Bendy DNA Nanorods Slip Through Mucus Where Rigid Ones Get Stuck

Mucus is one of the body’s most deceptively difficult barriers. The gel-like coating that lines the intestines, stomach, lungs, and other organs is a viscoelastic mesh of mucin fibers, proteins, and lipids, riddled with pores that vary wildly in size and shape. For drug developers hoping to deliver nanoparticles across this barrier, mucus has long been a formidable adversary. Now, a team of researchers has shown that one of the most overlooked properties of a nanocarrier—how much it can bend—may determine whether it glides through mucus or becomes hopelessly trapped. Using programmable DNA origami structures, the scientists demonstrated that mechanical flexibility can dramatically improve diffusion through mucus, but only under the right biochemical conditions.

The study, published in Advanced Science, tackles a problem that has frustrated the field for years. Researchers have extensively studied how nanoparticle size, shape, and surface chemistry influence transport through mucus, but two factors have remained comparatively neglected: the mechanical flexibility of the particle itself, and the biological variability of the mucus barrier across different organs and physiological states. The difficulty is that flexibility is nearly impossible to tune in isolation. Modifying a particle’s mechanical properties typically changes its geometry or surface chemistry at the same time, making it hard to know whether observed effects stem from deformability or from some other confounding variable.

DNA origami offered a way out of this impasse. The technique folds a long single-stranded DNA scaffold, in this case from the M13mp18 bacteriophage, using hundreds of short complementary staple strands into precisely defined nanoscale shapes. The researchers built a rod-shaped structure called a 14-helix bundle, roughly 150 nanometers long—a size deliberately chosen to match the reported mesh size of mucus, which ranges from about 100 to 200 nanometers. By selectively removing staples from a central hinge region, the team could systematically increase the structure’s bending flexibility while keeping its overall dimensions and surface chemistry essentially unchanged.

The result was a family of five variants, designated Hinge 0 through Hinge 4, ranging from fully rigid to maximally flexible. Transmission electron microscopy confirmed that all five assembled correctly and retained their rod-like geometry, with only modest and statistically insignificant differences in effective length. The bending angles told a clear story: the rigid Hinge 0 structures remained nearly linear at close to 180 degrees, while the most flexible Hinge 4 constructs averaged around 120 degrees, with individual particles bending as far as 75 degrees. The most compliant designs also showed pronounced twisting, a sign of increased rotational freedom.

Before introducing the structures to biological samples, the team measured their diffusion in simple buffer and in a viscous polyethylene glycol solution that mimics mucus’s viscosity without any specific biochemical interactions. In both inert environments, flexibility paid off. The most flexible rods diffused roughly 45 percent faster than the rigid ones in buffer, and about 48 percent faster in the viscous medium. The explanation is hydrodynamic: bending and shape fluctuations reduce the effective drag a rod experiences as it moves through fluid, making it easier to translate forward even before any biological interactions come into play.

The real test came in mucus. The researchers tracked fluorescently labeled particles in three physiologically distinct porcine mucus environments: fasted intestinal mucus, fed intestinal mucus, and stomach mucus. In fasted intestinal mucus, the trend from the inert media held—more flexible rods moved farther and faster than rigid ones, supporting the idea that deformability helps particles squeeze through the sterically heterogeneous mucus mesh. Surprisingly, coating the particles with bovine serum albumin, a common surface-passivation strategy, actually reduced diffusion of all variants, likely because the protein layer increases hydrodynamic size and adds steric interactions at the particle-mucus interface. Yet even with this burden, flexible rods retained a measurable advantage over rigid ones.

The other two mucus environments revealed a more complicated picture. Fed intestinal mucus and stomach mucus both slowed particle diffusion overall, suggesting stronger adhesive interactions. To understand why, the team characterized each mucus sample using cryogenic scanning electron microscopy, rheology, and proteomics. The two intestinal samples, regardless of feeding state, looked structurally similar under the microscope, with elongated, oval-shaped pores, while stomach mucus displayed a distinctly different architecture of predominantly circular pores. Rheological measurements confirmed that stomach mucus was significantly stiffer than either intestinal sample. Proteomics identified roughly 6,300 proteins per sample, with about 88 percent shared across all three sources—but stomach mucus contained 258 unique proteins, compared with just 15 and 30 for the fasted and fed intestinal samples.

Single-particle tracking then exposed a critical mechanistic divide that bulk measurements would have missed. In stomach and fasted intestinal mucus, particles moved mostly as individuals, and their transport appeared limited by steric hindrance within the polymer network—conditions under which flexibility clearly helps. In fed intestinal mucus, however, particles clustered into aggregates, indicating that adhesive surface interactions, including electrostatic and hydrophobic binding to mucins, dominated the transport behavior. Under those conditions, adding flexibility alone accomplished little. Instead, BSA passivation was needed first to suppress aggregation and restore mobility—and once that happened, flexibility again provided an additional boost to diffusion. In other words, the right design strategy depends entirely on which barrier mechanism dominates in a given mucus environment.

The team also probed a scenario closer to real oral drug delivery: sequential exposure to intestinal fluid followed by mucus. Particles first incubated in intestinal fluid—a complex soup of enzymes, bile salts, and macromolecules—showed reduced mobility compared with particles introduced directly from buffer, and their subsequent diffusion in mucus was further diminished. Prior work has shown that DNA origami structures remain stable in intestinal mucus, so structural degradation was not the culprit; instead, fluid components appear to alter particle surface properties or create transient binding events that hinder movement. Crucially, the relative advantage of flexible designs persisted even after this fluid preconditioning, suggesting that mechanical compliance remains valuable under physiologically realistic conditions.

The findings carry practical weight for nanomedicine. Widely used surface-passivation strategies such as PEGylation can improve mucus penetration but may simultaneously compromise targeting and cellular uptake, so complementary approaches are needed. By decoupling flexibility from geometry and surface chemistry, this work establishes structural mechanics as a legitimate, independently tunable design parameter for mucosal drug carriers. The authors suggest the principle may extend beyond the gastrointestinal tract to pulmonary, nasal, and cervical mucus, though its impact will always depend on whether a given barrier is governed primarily by mechanical confinement or by surface-driven interactions. The broader message is that rational nanocarrier design demands a mechanistic diagnosis first: identify whether steric obstruction, interfacial adhesion, or aggregation is the limiting factor, and only then choose between flexibility, passivation, or a combination of both.

Subject of Research: Effect of DNA origami mechanical flexibility on nanoparticle transport through gastrointestinal mucus

Article Title: Mechanical Flexibility Enables DNA Origami to Overcome Steric Confinement in Mucus

Article References: Tollemeto, M., Tsang, E., Hong Lin, M. K. T., Mannino, L., Gothelf, K. V., & Boisen, A. (2026). Mechanical Flexibility Enables DNA Origami to Overcome Steric Confinement in Mucus. Advanced Science, 13(55), Article e76493. https://doi.org/10.1002/advs.76493

Image Credits: AI Generated

DOI: 10.1002/advs.76493

Keywords: DNA origami, mucus, nanoparticle transport, drug delivery, mechanical flexibility, single-particle tracking, mucosal barriers, surface passivation, 14-helix bundle, proteomics, rheology, gastrointestinal mucus