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Nanoscale

Royal Society of Chemistry (RSC)

All preprints, ranked by how well they match Nanoscale's content profile, based on 39 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Co2+-mediated adsorption facilitates atomic force microscopy of DNA molecules at double-helix resolution

Pailing, M.; Maia de Oliveira, T.; Flocco, M.; Hoogenboom, B. W.

2025-05-30 biophysics 10.1101/2025.05.29.655787 medRxiv
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Atomic force microscopy (AFM) has demonstrated the ability to resolve single DNA molecules in liquid at a spatial resolution that is sufficient to visualize the double helix structure and variations therein. Such variations can be due to inherent configurational flexibility and may be related to, e.g., DNA sequence, ionic screening, supercoiling, or protein binding. These AFM experiments require DNA to be adhered to a solid and preferably flat support. For high-resolution, in-liquid AFM studies so far, such adhesion has commonly been achieved using Ni2+ ions to electrostatically bridge between the negatively charged DNA and a negatively charged, atomically flat mica surface, yet Ni2+ ions tend to cause precipitation of salts on the surface, increasing the risk of AFM tip contamination and increasing the corrugation of the support surface, making it harder to distinguish secondary DNA structure. Here, we report on a sample preparation protocol that, instead, relies on Co2+ ions to adhere DNA to mica. While the Co2+ is similarly effective as Ni2+ for facilitating DNA adsorption onto mica, it leads to significantly reduced salt precipitation with the potential to provide enhanced reproducibility in high-resolution DNA imaging by AFM. We expect this to substantially facilitate high-resolution AFM studies of DNA in aqueous solutions.

2
Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics

Muthukumar, M.; Mahalik, J. P.

2021-06-22 biophysics 10.1101/2021.06.21.449276 medRxiv
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The full potential of solid state nanopores is yet to be realized for genome sequencing. Due to its robustness it can handle strong voltage amplitude and frequency. The effect of strong alternating voltage on the dynamics of nucleotides during translocation has been explored. We proposed a setup consisting of single stranded DNA covalently linked with symmetric polycations at both ends fashioned after the proposal of Kasianowicz. 1 Such a setup allows for repeated back and forth motion of the DNA along the nanopore (1.45 nm diameter and 1.53 nm thick) by simply switching the voltage polarity if the polycation tail is sufficiently long ([≥] 10) and the applied voltage is below 0.72 volts, but the average residence time of the nucleotides are too small to be of any practical use (6-30 ns). When alternating voltage of higher frequency is applied, it enhances the average residence time of the nucleotides by an order of magnitude to [~] 0.1 {micro}s relative to direct voltage but the individual trajectories are too stochastic. Since, we are able to collect repeated read on the dynamics of individual nucleotides, we obtained the most probable time of appearance of a nucleotide within the nanopore. With such construct we were able to get almost linear dependence of most probable time versus nucleotide index, after gaussian fitting.

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Magnetically controlled tension of cytoskeletal elements with magnetic nanoparticles affects the expression of signaling pathway genes associated with cytoskeletal elements

Pozdina, V.; Karavashkova, O.; Minin, A. S.; Zubarev, I.

2025-05-13 bioinformatics 10.1101/2025.05.08.652598 medRxiv
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Interactions with the extracellular environment and biological responses are based on biochemical pathways. Cytoskeletal reorganization is a dynamic process accompanied by filament polymerization and depolymerization, that allows the cell to effectively perceive and respond to external mechanical stimuli by altering their biomechanical properties. The contribution of mechanical deformations of individual cytoskeletal elements to changes in intracellular signaling has not been covered in the existing literature. In our article, we investigated changes in gene expression after regulated cytoskeletal deformation using a constant magnetic field and magnetic nanoparticles associated with antibodies to cytoskeletal proteins (vimentin, beta-actin and acetylated tubulin). For the first time, we have identified and described the biological pathways involved in the regulation of mechanical deformations of cytoskeletal elements.

4
Principles of Dopamine Binding to Carbon Surfaces

Khot, G.; Shirtcliffe, N.; Celikel, T.

