DNA origami vaccines could be the next leap beyond mRNA

The COVID-19 pandemic unequivocally propelled messenger RNA (mRNA) vaccines into the forefront of global public health. Following an expedited development and clinical trial process, the first COVID-19 mRNA vaccine was administered on December 8, 2020, marking a pivotal moment in medical history. Subsequent sophisticated epidemiological modeling efforts have since underscored their profound impact, estimating that these innovative vaccines were instrumental in preventing at least 14.4 million deaths worldwide during their inaugural year alone. This unprecedented success not only demonstrated the rapid response capability of mRNA technology but also ignited a widespread scientific enthusiasm, prompting researchers globally to pivot towards developing similar vaccine strategies for a myriad of other infectious diseases. Currently, a robust pipeline of clinical trials is underway, exploring mRNA vaccine applications against persistent global health threats such as influenza virus, Respiratory Syncytial Virus (RSV), Human Immunodeficiency Virus (HIV), Zika virus, Epstein-Barr virus, and even the challenging tuberculosis bacteria. However, parallel to these advancements, ongoing scrutiny and real-world data from the deployment of COVID-19 mRNA vaccines have concurrently brought to light several important inherent limitations, thereby signaling a critical need for the exploration and development of novel, complementary vaccine strategies to bolster future pandemic preparedness and response.

The Double-Edged Sword of mRNA Vaccine Performance and Production

While groundbreaking, the widespread deployment of COVID-19 mRNA vaccines has illuminated significant challenges, particularly concerning their performance variability and logistical demands. The immune protection conferred by these vaccines can exhibit considerable differences from person to person, influenced by factors such as age, underlying health conditions, genetic predisposition, and prior immune exposures. Furthermore, the durability of this protection is not indefinite; studies have consistently shown a gradual waning of immunity over time, necessitating booster doses to maintain adequate defense. This issue is critically exacerbated by the relentless evolutionary pressure on SARS-CoV-2, which continually generates new variants capable of partially or significantly evading existing immune defenses—a phenomenon that has led to a cyclical need for vaccine updates and reformulations to match the circulating strains. The emergence of variants like Alpha, Delta, and particularly Omicron, with its numerous spike protein mutations, exemplified this challenge, requiring rapid adaptation of vaccine targets.

Beyond these immunological complexities, the practical hurdles associated with mRNA vaccines are substantial. The manufacturing process is inherently intricate and costly, demanding highly specialized facilities and stringent quality control. A persistent technical challenge involves precisely controlling the encapsulation of mRNA molecules within lipid nanoparticles (LNPs), which are crucial for delivering the genetic material safely and effectively into cells. Maintaining a consistent number of mRNA molecules per LNP remains a complex endeavor, impacting batch uniformity and efficacy. Moreover, a major logistical impediment is the requirement for ultra-cold storage, typically between -70°C and -80°C, to preserve the fragile mRNA molecules. This "cold chain" necessity presents enormous distribution challenges, especially in low-resource settings lacking advanced infrastructure, limiting global accessibility and equitable distribution. There are also ongoing investigations into potential unintended off-target effects, though generally rare, associated with LNP delivery or the robust immune activation triggered by the mRNA itself. Overcoming these multifaceted limitations is not merely a scientific pursuit but a global imperative, crucial for fortifying the world’s capacity to prepare for and effectively respond to future infectious disease threats with greater agility, equity, and sustainability.

Introducing DoriVac: A DNA Origami Nanotechnology Platform

In direct response to the identified limitations of existing vaccine technologies, particularly mRNA platforms, a multidisciplinary consortium of researchers from the Wyss Institute at Harvard University, Dana-Farber Cancer Institute (DFCI), and their esteemed partner institutions has pioneered a fundamentally different approach. Their innovative solution is a DNA origami nanotechnology platform named DoriVac, a sophisticated system designed to function simultaneously as both a vaccine antigen presentation system and an intrinsic adjuvant. This novel platform represents a significant leap forward in vaccine design, leveraging the precision of nanotechnology to overcome some of the most persistent challenges in vaccinology.

