The field traces its origins to the 1980s, when Ned Seeman proposed using cross-shaped Holliday junctions as modular building blocks for larger assemblies. By adjusting the sticky ends of these four-arm junctions, researchers could link tiles into increasingly complex two-dimensional patterns, culminating in Winfree’s 1998 demonstration of 2D DNA crystals built from double-crossover tiles. The pivotal breakthrough came in 2006, when Paul Rothemund introduced DNA origami: a long single strand of bacteriophage DNA folded by hundreds of short staple strands into pre-designed shapes of roughly 100 nanometers, from simple triangles to intricate patterns. In 2012, Peng Yin’s group added a third pillar with DNA bricks—short synthetic strands that self-assemble into stable three-dimensional constructs without any long scaffold, each brick functioning as a removable module. Today, complementary strategies such as rolling circle amplification and enzyme-free reactions like hybridization chain reaction and catalytic hairpin assembly allow structural construction and signal amplification to proceed simultaneously under mild, isothermal conditions.

What makes DNA nanostructures so attractive for fighting pathogens is a constellation of biophysical properties. Their geometry can be engineered with near-atomic precision, and that geometry directly governs biological behavior. Tetrahedral DNA nanostructures (TDNs) decorated on nanoparticle cores mimic the spiky architecture of coronaviruses, boosting small interfering RNA delivery efficiency from roughly 20 percent to 95 percent. The structures enter cells through caveolin-dependent and macropinocytosis pathways despite their negative charge, with size, shape, and rigidity each modulating uptake; medium-sized, compact, three-dimensional particles generally perform best. They also penetrate remarkable biological barriers: structures of 75 nanometers or less can reach the dermis, TDNs traverse up to 450 micrometers of skin, and the structures diffuse into bacterial biofilms—the dense, antibiotic-resistant fortresses that thwart conventional therapies.

Equally striking is their antioxidant chemistry. DNA origami scavenges singlet oxygen approximately 50,000 times more efficiently than double-stranded DNA, because folded architectures concentrate guanine active sites at high density. TDNs bind the antioxidant enzyme copper-zinc superoxide dismutase with extraordinary affinity, a dissociation constant of 7.59 × 10⁻¹² molar, and can dampen oxidative stress through the Nrf2/HO-1, MAPK, and NF-κB signaling pathways. Combined with low cytotoxicity below 250 nanomolar concentrations, negligible effects on platelets and red blood cells, high drug-loading capacity through intercalation, groove binding, electrostatic adsorption, or sequence hybridization, and rapid renal clearance of small constructs, these features position DNA nanostructures as unusually benign yet capable nanocarriers.

On the diagnostic front, the review documents detection limits that routinely rival or surpass polymerase chain reaction and ELISA. DNA walkers—dynamic structures that move along programmed tracks—have been coupled with electrochemical readouts to detect Staphylococcus aureus at just 9 colony-forming units per milliliter. A polymethylene blue nanoparticle sensor built on dumbbell hybridization chain reaction pushed S. aureus detection down to a single cell per milliliter in human serum and food samples. Dual-mode photoelectrochemical and surface-enhanced Raman spectroscopy platforms now allow hierarchical screening and confirmation in complex matrices such as fruit juices, while cyclic DNA nanostructure gold nanoparticle tags combined with cascade primer exchange reactions detect E. coli O157:H7 at 1.91 colony-forming units per milliliter with recoveries between roughly 88 and 108 percent in real samples.

Against viruses, tetrahedral frameworks have proven especially powerful. TDN-supported field-effect transistors detect SARS-CoV-2 nucleic acid in about 80 seconds without extraction or amplification, reaching limits of one to two copies per 100 microliters of clinical sample. DNA nanobait structures identify multiple respiratory viruses simultaneously at the single-molecule level without reverse transcription or pre-amplification, and a bipedal DNA walker paired with strand displacement amplification achieves attomolar sensitivity with single-base resolution in 15 minutes. Beyond detection, spatially patterned icosahedral DNA nanocages carrying up to 30 neutralizing aptamers block the SARS-CoV-2 spike–ACE2 interaction across variants including Omicron, and cone-shaped DNA origami traps physically engulf pleomorphic virus particles larger than 100 nanometers, from influenza A to Zika and chikungunya. Star-shaped designer DNA architectures display aptamers in patterns that precisely match dengue virus surface antigens, functioning as both sensor and inhibitor.

Therapeutic applications extend deep into antibacterial medicine. TDNs delivering the antimicrobial peptide GL13K enhanced activity against E. coli and restored efficacy against Porphyromonas gingivalis, and an injectable thermosensitive hydrogel system co-delivering GL13K with C/EBPα small activating RNA is being developed for periodontitis, offering anti-inflammatory and osteogenic benefits alongside antibacterial action. TDN–clindamycin complexes lowered the minimum inhibitory concentration eightfold against methicillin-resistant S. aureus in infected bone defect models. DNA origami platforms carrying lysozyme within five wells and 14 targeting aptamers homed in on Bacillus subtilis and E. coli, while a bactericidal origami co-loading G4/hemin DNAzyme and levofloxacin breached bacterial membranes and accelerated infected wound healing in vivo. Antisense oligonucleotide delivery by TDNs has silenced biofilm-forming genes in Streptococcus mutans, and six-helix bundle structures co-delivering antisense RNA with silver ions showed synergistic killing of both gram-positive and gram-negative bacteria.

