19 April 2026 | Sunday | Expert Opinion
The demand for nucleic acid therapeutics (NATs) is rapidly altering the therapeutic landscape across a wide range of diseases. Recent industry data highlights this momentum, with 1,248 RNA therapeutics in development and 480 active clinical trials worldwide at the end of Q4 in 2025 [1]. Meeting the rising demand for these advanced therapeutics introduces the operational challenge of scaling production quickly while reducing environmental impact.
The growing number of mRNA and oligonucleotide-based therapeutics in clinical development is increasing demand for active pharmaceutical ingredients (APIs), including small interfering RNAs (siRNAs), antisense oligonucleotides (ASOs), gene editing single guide RNAs (sgRNAs), and mRNA therapeutics. Expanding global production to supply these and future commercial volumes, especially for cardiometabolic disease targets such as APOC3, LPA, AGT, INHBE and PCSK9 [2,3], is raising concerns about the environmental footprint of NAT production.
While their programmable nature and high specificity offer compelling advantages for targeted intervention, the molecular complexity of mRNA and oligonucleotide therapeutics requires highly specialized production capabilities [4,5]. That challenge is made worse by rising demand and fragmented supply chains that often stretch across multiple regions. To meet future demand more sustainably, drug developers are investigating alternative synthesis technologies and integrated supply models that can improve efficiency and reduce process mass intensity (PMI).
The sustainability limits of conventional synthesis
Solid-phase oligonucleotide synthesis (SPOS) remains a mainstay technology and works effectively for many programs, especially those with lower-volume needs. As target populations grow, the material requirements of this chemical synthesis approach become harder to manage, driving up both the cost of goods and environmental impact. Industry analyses quantify this burden, estimating an average process mass intensity (PMI) of 4,299 kg of raw material for every kilogram of API produced [6].
From an operations standpoint, the synthesis stage alone accounts for about 50% of the total material footprint [6]. Within this stage, wash solvents account for roughly a quarter of the baseline PMI, while the detritylation step (comprising the acid deprotection and associated wash cycles) consumes nearly half of all materials used.
Driving these sequential SPOS reactions to completion consumes large volumes of reagents and generates substantial chemical waste. Traditional SPOS also relies on flow-through synthesizers that are typically limited to around 10 kg per batch. That means meeting multi-ton demand requires multiple parallel production lines, which in turn multiply solvent use and repeat resource-intensive downstream chromatography steps.
As sequences get longer, chemical synthesis becomes less efficient. Even with coupling efficiencies of 99%, the theoretical yield for a 150-nucleotide sequence drops to approximately 22% [7]. Because of the stepwise nature of SPOS, there are many opportunities for impurities to form and accumulate during synthesis. For long single guide RNA (sgRNA), these synthesis-related impurities are particularly challenging to control during synthesis and costly to remove during purification, reducing purity, affecting batch-to-batch consistency, and further lowering the overall yield.
Making the case for chemoenzymatic ligation
To address these scalability and sustainability constraints, manufacturers are exploring alternative technologies such as chemoenzymatic ligation. This approach uses an enzymatic ligation reaction to join short oligonucleotide fragments that are synthesized in high yield and good purity by SPOS. Because enzymatic ligation is highly specific and only works when the 5′-phosphate and 3′-hydroxyl groups are correctly positioned, non-ligatable fragment impurities are excluded from the final assembled sequence. The result is a crude oligonucleotide with a cleaner impurity profile that is easier to purify and requires less hazardous organic solvents during downstream chromatography.
This precise fragment-level assembly also supports workflows that reduce or eliminate the need for chromatography. For example, oligonucleotide fragments or siRNA that are sufficiently pure in crude form can be processed by ultrafiltration/diafiltration (UF/DF) instead. These workflows include taking unpurified fragments through to a purified final product (crude-to-purified), or removing chromatography entirely (crude-to-crude). Engineered enzymes are also important to making the crude-to-crude workflow effective. A T4 RNA ligase engineered for thermostability facilitates ligation at higher operating temperatures (52–57°C). At these temperatures, RNA substrates are less likely to form problematic secondary structures, which improves fragment alignment and helps deliver higher purity in the final duplex or single-stranded construct.