The foundational principle of DoriVac lies in DNA origami, a technique that allows scientists to fold single strands of DNA into intricate, predetermined three-dimensional nanostructures. This precision engineering enables the creation of highly customizable and stable vaccine "chassis" at the nanoscale. The researchers specifically engineered DoriVac vaccines to target a conserved peptide region known as HR2, which is critical for viral fusion and found within the spike proteins of several formidable viruses, including SARS-CoV-2, HIV, and Ebola. This strategic targeting of a conserved region aims to elicit broader and potentially more durable immune responses, less susceptible to viral mutation.

Initial preclinical studies conducted in mice yielded highly promising results. The SARS-CoV-2 HR2 vaccine formulated with DoriVac elicited robust and comprehensive immune responses, encompassing both antibody-driven (humoral) activity, which involves the production of neutralizing antibodies, and T cell-driven (cellular) activity, crucial for long-term immunity and clearance of infected cells. To further validate these findings and bridge the gap between animal models and human physiology, the team ingeniously utilized a cutting-edge preclinical human model: the Wyss Institute’s proprietary microfluidic human Organ Chip technology. Specifically, they employed a human lymph node-on-a-chip, which exquisitely simulates the complex cellular interactions and immune responses of a human lymph node in vitro. Within this sophisticated system, the SARS-CoV-2 HR2 DoriVac vaccine similarly generated potent antigen-specific immune responses in human cells, lending significant credence to its potential efficacy in humans.

A crucial comparative analysis directly pitted a DoriVac vaccine, presenting the same spike protein variant, against conventional SARS-CoV-2 mRNA vaccines delivered via lipid nanoparticles. In these human Organ Chip models, the DoriVac platform demonstrated a similarly strong immune activation profile. However, it exhibited distinct advantages in terms of stability, proving significantly easier to store and manufacture. These groundbreaking findings were meticulously documented and subsequently published in the esteemed scientific journal Nature Biomedical Engineering, signaling a new era in vaccine development.

The Precision Engineering of DNA Origami Vaccines

The conceptualization and realization of DoriVac as a DNA nanotechnology-based vaccine platform with broad potential applications were spearheaded by William Shih, Ph.D., a co-corresponding author and Wyss Institute Core Faculty member, whose pioneering group laid the groundwork for this innovative vaccine concept. Shih, who also holds professorships at Harvard Medical School and DFCI, emphasized the platform’s unparalleled flexibility and control. "With the DoriVac platform, we have developed an extremely flexible chassis with a number of critical advantages, including an unprecedented control over vaccine composition, and the ability to program immune recognition in targeted immune cells on a molecular level to achieve better responses," stated Dr. Shih. He added, "Our study demonstrates DoriVac’s versatility and potential by taking a close look at the immune changes that are required to fight infectious viruses."

The detailed architecture of DoriVac vaccines was first introduced by Shih’s team in 2024. Yang (Claire) Zeng, M.D., Ph.D., a leading figure in this collaborative effort and a co-corresponding author on the new study, meticulously demonstrated DoriVac’s capacity to precisely present immune-stimulating adjuvant molecules to cells at the nanoscale. These tiny, self-assembling square DNA nanostructures form the backbone of the DoriVac platform. One meticulously designed side of this nanostructure displays adjuvant molecules, strategically arranged at carefully controlled nanometer distances to optimize immune cell activation. Conversely, the opposite side presents selected antigens, which can be peptides or proteins derived from tumors or, in the case of infectious diseases, from pathogens.

Earlier studies, particularly in tumor-bearing mice, had already provided compelling evidence of the platform’s power, demonstrating that DoriVac vaccines elicited significantly stronger immune responses compared to versions lacking the precise DNA origami structure. This prior success in oncology applications provided a strong foundation. "While we were developing the platform for cancer applications, the COVID-19 pandemic was still moving with full force," Dr. Zeng recounted. "So, the question quickly arose whether DoriVac’s superior adjuvant activity could also be leveraged in infectious disease settings." Dr. Zeng, now the cofounder and CEO/CTO of DoriNano, is actively leading the translation of this technology into clinical applications, highlighting the urgent need and potential for this platform.