2021-08-24 biochemistry 10.1101/2021.08.24.457508 medRxiv
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Fast Scan Cyclic Voltammetry (FSCV) combined with carbon electrodes is considered as the gold standard method for real-time detection of oxidizable neurotransmitters. The bioinert nature, rapid electron transfer kinetics and long-term stability make carbon an attractive material for probing brain electrochemistry. Herein, we first demonstrate a rapid fabrication process of carbonized nanopipettes and subsequently perform experimental measurements and theoretical simulations to study mechanisms of dopamine binding on carbonized surfaces. To explain the kinetics of dopamine oxidation on carbonized electrodes we adapted the electron-proton transfer model originally developed by Compton and found that the electron-proton transfer model best explains the experimental observations. We further investigated the electron-proton transfer theory by constructing a Density Function Theory (DFT) for visualization of dopamine binding to graphite-like surfaces consisting of heteroatoms. For graphite surfaces that are capped with hydrogen alone, we found that dopamine is oxidized, whereas, on graphite surfaces doped with heteroatoms such as nitrogen and oxygen, we found deprotonation of dopamine along with oxidation thus validating our experimental and theoretical data. These observations provide mechanistic insights into multistep electron transfer during dopamine oxidation on graphite surfaces. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/457508v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@8bee9corg.highwire.dtl.DTLVardef@de66ecorg.highwire.dtl.DTLVardef@1373032org.highwire.dtl.DTLVardef@3d61d0_HPS_FORMAT_FIGEXP M_FIG A: Pictorial view of the experimental setup of carbonized electrodes. The application of waveform causes the oxidation of dopamine. B. Background subtracted voltammogram of dopamine, wherein the waveform applied is -0.4V to 1.3V and cycled back at -0.4V at 200 V s-1 at 10 Hz. C: A hotspot showing the oxidation and reduction of dopamine, wherein two distinct redox spots can be seen. The first redox spot can be seen at 0.0V and the second one at 0.5V. Thus showing a multistep electron transfer for dopamine. D: A DFT model for dopamines interaction with graphite surfaces doped with nitrogen atoms. Oxidation of oxygen (red) can be seen with loss of protons. C_FIG

5
Indenting multi-cellular spheroids with various cantilever tip geometry

GNANACHANDRAN, K.; Lorenc, E.; Podesta, A.; Lekka, M.

2025-07-08 biophysics 10.1101/2025.07.05.663257 medRxiv
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Spheroids are of great interest in the study of cancer as they can partially mimic the tumour microenvironment, thus allowing to investigate several aspects of cell - microenvironment interactions in healthy and diseased conditions, including those pertaining to mechanobiology. Atomic Force Microscopy (AFM) is a versatile tool for studying biological samples and their mechanobiological properties. In AFM, the tip shape and dimensions determine the contact geometry between the tip and the sample and the length scales at which the mechanical properties are probed. Given the complex multiscale structure of spheroids, the choice of tip geometry and size would allow, in principle, to dissect the mechanical response of the overall system into the contributions of the constituents, from the single cell level to the cellular aggregate. In this work, we studied the mechanical properties of spheroids derived from four cell lines (A549, NHLF, HT-29, CCD-18Co). Our studies revealed that using different contact geometries in the fitting procedure results in significantly different Youngs modulus values, highlighting the multiscale response of these complex cellular systems and the importance of a precise experiment design and choice of the AFM probe for the nano-mechanical measurements. We observed that the location of F-actin filaments is correlated to the rigidity of the spheroids.

6
Targeted Molecular MRI of Colorectal Cancer by Antibody Functionalized Hyperpolarized Silicon Particles

Whiting, N.; Hu, J.; Pudakalakatti, S.; McCowan, C.; Ramezani, S.; Davis, J.; Millward, N. Z.; Engel, B.; Liu, J.; Gellci, K.; Seo, H.; Brown, D.; Enriquez, J. S.; Menter, D. G.; Millward, S. W.; Gammon, S. T.; Piwnica-Worms, D.; Farach-Carson, M. C.; Carson, D.; Constantinou, P. E.; Bhattacharya, P.

