Oligonucleotides are expanding the frontiers of modern medicine, offering a level of precision treatment that was unimaginable just a few decades ago. Unlike conventional small-molecule drugs, oligonucleotide-based therapies work at the genetic level, silencing, modifying, or even activating genes to address the root causes of disease.
With rapid improvements in genomics and sequencing technology, oligonucleotides could become a cornerstone of precision medicine – where treatments can be tailored to the unique genetic profile of individual patients rather than a one-size-fits-all approach. Their applications extend beyond gene silencing and editing, revolutionizing drug discovery and cellular therapies. But as with any breakthrough, challenges remain. Despite their promise, bringing oligonucleotide-based therapies to market at scale requires overcoming significant hurdles in manufacturing, purification, bioinformatics and cost-effectiveness.
The pharmaceutical industry is now racing to optimize production processes, streamline regulatory pathways, and enhance the accessibility of these exciting new treatments.
From research to real-world impact
Early research in the 1990s provided proof of concept of oligonucleotide therapies, but it wasn’t until 2018, with the approval of Alnylam Pharmaceuticals’ Onpattro (patisiran), that the first FDA-approved small interfering RNA (siRNA) therapy entered the market, marking a turning point for the field.
Since then, the development of oligonucleotide-based drugs has accelerated, with therapies such as Inclisiran, developed by Alnylam and Novartis, offering a novel RNA-based approach to lowering LDL cholesterol in patients with cardiovascular disease. Another example is the approval of Amvuttra (vutrisiran), a siRNA therapy also developed by Alnylam, targeting hereditary transthyretin-mediated amyloidosis (hATTR), a rare condition affecting multiple organs.
Perhaps one of the most personalized examples of oligonucleotide therapeutics’ potential is Milasen, a fully customized antisense oligonucleotide (ASO) developed in just nine months for a single patient with Batten disease, a fatal, inherited disorder of the nervous system. This groundbreaking case demonstrated the speed and personalization possible with oligo-based therapies, highlighting their ability to address highly specific genetic mutations.
Addressing the synthesis and manufacturing challenges
While oligonucleotides hold great therapeutic potential, their journey from lab to patient is anything but simple. Sequencing data is used to design and evaluate oligonucleotide candidates, which means that there is a significant need for advanced bioinformatic tools to process and interpret vast amounts of genetic information. Emerging AI-driven approaches are enabling researchers to analyze large-scale sequencing datasets, optimize oligonucleotide design and predict therapeutic outcomes with greater accuracy. One of the most promising developments is the integration of next-generation sequencing (NGS) with machine learning. By leveraging AI-driven platforms, researchers can optimize oligonucleotide sequences before clinical trials begin, reducing costly late-stage failures and improving the efficiency of drug design.
One of the most pressing challenges with oligonucleotides, however, is the complexity of their manufacturing process. Unlike traditional pharmaceuticals, which rely on well-established chemical synthesis methods, oligonucleotide production requires highly controlled conditions to ensure precision. The process involves solid-phase synthesis, where nucleotides are sequentially added in a precise order, followed by capping, oxidation and purification steps to stabilize the final product and ensure it is thoroughly cleaned of incomplete sequences, byproducts, and immune-triggering impurities. Maintaining consistency across large-scale production, while minimizing impurities, is a significant hurdle as even minor variations can impact product purity and potentially therapeutic efficacy.
While small-scale oligonucleotide synthesis is a well-established and routine procedure in research settings, scaling up to commercial production presents a significantly greater challenge. Unlike the relatively straightforward lab-scale processes, large-scale manufacturing demands advanced automation, rigorous process control, and meticulous optimization to ensure high fidelity and batch-to-batch consistency – capabilities that have only recently become feasible through new technologies. Companies are also investing in automated synthesis platforms to increase throughput and ensure consistency. Efforts to develop more sustainable production methods, such as solvent recycling and alternative synthesis pathways, are also gaining traction.
Understanding analysis and raw materials
The complex chemical reactions and challenges in separating similar sequences mean that there is the potential for adulteration. Highly sensitive analytical methods are required to detect trace-level impurities. Fortunately, a range of approaches have been devised to overcome these problems.
Oligonucleotides are commonly analyzed using liquid chromatography/mass spectrometry (LC/MS) in negative ion polarity mode using ion-pairing reversed-phase (IP-RP) methods. As a rule, this approach provides good chromatographic separation and MS response for a wide range of oligo samples. However, many ion-pairing reagents persist in the analytical system long after their use, presenting a strong MS response in positive ion polarity, which can be detrimental to subsequent analyses.
Using ion-pairing methods on multipurpose systems can therefore be challenging. These analytical instruments normally require substantial cleaning in between sample runs with IP-RP and non-ion-pairing conditions to provide optimal results. As a result, LC/MS methods that deliver high-quality data without relying on ion-pairing reagents – such as hydrophilic interaction liquid chromatography (HILIC) – are gaining attention. HILIC offers effective separation and strong mass spectrometry response without the complications associated with ion-pairing agents.
Another key challenge is the availability and cost of raw materials. These include essential building blocks such as nucleoside phosphoramidites and high-purity solvents like acetonitrile, which must meet appropriate quality standards. Historically, the supply of these materials was limited because of low demand, complex manufacturing requirements, and a small number of qualified suppliers. However, as demand for oligonucleotide-based therapeutics has grown, increased investment in raw material production is beginning to ease these constraints and drive down costs, making large-scale manufacturing more feasible. In parallel, companies are actively exploring alternative synthesis methods and sustainable sourcing strategies to further optimize material supply and enhance production efficiency.
The future of oligonucleotide-based therapies
Without doubt, oligonucleotides represent one of the most exciting frontiers in modern medicine, offering hope for a broadening array of patients and conditions. As manufacturing processes improve and sequencing technology advances and, companies specializing in oligo production are poised to scale these therapies to broader patient applications. Innovations in synthesis, purification and bioinformatic solutions will be key in making this a reality.
Realizing the full potential of oligonucleotide-based therapies will require not only technological breakthroughs, but also strong collaboration across the industry. Researchers, manufacturers, and technology providers must work together to overcome scalability and production challenges.
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