Skip to main content
SpringerLink
Log in

Large-Scale Oligonucleotide Manufacturing

  • Chapter
  • First Online:
Book cover Synthesis of Therapeutic Oligonucleotides

Abstract

In the past decades, synthetic oligonucleotides have been explored for therapeutic purposes and seven oligonucleotide drugs have been successfully approved by FDA with many oligonucleotides, approximately 100, are in clinical trials worldwide. The increase in demand for a large quantity of oligonucleotide material for therapeutic applications has led to more cost-effective manufacturing technologies. Synthetic oligonucleotide quality has been improved by using raw materials with the highest possible purity. At the same time, yields and throughput have been increased significantly by the introduction of high loaded polymer supports like NittoPhase™ and by continuous development and optimization of oligonucleotide manufacturing processes that allow oligonucleotide manufacturers to access to a wide variety of oligonucleotide modifications. However, large scale oligonucleotide manufacturing is still not straight forward. In this chapter, considerations on large scale manufacturing equipment and a small scale modeling approach for scaling up each of the manufacturing processes are described.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. (a) Katzhendler J, Cohen S, Rahamim E, Weisz M, Ringel I, Deutsch J (1989) The effect of spacer, linkage and solid support on the synthesis of oligonucleotides. Tetrahedron 45:2777–2792; (b) Kozlov IA, Dang M, Sikes K, Kotseroglou T, Barker DL, Zhao C (2005) Significant improvement of quality for long oligonucleotides by using controlled pore glass with large pores. Nucleosides Nucleotides Nucleic Acids 24(5–7):1037–1041

    Google Scholar 

  2. Yip KF, Tsou KC (1971) A new polymer-support method for the synthesis of ribooligonucleotide. J Am Chem Soc 93:3272–3276

    Article  CAS  PubMed  Google Scholar 

  3. Alul RH, Singman CN, Zhang GR, Letsinger RL (1991) Oxalyl-CPG: a labile support for synthesis of sensitive oligonucleotide derivatives. Nucleic Acids Res 19(7):1527–1532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. (a) Pon RT, Yu S (1997) Hydroquinone-O,O′-diacetic acid (‘Q-linker’) as a replacement for succinyl and oxalyl linker arms in solid phase oligonucleotide synthesis. Nucleic Acids Res 25(18):3629–3635; (b) Pon RT, Yu S (1997) Hydroquinone-O,O′-diacetic acid as a more labile replacement for succinc acid linkers in solid-phase oligonucleotide synthesis. Tetrahedron Lett 38(19):3327–3330

    Google Scholar 

  5. Gough GR, Brunden MJ, Gilham PT (1983) 2′(3′)-O-benzoyluridine 5′ linked to glass: an all-purpose support for solid phase synthesis of oligodeoxyribonucleotides. Tetrahedron Lett 24(48):5321–5324

    Article  CAS  Google Scholar 

  6. Vargeese C, Wang W (2007) Methods and reagents for oligonucleotide synthesis. US7205399, 04/17/2007

    Google Scholar 

  7. Kurata C, Bradley K, Gaus H, Luu N, Cedillo I, Ravikumar VT, Van Sooy K, McArdle JV, Capaldi DC (2006) Characterization of high molecular weight impurities in synthetic phosphorothioate oligonucleotides. Bioorg Med Chem Lett 16(3):607–614

    Article  CAS  PubMed  Google Scholar 

  8. (a) Nelson PS, Muthini S, Vierra M, Acosta L, Smith TH (1997) Rainbow universal CPG: a versatile solid support for oligonucleotide synthesis. Biotechniques 22(4):752–756; (b) Lyttle MH, Dick DJ, Hudson D, Cook RM (1999) A phosphate bound universal linker for DNA synthesis. Nucleosides Nucleotides 18:1809–1824; (c) Schcuer-Larsen C, Rosenbohm C, Jøgensen TJD, Wengel J (1997) Introduction of a universal solid support for oligonucleotide synthesis. Nucleosides Nucleotides 16:67–80; (d) Scott S, Hardy P, Sheppard RC, McLean MJ (1994) A universal support for oligonucleotide synthesis. In: Epton R (ed) Innovations and perspectives in solid phase synthesis. 3rd international symposium. mayflower worldwide. pp 115–124; (e) Kumar P, Dhawan G, Chandra R, Gupta KC (2002) Polyamine-assisted rapid and clean cleavage of oligonucleotides from cis-diol bearing universal support. Nucleic Acids Res 30(23):e130; (f) Kumar P, Mahajan S, Gupta KC (2004) Universal reusable polymer support for oligonucleotide synthesis. J Org Chem 69(19):6482–6485; (g) Anderson E, Brown T, Picken D (2003) Novel photocleavable universal support for oligonucleotide synthesis. Nucleosides Nucleotides Nucleic Acids 22(5–8):1403–1406; (h) Anderson KM, Jaquinod L, Jensen MA, Ngo N, Davis RW (2007) A novel catechol-based universal support for oligonucleotide synthesis. J Org Chem 72(26):9875–80; (i) Morvan F, Meyer A, Vasseur JJ (2007) A universal and recyclable solid support for oligonucleotide synthesis. Curr Protoc Nucleic Acid Chem. Chapter 3, Unit 3.16

    Google Scholar 

  9. (a) Guzaev AP, Manoharan M (2003) A conformationally preorganized universal solid support for efficient oligonucleotide synthesis. J Am Chem Soc 125(9):2380–2381; (b) Ravikumar VT, Kumar RK, Olsen P, Moor MN, Carty RL, Andrade M, Gorman D, Zhu X, Cedillo I, Wang Z, Mendez L, Scozzari AN, Aguirre G, Somanathan R, Bernees S (2008) UnyLinker: an efficient and scaleable synthesis of oligonucleotides utilizing a universal linker molecule: a novel approach to enhance the purity of drugs. Org Process Res Dev 12:399–410

