910; b) Donga RA, Hassler M, Chan TH et al (2007) Oligonucleotide synthesis using ionic liquids as soluble supports. Nucleosides Nucleotides Nucleic Acids 26:1287–1293; c) Donga RA, Chan TH, Damha MJ (2007) Ion-tagged synthesis of an oligoribonucleotide pentamer—the continuing versatility of TBDMS chemistry. Can J Chem 85:274–282
a) Wada T (2013) Methods for the synthesis of functionalized nucleic acids. International Patent WO 2005/070859 A1, 24 Jan 2013; b) Oka N, Murakami R, Kondo T et al (2013) Stereocontrolled synthesis of dinucleoside phosphorothioates using a fluorous tag. J Fluorine Chem 150:85–91
a) Pearson WH, Berry DA, Stoy P et al (2005) Fluorous affinity purification of oligonucleotides. J Org Chem 70:7114–7122; b) Berry DA, Pearson WH (2006) Fluorous oligonucleotide reagents and affinity purification of oligonucleotides acids. International Patent WO 2006/081035 A2, 3 Aug 2006; c) Dandapani S (2006) Recent applications of fluorous separation methods in organic and bioorganic chemistry. QSAR Comb Sci 8:681–688
a) Mishra R, Mishra S, Misra K (2006) Synthesis and application of fluorous-tagged oligonucleotides. Chemistry Lett 35:1184–1185; b) Tripathi S, Misra K, Sanghvi YS (2005) Group for 5′-hydroxyl protection of oligonucleosides. Org Prep Proc Int 37:257–263
a) Biernat J, Wolter A, Köster H (1983) Purification orientated synthesis of oligodeoxynucleotides in solution. Tetrahedron Lett 24:751–754; b) Wörl R, Köster H (1999) Synthesis of new liquid phase carriers for use in large scale oligonucleotide synthesis in solution. Tetrahedron 55:2941–2956; c) Kungurtsev V, Laakkonen J, Molina AG et al (2013) Solution-phase synthesis of short oligo-2-deoxyribonucleotides by using clustered nucleosides as a soluble support. Eur J Org Chem:6687–6693; d) Kungurtsev V, Virta P, Lönnberg H (2013) Synthesis of short oligodeoxyribonucleotides by phosphotriester chemistry on a precipitative tetrapodal support. Eur J Org Chem 7886:7890
de Koning MC, Ghisaidoobe ABT, Duynstee HI et al (2006) Simple and efficient solution-phase synthesis of oligonucleotides using extractive work-up. Org Proc Res Dev 10:1238–1245
a) Chiba K, Kin S, Soichiro T et al (2010) Hydrophobic group-linked nucleoside, hydrophobic group-linked nucleoside solution and method of synthesizing hydrophobic group-linked oligonucleotide. Japanese Patent JP 2010-275254, 9 Dec 2010; b) Kim S, Matsumoto M (2013) Oligonucleotide synthesis method using highly dispersible liquid-phase support. International Patent WO 2013/179412 A1, 5 Dec 2013; c) Kim S, Matsumoto M, Chiba K (2013) Liquid-phase RNA synthesis by using alkyl-chain-soluble support. Chem Eur J 19:8615–8620; d) Shoji T, Kim S, Chiba K (2014) Synthesis of conjugated oligonucleotide in solution phase using alkyl-chain-soluble support. Chem Lett 43:1251–1253
Mihaichuk JC, Hurley TB, Vagle KE (2000) The dimethoxytrityl resin product anchored sequential synthesis method (DMT PASS): a conceptually novel approach to oligonucleotide synthesis. Org Proc Res Dev 4:214–224
a) Dueymes C, Schönberger A, Adamo I et al (2005) High-yield solution-phase synthesis of di- and trinucleotide blocks assisted by polymer-supported reagents. Org Lett 7:3485–3488; b) Adamo I, Dueymes C, Schönberger A et al (2006) Solution-phase synthesis of phosphorothioate oligonucleotides using a solid-supported acyl chloride with H-phosphonate chemistry. Eur J Org Chem 436–448; c) Adamo I, Dueymes C, Schönberger A et al (2004) Method for preparing oligonucleotides. International Patent WO2004/013154 12 Feb 2004; d) Mohe N, Heinonen P, Sanghvi Y-S et al (2005) A solid supported reagent for internucleoside H-phosphonate linkage formation. Nucleosides Nucleotides Nucleic Acids 24:897–899
a) Takahashi D (2009) Method for production of peptide. International Patent WO 2009014176, 29 Jan 2009; b) Takahashi D (2009) Method for selective removal of dibenzofulvene derivative. International Patent WO 2009014177 29 Jan 2009; c) Takahashi D (2010) Fluorene compound. International Patent WO 2010104169, 16 Sep 2010; d) Takahashi D (2010) Diphenylmethane compound. International Patent WO 20100249374, 30 Sep 2010; e) Takahashi D (2011) Benzyl compound. International Patent WO 2011078295, 30 Jun 2011; f) Takahashi D, Yano T, Fukui T (2012) Novel diphenylmethyl-derived amide protecting group for efficient liquid-phase peptide synthesis: AJIPHASE. Org Lett 14:4514–4517; g) Takahashi D, Yamamoto T (2012) Development of an efficient liquid-phase peptide synthesis protocol using a novel fluorene-derived anchor support compound with Fmoc chemistry; AJIPHASE®. Tetrahedron Lett 53:1936–1939; h) Takahashi D (2012) Aromatic compound containing specific branch. International Patent WO 2012029794 Mar 8 2012; i) Takahashi D (2012) Method for producing peptide. International Patent WO 2012165545, 6 Dec 2012; j) Takahashi D (2012) Method for producing peptide. International Patent WO 2012165546, 6 Dec 2012; k) Takahashi D (2013) Method for removing Fmoc group. International Patent WO 2013089241, 20 Jun 2013
a) Hirai K, Katayama S (2012) Method for producing oligonucleotide. International Patent WO 2012157723, 22 Nov 2012; b) Hirai K, Katayama S, Torii T et al (2013) Base-protected oligonucleotide. International Patent WO 2013122236, 22 Aug 2013
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Katayama, S., Hirai, K. (2018). Liquid-Phase Synthesis of Oligonucleotides. In: Obika, S., Sekine, M. (eds) Synthesis of Therapeutic Oligonucleotides. Springer, Singapore. https://doi.org/10.1007/978-981-13-1912-9_5
Download citation
DOI: https://doi.org/10.1007/978-981-13-1912-9_5
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-1911-2
Online ISBN: 978-981-13-1912-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)