The technology is not without serious bottlenecks. DNA nanostructures depend on cations such as magnesium to neutralize electrostatic repulsion, so physiological media can trigger disassembly, and nucleases degrade unprotected structures rapidly. The hundreds of custom oligonucleotides required for origami are expensive, and laboratory fabrication resists scale-up to good manufacturing practice standards. Regulatory pathways remain ambiguous, batch-to-batch consistency is difficult to guarantee, and assembly byproducts arising from kinetic traps and thermodynamic competition depress yields. Pathogen-specific obstacles compound these challenges: biofilm extracellular matrices impede penetration even though TDNs achieve 44-fold stronger fluorescence at 20-micrometer biofilm depth than linear structures; RNA viruses mutate rapidly enough to escape single-target therapeutics, though multivalent, multi-epitope DNA scaffolds offer a hedge; and fungal cell walls of bewildering structural variability limit drug access, even as TDNs improve delivery of the antifungal peptide Histatin 5 against Candida albicans.

The outlook nevertheless points toward integration. The review’s authors propose stability benchmarks—structures retaining more than 80 percent integrity after 24 hours in human serum—alongside xenonucleic acid backbones, disulfide crosslinking, and oligolysine-PEG coatings to harden constructs against serum and nucleases. Double-blind validation across at least 500 clinical samples is framed as the gateway to diagnostic approval, while microfluidic chips, lyophilized paper-based formats, and artificial intelligence-assisted design promise point-of-care deployment by non-specialists. On the preventive side, DNA origami vaccine scaffolds have orchestrated antigen and CpG adjuvant spacing to elicit durable immune responses, DNA–RNA hybrid origami shows ribonuclease resistance suitable for mRNA vaccines, and inhalable DNA nano-adjuvants have activated lung-resident memory immunity against pneumonic plague in mice. Perhaps most compelling is the prospect of convergent platforms: single DNA nanostructures that detect an infection, deliver the therapeutic payload, and prime immunity—all from the same molecule that carries life’s code.

Subject of Research: Applications of DNA nanostructures in the detection, treatment, and prevention of pathogenic microorganisms

Article Title: Advances in DNA nanostructures for pathogenic microorganisms

Article References: Han, X., Zhang, J., Pang, S., Wei, G., Niu, J., Lu, Y., & Xi, J. (2026). Advances in DNA nanostructures for pathogenic microorganisms. Materials Today Bio, 40, Article 103591. https://doi.org/10.1016/j.mtbio.2026.103591

Image Credits: AI Generated

DOI: Not provided

Keywords: DNA nanostructures, DNA origami, tetrahedral DNA nanostructures, pathogen detection, antibacterial therapy, antiviral therapy, biosensors, drug delivery, biofilms, SARS-CoV-2, CRISPR diagnostics, nanomedicine

“ If you don’t know how something moves, you don’t know what it does,” says Pallav Kosuri, PhD, an assistant professor at Salk and senior author of the study. Kosuri’s laboratory is pursuing a view of biology in which movement is as fundamental as chemistry. Chemical reactions may determine which bonds are formed or broken, but the motions of atoms, proteins, and larger molecular assemblies often determine how those reactions occur in real time. According to Kosuri, biology has a relatively comprehensive catalog of chemical reactions, while the mechanical side remains far less explored. The new method is designed to reveal that missing layer by converting molecular-scale motion into a signal visible through a conventional fluorescence microscope.

The approach is based on DNA origami, a form of molecular engineering that uses the predictable pairing of DNA bases to build custom structures. DNA contains four nucleic-acid bases—adenine, thymine, cytosine, and guanine—that pair in specific combinations, with adenine pairing with thymine and cytosine pairing with guanine. Researchers can design a long scaffold strand and hundreds of shorter “staple” strands so that the DNA folds into a predetermined three-dimensional shape. Because the structure assembles from the bottom up according to the sequence of its components, DNA origami can produce objects with nanometer-scale precision without the machinery required for conventional manufacturing. The technology has been explored for applications including drug delivery and nanoscale devices, but Kosuri’s group is using it as a tool for foundational molecular biology.

The challenge is that the movements the researchers want to measure are far smaller than the resolution of visible-light microscopy. DNA has a helical structure, and proteins that travel along it must rotate as they follow the twisting molecular track. The diameter of this rotation is roughly 100 times smaller than the wavelength of visible light, making the motion impossible to observe directly with a standard microscope. Rather than attempting to image DNA’s tiny rotation itself, Kosuri and his colleagues designed a much larger DNA-origami rotor that can be attached to the DNA-protein system. When the molecular machinery rotates, the origami device rotates with it, amplifying the movement into a fluorescent signal that can be recorded over time.