Transitioning to chemoenzymatic ligation introduces new quality and regulatory considerations. One is the need to monitor residual enzyme in the final product, using methods such as hybridization ELISA and mass spectrometry to confirm clearance. Moving from chemical synthesis to ligation can also affect phosphorothioate stereochemistry, changing the diastereomeric distribution of the final product. To address this, comparative analytical studies between materials from the two processes may be required to demonstrate equivalence and justify differences to regulatory authorities. There are also differences in how product quality is assessed. For SPOS-derived duplexes, identity, purity and impurities are measured strand by strand by HPLC/MS before hybridization. For ligation-based products, these CQAs are measured directly on the duplex.
The promise of fully enzymatic synthesis
Fully enzymatic synthesis is an emerging approach to more sustainable RNA manufacturing. Because sequence assembly takes place entirely in an aqueous buffer, it offers a way to remove hazardous organic solvents from the production process.
To carry out fully enzymatic synthesis, researchers are studying template-independent polymerases, notably CID1 mutants and terminal deoxynucleotidyl transferase (TdT), as well as RNA-specific enzymes such as poly(A) polymerase (PAP) and poly(U) polymerase (PUP). These enzymatic cycles generally rely on nucleoside triphosphate monomers with reversible 3′-hydroxyl protecting groups. These groups are described as clippable because they require selective deprotection reactions for removal, and they include cis-diols, 3′-O-allyl ethers, and monophosphates [7,8,9]. This approach allows sequence assembly to be controlled one base at a time without uncontrolled polymerization. Scaling the platform for commercial use will require further process and enzyme engineering to compete with SPOS and chemoenzymatic ligation and support the range of therapeutic modifications used in today’s clinical pipelines, although it is clear that significant progress is being made [10].
Why vertical integration and operations matter
Beyond changes in synthesis technology, the environmental impact of NAT manufacturing is also affected by the supply chain. Fragmented supply chains, with production spread across multiple locations, increase transport distances and inventory redundancies, adding to greenhouse gas emissions across the product lifecycle.
A fragmented supply chain also means multiple material handoffs between vendors. Each handoff can trigger repeated tech transfers, duplicate quality control testing and extra packaging waste. A vertically integrated supply model brings these critical production stages together within one company, allowing close alignment between raw material production and cGMP drug substance and drug product manufacturing.
Improving sustainability in oligonucleotide manufacturing also depends on changes at the operational level. Direct control over facilities can also support energy-saving measures, from solvent recycling to electrifying on-site logistics and using 100% solar-powered exterior lighting.
Further progress will also require collaboration across the sector. Initiatives such as the ACS Green Chemistry Institute Pharmaceutical Roundtable help define best practices for more sustainable oligonucleotide manufacturing. Sharing data on solvent recycling, biocatalysis, PMI and other green chemistry metrics helps developers and CDMOs compare progress and promote more sustainable manufacturing approaches across the industry. Large pharmaceutical companies are also paying closer attention to Scope 3 indirect emissions and the measured sustainability performance of manufacturing partners, alongside technical capability and supplier assessments such as EcoVadis.
The future of sustainable NAT manufacturing
Meeting future multi-ton demand will require lower-waste synthesis approaches and more integrated manufacturing. Chemoenzymatic ligation, and potentially fully enzymatic workflows, will help the industry produce NATs at a global scale with a lower environmental impact. Pairing these advanced synthesis methods with a vertically integrated supply model can also improve process control and reduce handoffs between vendors, helping manufacturers scale more efficiently as demand accelerates.
Beyond environmental sustainability, better nucleic acid manufacturing can also improve global patient access. Reducing the cost of goods and accelerating production timelines through vertically integrated manufacturing models will make it more feasible to serve smaller patient populations, including those targeted by personalized cancer vaccines and nano-rare disease programs.
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