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Oligonucleotide Process Development

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Oligonucleotide Process Development

Design & Feasibility • Pilot Synthesis • Purification Optimization • Scale-Up • Analytical Methods • Formulation • Regulatory

Overview

Custom oligonucleotide process development is far more than linking bases — it’s a multi-step R&D and manufacturing pipeline that must balance chemistry, scalability, purity, and compliance, especially for therapeutic and diagnostic use.

At Bio-Synthesis, Inc., we deliver end-to-end solutions, transforming concepts into scalable, reproducible, and regulatory-ready processes. Our expertise covers DNA, RNA, LNA, PNA, Morpholino, and mixed-backbone chemistries, with decades of experience in integrating complex modifications, conjugates, and novel chemistries into robust workflows.

We guide projects from design and feasibility through pilot synthesis, purification optimization, scale-up, analytical validation, and formulation — all within a rigorous quality framework. Whether your goal is research-use, ISO13485, or GLP-compliant production, every step is data-driven and quality-controlled.

ISO 9001:2015 / ISO13485:2016 45+ Years of Expertise U.S.A. Facilities-Texas
  • Complex and highly modified oligos, including rare/custom monomers
  • Integrated analytical capabilities: HPLC, LC-MS, CE, UV, stability studies
  • Flexible scale — from µmol R&D batches to multi-gram GMP lots
  • Full documentation and tech transfer for regulatory filings

At-a-Glance

  • Bioinformatics-assisted sequence & modification design
  • Pilot synthesis with real-time QC feedback (HPLC/MS/UV)
  • Purification route optimization (RP-HPLC, IEX, PAGE)
  • Process scaling for small to large production columns
  • ICH stability programs and validated analytical methods
  • Formulation development and sterile filtration for in vivo/IVD
  • Regulatory-ready documentation from COA to ISO13485 or GLPbatch records

Bio-Synthesis offers the rare combination of deep chemistry expertise, state-of-the-art facilities, and personalized technical support — ensuring your oligos are delivered exactly to spec, on time, and ready for their intended application.

Workflow

Oligo Process Development Workflow

1) Design & Feasibility

Sequence & Chemistry

  • Base/backbone selection with length/Tm constraints
  • Modification plan (e.g., 2′-OMe/2′-F, PS linkages, conjugation handles)
  • Protecting groups & coupling strategy compatibility

Synthetic Feasibility

  • Reagent availability vs. custom monomer development
  • Risk assessment: low-yield steps, sensitive linkers, scale risks
  • Initial process map and QC checkpoints

Bioinformatics

  • Specificity checks and off-target analysis
  • Secondary structure modeling (critical for siRNA/ASO)

2) Pilot Synthesis & Screening

Small-Scale Runs

Automated solid-phase synthesis (1–10 µmol) to evaluate coupling efficiency and stepwise yields.

  • Cycle timing, activators, capping, and oxidation/sulfurization
  • Early integration of non-standard bases, dyes, linkers

Rapid QC Feedback

  • Crude purity by HPLC/CE; identity by LC-MS
  • UV quantitation and molar extinction checks
  • Decision gates for purification route selection

3) Purification Process Development

Route Screening

  • RP-HPLC for hydrophobicity-driven separations
  • IEX for charge resolution of long/PS-rich oligos
  • PAGE for short oligos or ultra-high purity needs

Objectives

  • Removal of truncated sequences and deprotection by-products
  • Yield vs. purity trade-off curves and cycle-time targets
  • Solvent/gradient design scalable to prep columns
Case Preferred Method Notes
Short DNA (≤35 nt) RP-HPLC Fast cycles; strong resolution of truncateds
PS-rich ASO/Gapmer IEX Charge-based separation of isomers
siRNA Duplex RP-HPLC + Anneal Strand purification then duplexing

4) Scale-Up Development

Process Translation

  • Flow rates, reagent consumption, temperature profiles
  • Column loading, packing density, solvent recovery
  • Cycle-time modeling and throughput planning

Finishing & Stability

  • Drying: lyophilization or spray-dry, residual solvent testing
  • In-process controls and in-line analytics where applicable
  • Tech transfer package for manufacturing

5) Analytical Method Development

Identity & Purity

  • HPLC/UPLC, CE, and mass spectrometry fingerprints
  • Sequence-specific assays (hybridization, enzymatic)
  • Impurity profiling and reporting thresholds

Stability Programs

  • Accelerated/long-term per ICH guidance
  • Shipping/temperature excursion studies
  • Method validation (accuracy, precision, linearity, robustness)

6) Formulation & Delivery Readiness

Buffers & Formats

  • TE, PBS, or custom buffers; defined pH/ionic strength
  • Lyophilized cakes or liquid vials; tubes or plates
  • Sterile filtration and bioburden/endotoxin testing (as needed)

Conjugation Stability

  • Labels: dyes, biotin, peptides, lipids, GalNAc, PEG
  • Stress testing across storage/handling conditions
  • Functional assays to confirm activity post-formulation

7) Documentation & Regulatory

Standard Deliverables

  • COA with yield, purity, and identity data
  • HPLC traces and MS spectra
  • Sequence maps and formulation records

GMP Readiness

  • Batch records, raw-material traceability, QA oversight
  • Change control and deviation management
  • Documented tech transfer to manufacturing

Optional Add-On Services

Barcoding & Pooling

Custom labels/barcodes, plate maps, and pool design for screens.

Plate Formatting

96/384-well plates, normalized concentrations, and QC stamps.

Blinded Studies

Sequence masking and third-party shipping coordination.

How to Start

  1. Share sequence(s), application, and target product profile.
  2. Specify backbone/modifications and intended scale(s).
  3. Select desired purification and QC deliverables.
  4. Note formulation, packaging, and documentation needs.

Specs Checklist

  • Chemistry (DNA/RNA/LNA/PNA/etc.), length, and modifications
  • Purity targets and accepted impurity thresholds
  • Throughput (single to plate) and packaging format
  • Regulatory context (RUO, IVD, GLP, GMP)
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FAQ

What determines whether RP-HPLC or IEX is used?

Hydrophobic modifications and shorter oligos favor RP-HPLC; longer or PS-rich designs that differ by charge resolve better on IEX. We screen routes during pilot work.

Can you transfer the process to our site or a CMO?

Yes. We prepare a full tech-transfer package with parameters, specs, and in-process controls, and support on-site qualification if required.

Do you provide ICH stability data?

We run accelerated and long-term studies and generate protocols/reports aligned to ICH expectations for your filing context.

What QC is standard?

Analytical HPLC and MS identity are standard; additional methods (CE, sequencing/hybridization assays, endotoxin/bioburden) are available as needed.

Speak to a Scientist

Complete the form to receive a tailored quote. Your request will be emailed to info@biosyn.com and logged to your CRM endpoint (configure below).

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Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45+ years of delivering high quality, fast and scalable synthetic biology solutions.