Biology subjects

Asor, R.

Publications and source records attributed to Asor, R..

6 recordsLinked to original sources

bioRxiv2026

Modular DNA nanosensors enable state-aware multiplexed single-molecule mass photometry in complex media

Proteins exist in diverse biochemical states, including oligomers, complexes, heterogeneous proteoforms and shed fragments that encode functional and regulatory information. Yet, these molecular states remain difficult to resolve with existing analytical techniques, which typically require labelling, immobilisation or amplification and collapse this information into a single readout. Here, we introduce a modular platform that integrates programmable DNA nanostructures with single-molecule mass photometry for rapid, label-free and multiplexed protein analysis in native and complex media, without washing, enrichment or immobilisation, making native biochemical states observable directly in serum and plasma. DNA nanostructures act as nanosensors whose mass and mobility on supported lipid bilayers provide orthogonal identifiers for target identity and biochemical state, thereby decoupling recognition from readout. We define the analytical specificity and response window, demonstrate quantitative affinity determination, and resolve oligomeric and proteoform differences under native conditions. The nanosensors are rapidly reprogrammable to new targets, support multiplexed detection with internal controls for non-specific interactions, and enable selective resetting via strand displacement. Together, these capabilities establish nanoscale programmability as a route to state-resolved single-molecule protein profiling adaptable to both diagnostic and mechanistic applications.

biophysics↗

bioRxiv2026

Continuous mass photometry by single molecule trapping

The dynamic choreography of biomolecular interactions underpins the processes of life, but its direct observation remains challenging. Here, we introduce confined diffusion mass photometry, enabling hour-long, mass-resolved observation of individual biomolecules, their complexes and interactions with up to sub-kDa mass precision and ms temporal resolution. Our approach represents a quantitative time-resolved single-molecule measurement modality for studying complex biomolecular mechanisms in action.

biophysics↗

bioRxiv2026

Molecular-level observation of the self-assembly of a virus-like particle

Biomolecular assembly is a cornerstone of cellular organisation and function. Revealing its underlying principles is essential for understanding biological processes, and their malfunction in disease. Viral capsid assembly is the archetypal self-assembly system that has been central in establishing the fundamental principles of biological self-assembly, providing a conceptual and geometric framework that underpins the current understanding of supramolecular biomolecular systems, the development of new biomaterials, and advancing therapeutic design. Yet, despite decades of experimental efforts, observation and quantification of virus self-assembly pathways and dynamics have remained elusive. Here, we combine mass photometry with a non-perturbative single molecule trapping method, enabling direct, real-time monitoring of the self-assembly of individual virus-like particles (VLPs) with molecular resolution. We show that weak, diffusion-limited, and reversible multivalent interactions control the assembly process by facilitating stochastic selection of a limited set of on-path, topologically closed intermediates. Assembly is finely tuned by the transition rates between these topologically closed configurations and proceeds through a sequence of effectively irreversible first-passage events. The intrinsic first-passage times are a consequence of VLP symmetry, creating a separation of timescales between the formation of the first closed intermediate and subsequent elongation. This separation results in a nucleation and growth mechanism that yields an equilibrium distribution consistent with the law of mass action, despite the overall irreversibility of assembly. Our approach enables direct and complete characterisation of both the thermodynamics and the kinetics governing VLP assembly and reveals how the system achieves specific assembly of one final structure with high fidelity despite the availability of thousands of assembly intermediates. More broadly, our approach provides a general framework for visualising and quantifying the dynamics of multimeric biological machines at the molecular level.

biophysics↗

bioRxiv2024

NIPBL and STAG1 enable loop extrusion by providing differential DNA-cohesin affinity

DNA loop extrusion by cohesin has emerged as a critical pathway for chromosome organization. In vitro single-molecule experiments indicate that loop extrusion requires the assembly of an heteropentameric complex consisting of the SMC1/SMC3 heterodimer, STAG1, NIPBL and the kleisin SCC1. The multimeric nature of this complex and regulatoin of its dynamic DNA interactions that are modulated by ATP binding-hydrolysis cycles make it challenging to reveal the molecular mechanism of loop extrusion. Here, we use mass photometry to quantify the key interactions responsible for cohesin assembly, DNA binding, and their modulation by ATP binding and hydrolysis. We find that STAG1 binds tightly to the trimeric complex formed by the SMC1/SMC3 heterodimer and SCC1, creating a DNA binding site whose strength is modulated by the presence of ATP. NIPBL binds strongly to both DNA and the STAG1-tetramer, enabling assembly of the holoenzyme in the absence of DNA or ATP. Taken together, these results suggest that NIPBL acts as a DNA anchor, while a dynamic STAG1-Trimer binding site drives DNA loop formation.

biophysics↗

bioRxiv2023

Cooperativity and induced oligomerisation control the interaction of SARS- CoV-2 with its cellular receptor and patient-derived antibodies

Viral entry is mediated by oligomeric proteins on the virus and cell surfaces. The association is therefore open to multivalent interactions between these proteins, yet such recognition is typically rationalised as affinity between monomeric equivalents. As a result, assessment of the thermodynamic mechanisms that control viral entry has been limited. Here, we use mass photometry to overcome the analytical challenges consequent to multivalency. Examining the interaction between the spike protein of SARS-CoV-2 and the ACE2 receptor, we find that ACE2 induces oligomerisation of spike in a variant-dependent fashion. We also demonstrate that patient-derived antibodies use induced-oligomerisation as a primary inhibition mechanism or to enhance the effects of receptor-site blocking. Our results reveal that naive affinity measurements are poor predictors of potency, and introduce a novel antibody-based inhibition mechanism for oligomeric targets. One-Sentence SummaryMultivalent interactions between viral proteins, cell-surface receptors, and anti-viral antibodies regulate infection and inhibition.

biophysics↗

bioRxiv2022

Effect of Ionic Strength on the Assembly of Simian Vacuolating Virus Capsid Protein Around Poly(Styrene Sulfonate)

Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent like RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with combinatorial intermediates, and therefore the mechanism of the reaction is poorly understood. In this paper, we determined the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by solution small-angle X-ray scattering (SAXS) and cryo-TEM. To analyze the data, we performed Brownian dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures that were consistent with the experimental data. We found that close to physiological ionic strength, T=1 VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and T=1 particles. Including the simulation, structures were essential to explaining the SAXS data.

biophysics↗