Biology subjects

Veneziano, R.

Publications and source records attributed to Veneziano, R..

12 recordsLinked to original sources

bioRxiv2026

Direct Synthesis of Targeted Nanosized ICG J-aggregate for Photoacoustic Imaging

Indocyanine green (ICG) J-aggregates (JAs) are self-assembled particles characterized by a sharp and strong absorption peak in the near-infrared region ([~]890 nm), enhanced photostability, low fluorescence, and high photothermal conversion efficiency, compared to monomeric ICG. These attributes make ICG-JAs promising contrast agent candidates for photoacoustic imaging (PAI). However, traditional methods for synthesizing ICG-JAs often yield particles without targeting ability, which limit their applications. Thus, to synthesize targeted nanoscale JA, complex and multi-step encapsulation and filtration processes are generally required. To solve this issue, we introduce a robust and rapid strategy for direct synthesis of targeted nanoscale ICG-JA by co-assembling ICG and ICG-azide dyes under optimized formulation conditions that do not require encapsulation. The resulting nanoscale JAAZ particles (nJAAZ) exhibit diameters of [~]120-150 nm and are amenable to direct bio-orthogonal functionalization via copper-free click chemistry for the attachment of virtually any targeting ligands and/or biomolecules. We further demonstrate the strong photoacoustic signal generation of these nJAAZ in vitro and in vivo, highlighting their potential as a modular high-performance contrast agent platform for PAI. This work establishes a scalable and tunable platform for engineering functional JAs, opening new avenues for targeted molecular imaging and theranostic applications.

bioengineering↗

bioRxiv2026

DNA-Based Nanoprobes for Fluorescence K+ Sensing in Neural Systems

SignificanceAbnormalities in potassium ion concentrations across subregions of the hippocampus have been implicated in seizures and other pathologies. Direct measurements of potassium ion concentrations are largely made using invasive electrodes, which do not allow for wide spatial coverage. This fluorescent nanoparticle potassium sensor enables direct visualization of potassium dynamics and represents a minimally invasive alternative to electrode-based methods. AimHere, we present a DNA-based fluorescence nanoprobe capable of sensing relative concentrations of potassium ions within populations of neurons. We present its effectiveness in monitoring neuronal K+ dynamics in response to electrical stimulation ex vivo. ApproachWe used widefield fluorescence microscopy to monitor changes in fluorescence intensity in labeled brain tissue in response to electrical stimulation ex vivo. ResultsWe found that our nanoprobe could be retained within the intracellular compartment and modulate in fluorescence intensity linearly in response to induced electrical current. Our K+ Sensor showed a fractional fluorescence change of approximately 1% per 10 mA of applied stimulation current in brain tissue. Optical spectroscopy confirmed the selectivity of the nanoprobes to potassium ions over other endogenous ions. ConclusionsOur findings indicate that this nanoprobe can be used to detect more complex potassium dynamics implicated in various pathologies of the nervous system, such as migraines, seizures, and trauma.

bioengineering↗

bioRxiv2025

Synthesis and Characterization of ICG-based Near-infrared Photoacoustic Contrast Agents

Near-infrared photoacoustic imaging (NIR-PAI) integrates optical excitation with ultrasound detection to enable high-resolution, deep-tissue imaging by taking advantage of reduced light scattering and absorption in this spectral window. Despite its potential, clinical translation of contrast-enhanced NIR-PAI is limited by the scarcity of effective contrast agents. Indocyanine green (ICG), an FDA-approved NIR dye, is a strong candidate due to its biocompatibility and photoacoustic efficiency. However, its concentration-dependent aggregation, lack of facile targeting strategies, instability in aqueous environments, and low photostability result in variable signal, high background noise, and reduced reliability in vivo. To address these challenges, we developed three biocompatible ICG-based nanoprobe platforms amenable to facile, scalable synthesis: 5-arm DNA-ICG nanostructures (5-arm DNA-ICG), lipid-shelled ICG nanobubbles (ICG-NBs), and Azide-modified ICG J-aggregates (JAAZ). These platforms are designed to preserve ICG monomers or control aggregation, enabling enhanced NIR-PAI performance. Spectroscopic and photoacoustic analyses revealed consistent absorbance and photoacoustic profiles, showing enhanced signals compared to free ICG. The greatest improvement was observed for JAAZ, followed by ICG-NBs and 5-arm DNA-ICG. Photostability studies showed that JAAZ aggregation protects ICG from light-induced photodegradation, whereas monomer preservation in 5-arm DNA-ICG and ICG-NBs provides less protection and moderate signal stability. All three probes demonstrated stable performance under physiological conditions, achieved strong signal-to-noise ratios at depth and under tissue-mimicking conditions, and required markedly reduced probe concentrations to generate robust signals. Their modular architectures allow incorporation of targeting ligands, offering molecular specificity and multimodal functionality. Collectively, these contrast agent platforms provide noninvasive, deep-tissue molecular imaging and biosensing, with strong potential for future preclinical and clinical translation, and represent a promising alternative to free ICG for biomedical applications.