    Google Scholar 

  10. Capaldi DC, Gaus H, Krotz AH, Arnold J, Carty RL, Moore MN, Scozzari AN, Lowery K, Cole DL, Ravikumar VT (2003) Synthesis of high-quality antisense drugs. Addition of acrylonitrile to phosphorothioate oligonucleotides: adduct characterization and avoidance. Org Process Res Dev 7(6):832–838

    Article  CAS  Google Scholar 

  11. Eritja R, Robles J, Avino A, Albericio F, Pedroso E (1992) A synthetic procedure for the preparation of oligonucleotides without using ammonia and its application for the synthesis of oligonucleotides containing O-4-alkyl thymidines. Tetrahedron 48:4171–4182

    Article  CAS  Google Scholar 

  12. (a) Noll B, Seiffert S, Hertel F, Debelak H, Hadwiger P, Vornlocher HP, Roehl I (2011) Purification of small interfering RNA using nondenaturing anion-exchange chromatography. Nucleic Acid Ther XXX; (b) Gjerde DT, Hoang L, Hornby D (2009) RNA purification and analysis: sample preparation, extraction, chromatography. Wiley-VCH, Weinheim, p xi. 195 p; (c) Vargeese C (2006) Deprotection and purification of oligonucleotides and their derivatives. US6989442; (d) Shanagar J (2005) Purification of a synthetic oligonucleotide by anion exchange chromatography: method optimisation and scale-up. J Biochem Biophys Methods 64(3):216–225; (e) Deshmukh RR, Eriksson KO, Moore P, Cole DL, Sanghvi YS (2001) A case study: oligonucleotide purification from gram to hundred gram scale. Nucleosides Nucleotides Nucleic Acids 20(4–7):567–576; (f) Andrus A, Kuimelis RG (2001) Overview of purification and analysis of synthetic nucleic acids. Curr Protoc Nucleic Acid Chem. Chapter 10, Unit 10.3; (g) Deshmukh RR, Cole DL, Sanghvi YS (2000) Purification of antisense oligonucleotides. Methods Enzymol 313:203–226; (h) Wincott F, DiRenzo A, Shaffer C, Grimm S, Tracz D, Workman C, Sweedler D, Gonzalez C, Scaringe S, Usman N (1995) Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res 23(14):2677–2684

    Google Scholar 

  13. (a) Bergot BJ, Egan W (1992) Separation of synthetic phosphorothioate oligodeoxynucleotides from their oxygenated (phosphodiester) defect species by strong-anion-exchange high-performance liquid chromatography. J Chromatogr A 599:35–42; (b) Deshmukh RR, Miller JE, De Leon P, Leich WE II, Cole DL, Sanghvi YS (2000), Process development for purification of therapeutic antisense oligonucleotides by anion-exchange chromatography. Org Process Res Dev 4:205–213; (c) Metelev V, Agrawal S (1992) Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates. Anal Biochem 200(2):342–346; (d) Banerjee A, Bose HS, Roy KB (1991) Fast and simple anion-exchange chromatography for large-scale purification of self-complementary oligonucleotides. Biotechniques 11(5):650–656; (e) Cohn WE (1950) The anion-exchange separation of ribonucleotides. J Am Chem Soc 72:1471–1478

    Google Scholar 

  14. (a) Cramer H, Finn KJ, Herzberg E (2011) Purity analysis and impurities determination by reversed-phase HPLC. In: Bonilla J, Srivatsa GS (eds) Handbook of analysis of oligonucleotides and related products. CRC Press, Boca Raton, pp 1–46; (b) McCarthy SM, Gilar M, Gebler J (2009) Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA. Anal Biochem 390(2):181–188; (c) Lei B, Li S, Xi L, Li J, Liu H, Yao X (2009) Novel approaches for retention time prediction of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography. J Chromatogr A 1216(20):4434–4439; (d) McCarthy SM, Warren WJ, Dubey A, Gilar M (2008) Ion-pairing systems for reversed-phase chromatoraphy separation of oligonucleotides. In: TIDES Conference, Las Vegas, NV; (e) Kirkland JJ (2004) Development of some stationary phases for reversed-phase high-performance liquid chromatography. J Chromatogr A 1060(1–2):9–21; (f) Azarani A, Hecker KH (2001) RNA analysis by ion-pair reversed-phase high performance liquid chromatography. Nucleic Acids Res 29(2):E7

    Google Scholar 

  15. Cramer H (2015). In: Development of small scale models to predict large scale manufacturing results, Euro TIDES, Berlin, Berlin

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Nitto Avecia, Cincinnati, OH, USA

    Eduardo Paredes

  2. Nitto Denko Corporation, Osaki, Miyagi, Japan

    Tatsuya Konishi

Authors
  1. Eduardo Paredes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tatsuya Konishi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eduardo Paredes .

Editor information

Editors and Affiliations

  1. Osaka University, Suita, Osaka, Japan

    Satoshi Obika

  2. Tokyo Institute of Technology, Yokohama, Kanagawa, Japan

    Mitsuo Sekine

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Paredes, E., Konishi, T. (2018). Large-Scale Oligonucleotide Manufacturing. In: Obika, S., Sekine, M. (eds) Synthesis of Therapeutic Oligonucleotides. Springer, Singapore. https://doi.org/10.1007/978-981-13-1912-9_6

Download citation

Publish with us

Policies and ethics

Search

Navigation