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Oligonucleotide Process Development

Oligonucleotides are short single or double stranded nucleic acid fragments, formed by polymerization of RNA, DNA and their analogues. Initially, oligonucleotides were manufactured and used primarily as reagents in life science research such as PCR and in DNA-based diagnostic kits. Nowadays, oligonucleotide therapies have emerged as a novel therapeutic option in the field of rare and orphan diseases as a class of drugs with a wide range of indications. The complex linkages of nucleotides form the biologically-critical RNA and DNA biomolecules. These specific linkages of nucleotide create the target biomolecules that are used in biological, medical, forensic and clinical applications. However, the relative complexity of oligonucleotide synthesis can pose purification challenges. In recent years, advances in modern solid-phase synthesis techniques have made automated high-throughput custom oligonucleotide synthesis possible. In addition, some chemical modifications are necessary to improve their pharmacokinetics and enhance their stability in vivo. Therefore, the establishment of a robust oligonucleoside drug production process is essential to enable preclinical development and eventual clinical trials. With decades of experience in API development, manufacturing and regulatory support, BOC Sciencesis expanding its focus to oligonucleotides, and our team has developed a unique platform to develop a rapid oligonucleotide development process to continuously increase the manufacturing capabilities and capacity of oligonucleotide-based APIs. We are committed to providing a full range of CMC development services for oligonucleotide manufacturing, starting with the establishment of scalable manufacturing processes and ending with IND and NDA filings supported by BOC Sciences' in-house regulatory affairs experts.

Therapeutic  oligonucleotides. Figure 1. Therapeutic oligonucleotides. (Takakura, K.; Kawamura, A. et al. 2019)

Our Services

To make it easier and better for researchers, BOC Sciences provides oligonucleotide process development service in a competitive fashion. We have provided a more efficient way to increase the number of new drugs, greatly shorten the R&D cycle, and reduce the development costs. BOC Sciences is one of the world's leading companies in oligonucleotide drug development, providing technical challenges from development to commercial production. Our first-class services can greatly accelerate the oligonucleotide drug development process.

  • We provide expertise in solid-phase synthesis, protecting group chemistry, chromatographic purification, ultra/diafiltration techniques, precipitation and lyophilization required for the production of oligonucleotides
  • Our oligonucleotide manufacturing platform provides process development and GMP production services for synthetic oligonucleotides in the multi-kilogram scale with the ability to achieve tight process control and high yields
  • BOC Sciences' exceptional analytical chemistry team has expertise and project experience in developing and validating test methods for large and structurally complex molecules

Oligonucleotide production process

  1. Synthesis-We use solid-phase synthesis for the manufacture of oligonucleotides from microgram for research application, including a variety of chemical reactions such as delipidation, coupling, oxidation/thiolation and capping
  2. Cleavage and Deprotection (C&D)-This process is typically performed in a batch mode
  3. Purification-The purification of the oligonucleotide crude solution is usually achieved by chromatographic methods
  4. Desalting and Concentration-At BOC Sciences, we utilize tangential flow filtration (TFF) for therapeutic oligonucleotide isolation at manufacturing scales
  5. Lyophilization-Freezing and lyophilization of oligonucleotides are conducted to obtain the final product in powder form

Wide coverage

  • ASO, Native and modified DNA (single- and double-stranded), Small interfering RNA (siRNA), O-methyl/locked nucleic acids (LNA), aptamer, peptidic nucleic acids (PNA), microRNA, PMO, etc
  • Oligonucleotide conjugates including GalNAc-conjugated siRNA, phosphorodiamidate morpholino oligos (PMOs)-based conjugates, oligotoxins/oligobodies
  • Full suite of analytical tests

Clinical trials  of Oligonucleotide therapeutics for patients with pancreatic cancer. Figure 2. Clinical trials of Oligonucleotide therapeutics for patients with pancreatic cancer. (Takakura, K.; Kawamura, A. et al. 2019)


  • Solid phase + liquid phase synthesis
  • Conjugation chemistry
  • Linker and ligand synthesis
  • Custom phosphoramidite synthesis
  • Synthesis of GalNAc

Characterization of oligonucleotides

  • Molecular weight confirmation using ESI-MS, LC-MS and/or MALDI-TOF
  • Detailed structural analysis using LC-MS
  • Confirmation of sequence using LC- MS/MS and/or exonuclease treatment followed by MALDI-TOF MS analysis
  • Impurity profiling and identification using LC-MS
  • pI/charge variants using icIEF/IEX

Features of Our Oligonucleotide Services

  • High purity raw materials to improve the quality of synthetic oligonucleotides
  • Continuous development and optimization of oligonucleotide production processes
  • Large-scale oligonucleotide manufacturing
  • Competitive price and fast turnaround times

Typical  oligonucleotide synthesis process. Figure 3. Typical oligonucleotide synthesis process. (Kiesman, W. F.; Mcpherson, A. K. et al. 2021)

Why choose BOC Sciences?

Our dedicated CMC team has provided tailored solutions to our clients from engagement to launch. With many years of industry experience, we provide clients with the following:

  • Comprehensive, integrated CMC services with a flexible service model that grows with your programs
  • Knowledgeable industry experts who deliver scalable, actionable insights
  • World-class facilities and equipment that remain at the forefront of the global pharmaceutical research, analytical and development standards
  • Our comprehensive services support products at every stage of the product lifecycle, from early-stage discovery to full commercial cGMP manufacture
  • A focus on risk management that is designed to ensure completion of your technical goals

BOC Sciences provides professional, rapid and high-quality services of oligonucleotide process development at competitive prices for global customers. Personalized and customized services of oligonucleotide process development can satisfy any innovative scientific study demands. Our clients have direct access to our staff and prompt feedback to their inquiries. If you are interested in our services, please contact us immediately!


  1. Takakura, K.; Kawamura, A. et al. The Clinical Potential of Oligonucleotide Therapeutics against Pancreatic Cancer. International Journal of Molecular Sciences. 2019. 20(13).
  2. Kiesman, W. F.; Mcpherson, A. K. et al. Perspectives on the Designation of Oligonucleotide Starting Materials. Nucleic acid therapeutics. 2021. 31(2): 93-113.


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