The original version of this technology, known as ORBIT, uses a fluorescently labeled DNA-origami rotor to track rotation as RNA polymerase transcribes DNA into RNA. RNA polymerase is an enzyme that moves along a DNA template, assembling a complementary RNA molecule one nucleotide at a time. Since transcription proceeds base by base, the attached rotor can report the enzyme’s progress with single-base-pair resolution. The engineered structure resembles a nanoscale wine opener: a spiraling stem connects the DNA-interacting region to a large, X-shaped handle carrying a fluorescent label. The handle magnifies the underlying rotation, allowing researchers to follow the direction and timing of the enzyme’s movement with a microscope that cannot resolve the DNA helix itself.

However, fluorescence microscopy has a fundamental limitation. Fluorescent molecules emit light when excited, but the repeated illumination gradually damages them in a process known as photobleaching. Once the dye molecules are chemically altered, they no longer produce a sufficiently bright signal, and the molecular motion disappears from the image even if the biological process continues. In early ORBIT experiments, photobleaching restricted observations to only a few seconds and allowed RNA polymerase to be followed across just a small number of base pairs. That short time window made it difficult to study pauses, changes in speed, or other mechanical behaviors that emerge over longer transcriptional journeys.

To overcome the problem, first author Amanda Wacker, PhD, and her colleagues developed a dye-cycling strategy that continually replenishes the fluorescent signal. Instead of relying on one permanently attached fluorescent tag, the system allows fresh fluorescent probes to associate with the DNA-origami rotor during the observation period. As older dyes fade, new probes replace them, effectively refueling the rotor while it is being tracked. The cycling process preserves the spatial information encoded by the origami structure while extending the period during which the molecular motion can be detected. In their study, the researchers used dye-cycling ORBIT to observe DNA rotations associated with transcription for approximately 10 minutes, a major increase over the seconds available with the original method.

“Pairing dye-cycling with ORBIT allowed us to overcome photobleaching limitations and track RNA polymerase transcription over long timescales while maintaining our single base-pair resolution,” says Wacker, who recently completed her PhD in Kosuri’s laboratory. The extended measurements provide more than a longer video of the same process. They allow researchers to examine how a molecular machine behaves across an extended DNA sequence, including whether its rotation remains uniform, whether it pauses, and how its motion may change as it encounters different regions of genetic material. Kosuri says the technique has since been used in his laboratory to capture molecular movement for hours, suggesting that the method could be adapted to study biological processes whose most informative events occur slowly or intermittently.

The immediate focus of the work is transcription, but the researchers see dye-cycling ORBIT as a broader platform for studying proteins that interact mechanically with DNA. RNA polymerase must negotiate the structural constraints of the DNA helix as it reads genetic instructions, and its movement is influenced by the physical properties of both the enzyme and the nucleic-acid track. A longer-lasting rotor could help scientists connect biochemical events—such as nucleotide incorporation—to mechanical events, including rotation, forward stepping, and pausing. Such measurements may ultimately clarify how transcription is regulated, how errors are avoided, and how molecular motion changes when genetic processes malfunction. More broadly, the method could make it possible to investigate the largely unexplored “mechanical universe” of biology, in which enzymes and molecular complexes constantly twist, step, bend, and reorganize themselves to keep cells alive.

The study also illustrates how DNA origami is evolving from a nanoscale construction technique into an instrument for observing life. Kosuri’s laboratory previously drew global attention after helping engineer a functional miniature Nerf gun made entirely from DNA for an educational project with engineer and science communicator Mark Rober. That project highlighted the extraordinary design flexibility of DNA-based structures; dye-cycling ORBIT applies the same precision to a more fundamental biological question. By attaching a visible, programmable nanostructure to an invisible molecular process, the researchers have created a bridge between the scale of individual base pairs and the scale accessible to optical microscopy. Their paper, titled “Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution,” reports a method that could help turn molecular movement from an abstract model into an experimentally measurable feature of gene expression.

Subject of Research: DNA origami, molecular motion, RNA polymerase transcription, fluorescence microscopy, single-molecule analysis

Article Title: Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution

News Publication Date: August 13, 2026

Web References: https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(26)00251-1; https://www.salk.edu/scientist/pallav-kosuri/; https://doi.org/10.1016/j.crmeth.2026.101550

References: Wacker A, Tenner B, Liu B, Fantasia R, Monell N, Wu J, Kosuri P. “Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution.” Cell Reports Methods. Published August 13, 2026. DOI: 10.1016/j.crmeth.2026.101550.

Image Credits: Salk Institute

Keywords: DNA origami, dye-cycling ORBIT, RNA polymerase, transcription, DNA, fluorescence microscopy, photobleaching, molecular motion, biophysics, structural biology, single-molecule analysis, molecular biology, genetic material, polymerases, Salk Institute