2025-05-07 cancer biology 10.1101/2025.05.06.651536 medRxiv
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The development of non-invasive, non-ionizing sensitive molecular targeting approaches to detect colorectal cancer (CRC) lesions is warranted to improve high risk patient outcomes. Hyperpolarized silicon nanoparticles and microparticles are potentially well-suited to act as targeted molecular imaging agents because of their overall biocompatibility and long-lasting enhanced magnetic resonance imaging (MRI) signals. In this study, dynamic nuclear polarization was performed on silicon particles functionalized with an antibody to Mucin-1 (MUC1), a surface mucin glycoprotein aberrantly expressed in CRC. Antibody conjugation to the particle surface did not affect 29Si hyperpolarization characteristics. Similarly, conjugation and the dynamic nuclear polarization process did not adversely affect the affinity of the targeting antibody. In vivo MRI scans performed 10-15 minutes after luminal administration of targeted hyperpolarized particles into human MUC1-expressing orthotopic CRC mouse models showed that particles actively targeted tumor sites. These results were supported by chemical and biological controls and blocking experiments as well as correlative immunohistochemical analysis. These surface-functionalized silicon particles are under development as a platform technology that will allow non-invasive molecular targeting of CRC using hyperpolarized MRI. Single Sentence SummaryTargeted molecular MR imaging of colorectal cancer by hyperpolarized silicon particles functionalized with mucin 1 antibody.

7
Nanoscale Structure, Interactions, and Dynamics of Centromere Nucleosomes

Filliaux, S. B.; Sun, Z.; Lyubchenko, Y. L.

2024-02-12 biophysics 10.1101/2024.02.12.579909 medRxiv
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Centromeres are specific segments of chromosomes responsible for the accurate chromosome segregation process. Centromeres are comprised of two types of nucleosomes: canonical nucleosomes containing an octamer of H2A, H2B, H3, and H4 histones, and CENP-A nucleosomes in which H3 is replaced with its analog CENP-A histone. This modification leads to the difference in the nuclear of DNA turns around the histone core, wrapping efficiency. This value is 121 bp of DNA, considerably less than 147 bp found in canonical nucleosomes. We used Atomic Force Microscopy (AFM) to characterize nanoscale features for both types of nucleosomes assembled on the same template, enabling us to evaluate the effect of internucleosomal interaction. We found that CENP-A mononucleosomes have a lower internucleosomal affinity than canonical H3 nucleosomes. We applied time-lapse, high-speed AFM (HS-AFM) to characterize the dynamics of nucleosomes. For both nucleosomes, spontaneous unwrapping of DNA was observed, and this process occurs via a transient state with [~]100 bp DNA wrapped around the core, followed by a rapid dissociation of DNA. The unwrapping process is asymmetric, so when the dissociation starts on one arm, it enlarges the size of the dissociated arm. Additionally, HS-AFM revealed higher stability of CENP-nucleosomes compared with H3 ones, in which dissociation of the histone core occurs prior to the nucleosome dissociation. The histone core of CENP-A nucleosomes remains intact even after the dissociation of DNA.

8
A Possible Inductive Mechanism for Magnetogenetics

Christiansen, M. G.; Hornslien, W.; Schuerle, S.

2020-07-17 neuroscience 10.1101/2020.07.16.207126 medRxiv
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Single domain magnetic nanoparticles are increasingly investigated as actuators of biological and chemical processes that respond to externally applied magnetic fields. Although their localized effects are frequently attributed to nanoscale heating, recent experimental evidence casts doubt on the existence of nanoscale temperature gradients in these systems. Here, using the stochastic Landau-Lifshitz-Gilbert equation and finite element modelling, we critically examine an alternative hypothesis that localized effects may be mediated by the induced electric fields arising from the detailed dynamical behavior of individual single domain magnetic particles. We apply our model to two significant case studies of magnetic nanoparticles in alternating magnetic fields: 1) magnetogenetic stimulation of channel proteins associated with ferritin and 2) catalytic enhancement of electrochemical hydrolysis. For the first case, while the local electric fields that ferritin generates are shown to be insufficient to perturb the transmembrane potential, fields on the surface of its mineral core on the order of 102 to 103 V/m may play a role in mass transport or release of iron ions that indirectly lead to stimulation. For the second case, our model indicates electric fields of approximately 300 V/m on the surface of the catalytic particles, with the highest interfacial electric field strengths expected during reversal events. This suggests that the nanoparticles best suited for hysteresis heating would also act as intermittent sources of localized induced electric fields in response to an alternating applied field. Finally, we put the magnitude and timescale of these electric fields in the context of technologically relevant phenomena, showing that they are generally weaker and faster. Popular SummaryThe possibility of using magnetic fields to exert wireless control over biological or chemical processes has stimulated vigorous research efforts across disciplines. Magnetic nanoparticles exposed to alternating magnetic fields have repeatedly been found to exert an influence at the nanoscale, for instance triggering biological responses or regulating chemical catalysis. While these effects have been attributed to nanoscale heating, recent experiments have shown that the temperature in the vicinity of magnetic nanoparticles may not differ appreciably from their surroundings. Could another nanoscale phenomenon be at work? Here, we critically examined the idea that electric fields induced in the immediate vicinity of magnetic nanoparticles might help explain nanoscale effects. The fact that magnetic nanoparticles thermally fluctuate is widely appreciated, but the process that dominates the generation of electric fields is the rapid (typically > 1 GHz) precession that the magnetic moment undergoes during reversal events. Combining a model of the detailed motion of a single magnetic moment with numerical calculation of the induced electric field, we consider the possible role of induced electric fields in two technologically important cases. The first is stimulation of neurons with weakly magnetic ferritin and the second is enhancement of hydrogen production by catalytic magnetic nanoparticles. Understanding the mechanism by which magnetic nanoparticles act on their surroundings is crucial to designing more optimal materials for triggering chemical and biological processes. The role of electric fields explored here also suggests the possibility of pairing magnetic nanoparticles with resonant stimuli to directly drive precession.