To rigorously explore this infectious disease application, Dr. Zeng and co-first author Olivia Young, Ph.D., a former graduate student in Shih’s group, initiated a crucial collaboration with Donald Ingber’s team at the Wyss Institute. Ingber’s group is renowned for its cutting-edge work in antiviral innovation, employing sophisticated AI-driven and multiomics approaches in conjunction with their advanced microfluidic human Organ Chip systems. Together with co-first author Longlong Si, Ph.D., a former postdoctoral researcher in Ingber’s lab, the interdisciplinary team developed DoriVac vaccines specifically targeting SARS-CoV-2, HIV, and Ebola. These vaccines strategically present HR2 peptides, which serve as highly conserved antigens within the respective viral spike proteins, aiming for broad and durable protection.

Reflecting on the comprehensive preclinical data, Dr. Zeng noted, "Our analysis of the immune responses provoked by these first DoriVac vaccines in mice led to several encouraging observations, including significantly greater and broader activation of humoral and cellular immunity across a range of relevant immune cell types than what the origami-free antigens and adjuvants could produce." She further elaborated, "We found that the numbers of antibody-producing B cells, activated antigen-presenting dendritic cells (DCs), and antigen-specific memory and cytotoxic T cell types that are vital for long-term protection were all increased, especially in the case of the SARS-CoV-2 HR2." These detailed immunological insights underscore DoriVac’s capacity to orchestrate a multifaceted and robust immune defense.

Bridging the Gap: From Mouse Models to Human Organ Chips

A longstanding and formidable challenge in the arduous journey of vaccine development is the inherent disconnect between immune responses observed in animal models, particularly mice, and the complex physiological realities of the human immune system. This translational gap has historically been a major bottleneck, leading to the unfortunate failure of numerous promising treatments during human clinical trials. To mitigate this risk and enhance the predictive accuracy of their preclinical evaluations, the DoriVac team ingeniously deployed the human lymph node-on-a-chip (human LN Chip) technology. This advanced microphysiological system is meticulously engineered to mimic key aspects of the human immune system in vitro, providing a more physiologically relevant testing ground than traditional cell cultures or animal models.

The development and refinement of this critical human LN Chip system were significantly advanced by co-first author Min Wen Ku and co-corresponding author Girija Goyal, Ph.D., Director of Bioinspired Therapeutics at the Wyss Institute. Their work enabled the precise assessment of DoriVac’s effects on human immune cells. The results from the human LN Chip were highly encouraging: the SARS-CoV-2-HR2 DoriVac vaccine effectively activated human dendritic cells (DCs), which are crucial antigen-presenting cells that initiate immune responses. Furthermore, it significantly boosted their production of inflammatory cytokines, essential signaling molecules for immune coordination, when compared with origami-free components. Critically, the platform also led to an increased proliferation of both CD4+ and CD8+ T cells, which are pivotal for orchestrating diverse protective functions, including helper T cell activity and direct killing of infected cells. These findings provide compelling human-relevant data, further buttressing the platform’s substantial potential for clinical translation.

Dr. Donald Ingber, M.D., Ph.D., a co-corresponding author and a luminary in the field, serving as the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital, and the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard John A. Paulson School of Engineering and Applied Sciences, emphasized the transformative role of this technology. "The predictive capabilities of human LN Chips gave us an ideal testing ground for DoriVac vaccines, and the induced, antigen-specific immune cell profiles and activities very likely reflect those that would occur in human recipients of the vaccines," Dr. Ingber stated. He further articulated the synergistic power of this approach: "This convergence of technologies enabled us to dramatically raise the chances of success for a new class of vaccines and create a new testbed for future vaccine developments." This integrated approach underscores a paradigm shift in preclinical evaluation, promising to accelerate the development of safer and more effective vaccines.

DoriVac Versus mRNA: A Head-to-Head Comparison

To firmly establish DoriVac’s competitive standing against the current gold standard, the research team undertook a rigorous head-to-head comparison with established mRNA vaccine platforms. Led by Dr. Zeng and co-author Qiancheng Xiong, the team evaluated a DoriVac vaccine designed to present the full SARS-CoV-2 spike protein, directly comparing its performance with commercially available Moderna and Pfizer/BioNTech mRNA lipid nanoparticle (LNP) vaccines that encode the identical spike protein sequence.

