Q&A feature with Dr. Michelle Kim: Perspectives on the future of mRNA
As the mRNA field continues to evolve, attention is increasingly turning to the technologies and processes that support its development and manufacture.
In this Q&A feature, we speak with Dr. Michelle Kim, Managing Director of the Johns Hopkins RNA Innovation Center, about the role of plasmid DNA in mRNA manufacturing and some of the challenges associated with current approaches.
Dr. Kim shares her perspective on how these challenges can influence the pace and scalability of mRNA development and explores the potential of synthetic DNA approaches to support the field as it continues to advance.
Dr. Kim's post on this site is made in a personal capacity and is independent of her affiliation with Johns Hopkins University.
As the biotech industry is heavily reliant on plasmid DNA, what limitations are becoming most apparent?
“Plasmid DNA has been the workhorse template for IVT mRNA for decades, but its limitations are becoming harder to ignore as demand scales. Production timelines pose potential bottlenecks: bacterial culture growth, fermentation, lysis, and multi-step purifications to remove host cell DNA, RNA, endotoxin, and protein. These workflows can take a couple of weeks or more for a single construct. That timeline is fundamentally at odds with the speed researchers now expect for iterative design-build-test cycles, especially for personalized therapeutics like neoantigen cancer vaccines where turnaround time directly affects patient outcomes.
There are also quality and consistency issues. Plasmids carry bacterial sequences such as CpG motifs that can trigger unwanted innate immune activation when residual template DNA carries over into the final product. They also contain elements like antibiotic resistance genes and origins of replication, which raise their own regulatory and biosafety considerations.
In addition, batch-to-batch variability from fermentation, plasmid topology heterogeneity (supercoiled vs. relaxed forms), and the risk of unwanted recombination or mutation during bacterial propagation all add complexity to QC and regulatory packages. From a supply chain perspective, plasmid manufacturing requires significant infrastructure – fermenters, biosafety containment, and specialized purification – which creates capacity constraints industry-wide, as we saw acutely during the COVID vaccine scale-up.”
Do you think there are some mRNA applications that are being delayed or deprioritized based on manufacturing limitations with plasmid DNA?
“I think personalized medicine is the clearest example. Individualized neoantigen cancer vaccines are scientifically compelling. You can design a construct that is specific to a patient's tumor mutational profile, but the plasmid-to-mRNA pipeline timeline doesn't match clinical reality. If it takes four to six weeks to get from sequence design to GMP-grade mRNA, that's a meaningful delay for a patient who may be progressing. I'd also point to rapid-response applications, including pandemic preparedness, emerging infectious disease, or even agile reformulation of existing vaccines against variants. The dream of "design today, dose this week" for platforms like mRNA vaccines is still constrained by upstream template production.
And research-stage work suffers too: academic and biotech groups doing high-throughput screening of mRNA constructs, testing dozens of UTR combinations, signal peptides, or codon-optimization strategies, are often rate-limited by how many plasmids they can realistically clone, propagate, and verify in parallel.”
What major benefits do you think synthetic DNA can offer in mRNA manufacturing?
“The most obvious benefit is speed. Going from a digital sequence to a usable DNA template without the days-to-weeks cycle of bacterial cloning and fermentation removes a major bottleneck. That alone changes what's possible for iterative design.
Beyond speed, there's a purity argument. Cell-free synthetic DNA templates avoid the bacterial contaminants that plague plasmid preps: host genomic DNA, endotoxins from the production host, antibiotic resistance markers that regulators increasingly scrutinize. These can simplify downstream purification, reduce unwanted immunogenicity, and strengthen the safety profile of the final mRNA product.
There's also a design freedom benefit. Synthetic DNA production isn't constrained by what a bacterial host can tolerate, so sequences that are toxic to propagate in E. coli, for example, highly repetitive sequences or regions with unusual GC-content, can be investigated. And for organizations thinking about decentralized or point-of-care manufacturing, a template technology that doesn't require fermentation infrastructure is a meaningful step toward smaller-footprint production models.”
What sort of projects would benefit most from swapping to a cell-free synthetic DNA template?
“High-throughput screening and early discovery work are obvious fits, particularly when a lab is testing many construct variants in parallel and where the cloning step is the rate-limiting step. Personalized therapeutics, especially individualized cancer vaccines, stand to benefit enormously given how time sensitive those workflows are.
I'd also highlight any program where sequence sensitivity has historically been a problem, such as constructs with toxic ORFs, highly repetitive elements, or sequences prone to recombination in bacterial hosts. Rapid response and pandemic-preparedness platforms are another strong candidate, since the value proposition is explicitly about compressing time-to-clinic. And smaller biotechs or academic groups without in-house fermentation and plasmid QC infrastructure could potentially access mRNA manufacturing capabilities that previously required significant capital investment.”
At the Johns Hopkins RNA Innovation Center, are you seeing growing interest in plasmid-free or synthetic DNA-based workflows from researchers or industry collaborators?
“I'll answer this from my broader vantage point in the field rather than speaking for any specific center. What I'm seeing across academic and industry conversations is a clear uptick in interest. Researchers are increasingly aware that template generation is often the long pole in their tent, and they're actively looking at alternatives as the technology matures and becomes more accessible. The interest tends to be strongest among groups working on personalized or rapidly-iterated constructs, where the time savings have the most direct impact on program timelines. I think we're at an inflection point where what was a niche, exploratory interest is becoming a more mainstream evaluation criterion when groups are designing new mRNA programs.”
What role can centers like the Johns Hopkins RNA Innovation Center play in helping validate and de-risk next-generation manufacturing approaches?
“Academic-industry partnership centers occupy a valuable middle ground. They can run rigorous, head-to head comparative studies between established and emerging manufacturing approaches without the commercial pressure of a vendor needing to show their own technology in the best light. That kind of independent, data-driven validation is exactly what newer manufacturing technologies need in order to build credibility with both the scientific community and regulators.
These centers can also serve as a translation layer, bridging fundamental RNA biology expertise with practical manufacturing and process development questions. By working with investigators, they can generate the comparative stability, potency, and immunogenicity data that helps the field understand where a new approach is a clear win versus where tradeoffs still exist.
There's also real value in training the next generation of scientists on these workflows so that as the technology matures, there's a talent pipeline that already understands it. Centers with strong industry partnerships are well-positioned to identify which applications are most ready for early adoption versus which need more development, helping the field deploy new approaches where they'll have the most impact first, rather than as a blanket replacement.”
Dr. Michelle Kim
Michelle Kim is the inaugural Managing Director of the Johns Hopkins RNA Innovation Center. Early in her career, she studied the mechanisms governing miRNA-mediated mRNA translation inhibition in Rachel Green’s lab. During her post-doctoral work in Bob Siliciano’s lab, she investigated features of the HIV RNA genome required for pathogenicity. Following that, Dr. Kim joined the core team at Circulomics, an early-stage, pre-commercial startup focused on creating innovative genomics tools. During her tenure there, she developed and commercialized multiple sample prep tools for long read sequencing across diverse taxa. By 2021, Circulomics had a global distribution network and was acquired by PacBio, a leader in long read sequencing technologies. At PacBio, Dr. Kim helped develop targeted solutions for agrigenomics and human clinical applications. She also led collaborations with large-scale, international genomics projects such as The Vertebrate Genome Project and The Darwin Tree of Life project. Dr. Kim earned her Bachelor of Arts from Columbia University and her PhD from the Johns Hopkins School of Medicine.