9
Nanotribology of Viruses Reveals Their Adhesion Strength and Modality of Motion on Surfaces

Ault, C. A.; Tsvetkova, I. B.; De Pablo, P.; Simon, C.; Dragnea, B.

2025-02-07 biophysics 10.1101/2025.02.03.636328 medRxiv
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We studied the friction dynamics of icosahedral viruses adsorbed to solid surfaces to probe their adhesion. Using the lateral torsion of cantilevers in atomic force microscopy to move individual capsids in a liquid environment, we found that the virions tend to roll rather than slide on the surface. In contrast, rigid, ligand-stabilized gold nanoparticles are more likely to combine rolling with sliding under the same conditions. The experiments indicate that the force required to drag the viruses on the surface is four times less than that of AuNPs, while the lateral force work needed to induce virus movement was [~] 104 kT, ten times less than that of the rigid gold nanoparticles. These results go beyond the paradigm that adhesion of nanoparticles is mainly governed by geometrical factors, such as size and area of contact, highlighting the need to amend modeling approaches to account for mechanically-compliant tribological response of biologically derived nanoparticles.

10
Single-nanoparticle electrophoretic mobility and trapping using active-feedback 3D tracking

Johnson, A.; Welsher, K.

2024-07-11 biophysics 10.1101/2024.07.08.602591 medRxiv
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Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EPM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EPM on a per-particle basis. Single-nanoparticle EPM is determined by using active feedback to "lock on" to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EPM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EPM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EPM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EPM in various ionic strengths (0.25-5 mM) and found decreased EPM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EPM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EPM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.

11
Optimised assembly of DNA-lipid nanostructures

Darley, E.; Ridone, P.; Singh, J. K. D.; Wickham, S. F.; Baker, M. A.

2020-06-02 biophysics 10.1101/2020.06.01.128686 medRxiv
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Liposomes are widely used as synthetic analogues of cell membranes and for drug delivery. Lipid-binding DNA nanostructures can modify the shape, porosity and reactivity of liposomes, mediated by cholesterol-modifications. DNA nanostructures can also be designed to switch conformations by DNA strand displacement. However, the optimal conditions to facilitate stable, high-yield DNA-lipid binding while allowing controlled switching by strand-displacement are not known. Here we characterised the effect of cholesterol arrangement, DNA structure, buffer and lipid composition on DNA-lipid binding and strand displacement. We observed that binding was inhibited below pH 4, and above 200 mM NaCl or 40 mM MgCl2, was independent of lipid type, and increased with membrane cholesterol content. For simple motifs, binding yield was slightly higher for double-stranded DNA than single-stranded. For larger DNA origami tiles, 4 - 8 cholesterol modifications were optimal, while edge positions and longer spacers increased yield of lipid-binding. Strand displacement achieved controlled removal of DNA tiles from membranes, but was inhibited by overhang domains, which are used to prevent cholesterol aggregation. These findings provide design guidelines for integrating strand-displacement switching with lipid-binding DNA nanostructures. This paves the way for achieving dynamic control of membrane morphology, enabling broader applications in nanomedicine and biophysics.