Utilizing a standard booster immunization approach in mice, the results were highly significant. Both the DoriVac platform and the mRNA-LNP vaccines produced strikingly similar and robust antiviral T cell and antibody-producing B cell responses. This direct comparability in immunogenicity is a powerful validation of DoriVac’s potential to match the efficacy of leading mRNA vaccines.

However, as Dr. Shih meticulously outlined, DoriVac distinguishes itself with a suite of compelling advantages that transcend mere immunological parity. "This underscored DoriVac’s potential as a DNA nanotechnology-enabled, self-adjuvanted vaccine platform," Dr. Shih affirmed. He continued, "But DoriVac vaccines have a number of other advantages: they don’t have the same cold-chain requirements as mRNA-LNP vaccines do and thus could be distributed much more effectively, especially in under-resourced regions; and they could overcome some of the enormous manufacturing complexities of LNP-formulated vaccines, to name two major ones." The elimination of ultra-cold storage requirements is a game-changer for global vaccine distribution, significantly reducing logistical costs and expanding access to remote and developing regions where specialized freezers are scarce or nonexistent. The simplified manufacturing process promises to lower production costs and increase scalability, addressing another critical bottleneck in global vaccine equity. Furthermore, recent studies conducted by DoriNano have also indicated that DoriVac exhibits a promising safety profile, an essential factor for any new vaccine technology.

Broader Implications and Future Outlook

The advent of the DoriVac platform represents more than just a new vaccine candidate; it signifies a pivotal advancement in vaccine technology with far-reaching implications for global health security. Its inherent stability and reduced reliance on ultra-cold chain logistics could fundamentally transform vaccine accessibility, particularly in low- and middle-income countries that have historically struggled with the distribution challenges posed by temperature-sensitive vaccines. This enhanced accessibility could be a cornerstone of future pandemic preparedness, enabling a more rapid and equitable global response to emerging pathogens.

The versatility of the DNA origami platform also positions it as a highly adaptable tool for targeting a wide array of infectious diseases beyond those currently in clinical trials. Its ability to precisely present diverse antigens and integrate powerful adjuvants suggests potential applications for diseases that have proven recalcitrant to traditional vaccine approaches, including chronic viral infections or even complex bacterial diseases. Moreover, the platform’s origins in cancer research underscore its potential for dual application, offering a flexible framework for both infectious disease prevention and oncology.

From an economic perspective, the potential for simpler and less costly manufacturing could lead to significant reductions in the overall price of vaccines, making them more affordable for governments and healthcare systems worldwide. This economic advantage, coupled with ease of distribution, could facilitate more comprehensive vaccination campaigns and ultimately save more lives. The DoriVac platform exemplifies the power of interdisciplinary collaboration, bringing together nanotechnology, immunology, and bioengineering to address some of the most pressing challenges in public health. As this technology progresses towards human clinical trials, it holds the promise of ushering in a new generation of vaccines that are not only highly effective but also universally accessible, stable, and precisely engineered for optimal immune protection, thereby fortifying humanity’s defenses against current and future microbial threats.

The comprehensive research described in this study was supported by a diverse array of funding bodies, including the Director’s Fund and Validation Project program of the Wyss Institute; the Claudia Adams Barr Program at DFCI; the National Institutes of Health (U54 grant CA244726-01); the US-Japan CRDF global fund (grant R-202105-67765); the National Research Foundation of Korea (grants MSIT, RS-2024-00463774, RS-2023-00275456); the Intramural Research Program of the Korea Institute of Science and Technology (KIST); and the Bill and Melinda Gates Foundation (INV-002274). This broad support underscores the global recognition of DoriVac’s potential and the collaborative spirit driving its development. Additional authors on the study included Sylvie Bernier, Hawa Dembele, Giorgia Isinelli, Tal Gilboa, Zoe Swank, Su Hyun Seok, Anjali Rajwar, Amanda Jiang, Yunhao Zhai, LaTonya Williams, Caleb Hellman, Chris Wintersinger, Amanda Graveline, Andyna Vernet, Melinda Sanchez, Sarai Bardales, Georgia Tomaras, Ju Hee Ryu, and Ick Chan Kwon, whose collective efforts were instrumental in this groundbreaking research.