12
Real-time Biomechanical Characterisation of Cytoskeletal Remodelling

Zhang, K.; Reeves, C.; Berry, J. D.; Fox, K.; Elbourne, A.; Gelmi, A.

2024-06-02 biophysics 10.1101/2024.05.29.595860 medRxiv
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As progenitors for tissue, human mesenchymal stem cells (hMSCs) with ability of self-proliferation and differentiation into various cell types such as osteocytes and adipocytes show great potential applications for tissue engineering. Stem cell fate regulation is highly affected by the cytoskeleton structure and mechanical properties. In this paper, quantitative Atomic Force Microscopy (Q-AFM) was used to continuously characterise topography and biomechanical properties while applying cytoskeleton disruptors to hMSCs. The cell stiffness (quantified by Youngs modulus), primarily governed by the cytoskeleton network, had quantifiable changes associated with cytoskeleton polymerisation and depolymerisation when treatments were applied. Furthermore, with Q-AFM measurements, these changes were tracked in real time over a period of minutes to hours, and the biomechanical properties of the cells were tracked through the applied treatment and subsequent recovery post treatment. Here we present the capability of Q-AFM to perform real time biomechanical characterisation of living cells, directly correlated to intracellular structure and cytoskeletal remodelling.

13
Arktos: a simple tool for the design of polyhedral 1DNA nanostructures

Balaji, H.; Kolipakala, R. S.; Samprathi, A. H.; Pradeep, P.; Nagarajan, D.

2024-02-08 bioinformatics 10.1101/2024.02.07.576791 medRxiv
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DNA nanostructures are a class of self-assembling nanomaterials with a wide range of potential applications in biomedicine and nanotechnology. The history of DNA nanotechnology can be traced back to the 1980s with the development of simple DNA polyhedra using either human intuition or simple algorithms. Today the field is dominated by DNA origami constructs to such an extent that the original algorithms used to design non-origami nanostructures have been lost. In this work we describe Arktos: an algorithm developed to design simple DNA polyhedra without the use of DNA origami. Arktos designs sequences predicted to fold into a desired structure using simulated annealing optimization. As a proof-of-concept, we used Arktos to design a simple DNA tetrahedron. The generated oligonucleotide sequences were synthesized and experimentally validated via polyacrylamide gel electrophoresis, indicating that they fold into the desired structure. These results demonstrate that Arktos can be used to design custom DNA polyhedra as per the needs of the research community.

14
In vivo capture of bacterial cells by remote guiding

Rybkin, I. A.; Pinyaev, S. I.; Sindeeva, O. A.; German, S. V.; Koblar, M.; Pyataev, N. A.; Ceh, M.; Gorin, D. A.; Sukhorukov, G. B.; Lapanje, A.

2021-08-06 microbiology 10.1101/2021.08.06.455395 medRxiv
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Recently, it has been shown that several bacterial strains can be very efficient in cancer treatment since they possess many important properties such as self-targeting, ease of detection, sensing and toxicity against tumors. However, there are only a few relevant "candidates" for such an approach, as targeting and detection one of the biggest challenges as well as there are many limitations in the use of genetic approaches. Here, it is proposed the solution that enables surface modification of alive bacterial cells without interfering with their genetic material and potentially reduces their toxic side effect. By the electrostatic interaction fluorescently labeled polyelectrolytes (PEs) and magnetite nanoparticles (NPs) were deposited on the bacterial cell surface to control the cell growth, distribution and detection of bacteria. According to the results obtained in vivo, by the magnet entrapment of the modified bacteria the local concentration of the cells was increased more than 5 times, keeping the high concentrations even when the magnet is removed. Since the PEs create a strong barrier, in vitro it was shown that the division time of the cells can be regulated for better immune presentation.

15
Coincident Fluorescence Burst Analysis of dUTP-Loaded Exosome-Mimetic Nanovesicles

Sanaee, M.; Sandberg, E.; Ronquist, G.; Morrell, J.; Widengren, J.; Gallo, K.

2021-10-12 biophysics 10.1101/2021.10.11.463914 medRxiv
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O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/463914v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@13a85b2org.highwire.dtl.DTLVardef@11f6cd3org.highwire.dtl.DTLVardef@219a73org.highwire.dtl.DTLVardef@232f95_HPS_FORMAT_FIGEXP M_FIG C_FIG The targeting functionality and low immunogenicity of exosomes and exosome-mimetic nanovesicles make them promising as drug-delivery carriers. To tap into this potential, accurate non-destructive methods to load them and characterize their contents are of utmost importance. However, their small size, polydispersity and aggregation in solution make quantitative characterizations of their loading particularly challenging. Here we develop an ad-hoc methodology based on a burst analysis of dual-color confocal fluorescence microscopy experiments, suited for quantitative characterizations of exosome-like nanovesicles and of their loading. We apply it to study bioengineered nanovesicles, loaded with dUTP cargo molecules, synthetized from detergent-resistant membranes of animal extracellular vesicles and human red blood cells. For both classes of bioengineered nanovesicles we prove, by means of dual-color fluorescence cross-correlation spectroscopy (FCCS), successful loading. Furthermore, by a dual-color coincident fluorescence burst (DC-CFB) analysis of the experimental data, we retrieve size and loading statistics for both types of nanovesicles. The procedure affords single-vesicle characterizations, which are essential for reliable quantitative studies of loading processes in exosomes and exosome-mimetic nanovesicles, especially in light of the typically high heterogeneity of their populations. Moreover, the method implementation can be easily adapted to the investigation of a variety of combinations of different cargo molecules and biological nanovesicles besides the proof-of-principle demonstrations considered in this study. The results provide a powerful characterization tool, well-suited for the optimization of loading processes of biomimetic nanovesicles and their advanced engineering for therapeutic drug delivery.

16
Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness

Cantrall, G. R.; Chauhan, G.; Abel, S. M.

2025-09-06 biophysics 10.1101/2025.09.04.674235 medRxiv
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Macromolecular crowding can significantly impact the behavior of biopolymers, with crowding-induced depletion interactions influencing both the conformations and surface adsorption of individual polymers. Although previous studies have explored the influence of homogeneous polymer stiffness in crowded conditions, biomolecules such as DNA can exhibit sequence-dependent stiffness, and DNA origami nanoparticles can be designed with alternating stiff and flexible domains. In this work, we use Langevin dynamics simulations to characterize how nonuniform bending stiffness modulates the conformations and adsorption of polymers in crowded environments. By systematically varying the relative length and arrangement of flexible and semiflexible domains along a linear chain, we show that increasing osmotic pressure leads to a pattern-dependent collapse of the polymer, as revealed by a decrease in the radius of gyration. In general, large flexible regions promote polymer collapse, although flexible domains separating extended semi-flexible regions can facilitate their contact, leading to stable folded conformations. When a surface is present, large semiflexible domains promote adsorption, and the pattern of stiffness can be used to control the adsorption threshold. Our findings provide insight into the impact of spatially varying stiffness on the behavior of polymers in crowded environments, highlighting mechanisms relevant to biopolymers and deformable nanoparticles in both cellular and cell-free contexts.

17
Kinetics and dynamics of single-molecule multivalent interactions revealed by plasmon-enhanced fluorescence

Okholm, K. R.; Nooteboom, S. W.; Lamberti, V.; Dey, S.; Zijlstra, P.; Sutherland, D. S.

2023-12-08 biophysics 10.1101/2023.12.08.570798 medRxiv
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Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling and a current concept in drug design. Rapid binding and unbinding of monovalent constituent interactions during multivalent binding creates dynamics that require a single-molecule approach to be studied. Here, we use the high signals from plasmon enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real-time. We study mono-, bi-and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency. Furthermore, we introduce a model framework for binding kinetics that involves the binding restriction during multivalent interactions to take into account the structural conformation of multivalent molecules allowing quantitative comparison. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where overall binding strength decreased with spacer length. For trivalent systems increasing spacer length was found to activate binding in the trivalent state giving insight into the design of multivalent drug or targeting moieties. Interestingly we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal to position of the fluorophore to observe binding dynamics during single multivalent binding events.

18
Changes in Secondary Structure and Properties of Bovine Serum Albumin as a Result of Interactions with Gold Surface

Komorek, P.; Rakowski, K.; Szota, M.; Lekka, M.; Jachimska, B.

2023-11-18 biochemistry 10.1101/2023.11.18.567678 medRxiv
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Proteins can alter their shape when interacting with a surface. This study explores how bovine serum albumin (BSA) modifies structurally when it adheres to a gold surface, depending on the protein concentration and pH. We verified that the gold surface induces significant structural modifications to the BSA molecule using circular dichroism, infrared spectroscopy, and atomic force microscopy. Specifically, adsorbed molecules displayed increased levels of disordered structures and {beta}-turns, with fewer -helices than the native structure. MP-SPR spectroscopy demonstrated that the protein molecules preferred a planar orientation during adsorption. Molecular dynamics simulations revealed that the interaction between cysteines exposed to the outside of the molecule and the gold surface was vital, especially at pH = 3.5. The macroscopic properties of the protein film observed by AFM and contact angles confirm the flexible nature of the protein itself. Notably, structural transformation is joined with the degree of hydration of protein layers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/567678v1_ufig1.gif" ALT="Figure 1"> View larger version (81K): org.highwire.dtl.DTLVardef@525beborg.highwire.dtl.DTLVardef@110d1adorg.highwire.dtl.DTLVardef@135eed9org.highwire.dtl.DTLVardef@1d3ec41_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Volume and surface methods for microparticle traction force microscopy: a computational and experimental comparison

Brauburger, S.; Kraus, B. K.; Walther, T.; Abele, T.; Goepfrich, K.; Schwarz, U. S.

2026-03-31 biophysics 10.64898/2026.03.28.714997 medRxiv
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It is an essential element of mechanobiology to measure the forces of biological cells. In microparticle traction force microscopy, they are inferred from the deformation of elastic microparticles. Two complementary variants have been introduced before: the volume method, which reconstructs surface stresses from the displacements of fiducial markers embedded inside the particles, and the surface method, which infers stresses directly from the deformation of the particle surface. However, a systematic comparison of the two methods has been lacking. Here, we quantitatively compare both approaches using simulated traction fields representing biologically relevant loading scenarios. We find that the surface method consistently reconstructs traction profiles with substantially lower errors than the volume method, which suffers from displacement tracking and stress calculation at the surface. At high noise levels, however, the performance gap becomes smaller. To compare the performance of the two methods in a realistic experimental setting, we developed DNA-based hydrogel microparticles equipped with both fluorescent surface labels and embedded fluorescent nanoparticles, enabling the direct comparison of the two methods within the same system. Compression experiments produced traction profiles consistent with Hertzian contact mechanics and confirmed the trends observed in the simulations. While our computational workflow establishes a framework to apply both methods, our experimental workflow establishes DNA microparticles as versatile and biocompatible probes for measuring cellular forces.

20
Magnetic activation of electrically active cells

Duret, G.; Coffler, S.; Avants, B.; Kim, W.; Peterchev, A. V.; Robinson, J. T.

2025-02-08 biophysics 10.1101/2025.02.07.636926 medRxiv
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Magnetic control of cell activity has applications ranging from non-invasive neurostimulation to remote activation of cell-based therapies. Unlike other methods of regulating cell activity like heat and light, which are based on known receptors or proteins, no magnetically gated channel has been identified to date. As a result, effective approaches for magnetic control of cell activity are based on strong alternating magnetic fields able to induce electric fields or materials that convert magnetic energy into electrical, thermal, or mechanical energy to stimulate cells. In our investigations of magnetic cell responses, we found that a spiking HEK cell line with no other co-factors responds to a magnetic field that reaches a maximum of 500 mT within 200 ms using a permanent magnet. The response is rare, approximately 1 in 50 cells, but is fast and reproducible, generating an action potential within 200 ms of magnetic field stimulation. The magnetic field stimulation is over 10,000 times slower than the magnetic fields used in transcranial magnetic stimulation (TMS) and the induced electric field is more than an order of magnitude lower than necessary for neuromodulation, suggesting that induced electric currents do not drive the cell response. Instead, our calculation suggests that this response depends on mechanoreception pathways activated by the magnetic torque of TRP-associated lipid rafts. Despite the relatively rare response to magnetic stimulation, when cells form gap junctions, the magnetic stimulation can propagate to nearby cells, causing tissue-level responses. As an example, we co-cultured spiking HEK cells with beta-pancreatic MIN6 cells and found that this co-culture responds to magnetic fields by increasing insulin production. Together, these results point toward a method for the magnetic control of biological activity without the need for a material co-factor such as synthetic nanoparticles. By better understanding this mechanism and enriching for magneto-sensitivity it may be possible to adapt this approach to the rapidly expanding tool kit for wireless cell activity regulation.