bioengineering↗

bioRxiv2025

Rapid Prototyping of Microfluidic Devices with Stereolithographic 3D Printing

3D printing has become a prevalent technology in many fields such as manufacturing, architecture, and electronics. This additive manufacturing technique is also widely used for biomedical research and clinical applications to prototype or assemble biomedical devices and tools. 3D printing-based strategies for biocompatible materials offer greater design flexibility, enhanced versatility, and faster results than traditional fabrication techniques, advantages that could be especially beneficial to the development of microfluidic chips. The ability to simply and efficiently produce new chip molds from computer aided design (CAD) models would significantly transform the development process and expand its accessibility by removing the need for more complex and expensive lithography methods. However, with standard processing strategies, the use of 3D printed molds for casting functioning chips is limited by the poor quality of prints achievable with widely available 3D printers. To mitigate this issue and facilitate rapid microfluidic device prototyping, we have developed a simple procedure to print microfluidic molds using a stereolithographic (SLA) printer and produce functional polydimethylsiloxane (PDMS) microfluidic chips with height and width feature dimensions as low as 75 {micro}m. Molds printed using a commercially available liquid photopolymer-based resin and processed using our strategy exhibited high dimensional fidelity to intended designs and significantly reduced average surface roughness (< 3 {micro}m). Here, we describe a streamlined post-print processing workflow for SLA molds and its efficacy in reducing surface roughness while preserving dimensional fidelity and then demonstrate its utility by prototyping and optimizing a microfluidic extracellular vesicle (EV)-exchange platform. Graphical AbstractRapid prototyping of microfluidic device features using stereolithographic 3D printing. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/662041v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@126ff02org.highwire.dtl.DTLVardef@1301c7forg.highwire.dtl.DTLVardef@19edb96org.highwire.dtl.DTLVardef@6256b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

DNA six-way junction conformations and their use in a 2D square lattice

In this paper, we investigate the conformational landscape of the DNA six-way junction (6WJ), a higher-order extension of the DNA four-way junction (4WJ), to de-termine preferred structural isomers. The 6WJ allows for unique junction-level topolo-gies, and could be used to create novel DNA nanostructures, but the conformational landscape for the 6WJ is much more complex than the 4WJ. Our proposed confor-mational landscape for the 6WJ includes eight unique structural motifs, including an unstacked motif, five distinct stacked motifs, and two twisted motifs, and we estimate that there are forty structural isomers for the 6WJ, compared to only three for the 4WJ. To gain insight into these conformations, we perform all-atom molecular dynam-ics (MD) simulations on fourteen of the structural isomers. Our analysis shows that each 6WJ motif can be distinguished by its duplex stacking angles, and only a few of the 6WJ isomers have favorable free energies, which include the planar parallel isomers, the twisted isomers, and one of the orthogonal isomers. Lastly, to confirm that these stacked 6WJ motifs could be used to create larger-scale DNA nanostructures, we design a 2D square lattice using four orthogonal motifs connected in a 2x2 arrangement. Experimental characterization of this 2D lattice shows folding into the correct size and shape, further confirmed by AFM images of the DNA tiles, and an MD simulation that shows a slight twist of the lattice structure from orthogonality. This is the first 2D tile assembly built using an orthogonal junction-level topology for DNA nanotechnology, allowing a smaller mesh size than is possible with the 4WJ architecture.

bioengineering↗

bioRxiv2025

Designer DX-tile DNAns hydrogels

Pure deoxyribonucleic acid (DNA) hydrogels synthesized via the hybridization of multi-arm DNA tiles are uniquely programmable and functionalizable biomaterials suitable for applications ranging from biosensing to cell-free protein production and soft tissue engineering. However, the full potential of the design flexibility and functionalization offered by DNA molecules has not yet been leveraged for pure DNA hydrogels, thereby limiting their range of mechanical properties and reducing their versatility and broader use. In this study, we introduce multi-arm double-crossover (DX)-tile motifs, often used in DNA nanoparticle design, to enable greater control over the hydrogels mechanical properties and facilitate functionalization. Specifically, we demonstrate that modifying structural design parameters, such as the arm geometry, length, valency, and linker design, allows fine control of the elastic modulus and viscoelastic properties of the hydrogels. We also show that functionalization can be performed without compromising the hydrogels physical properties and exhibit enhanced mechanical strength and tunable properties, compared to simple duplex-based DNA hydrogels. Furthermore, these DNA hydrogels demonstrated printability and scalability, which pave the way towards the development of novel formulations and bioinks for the rational design of soft tissue engineering scaffolds and broaden the use of DNA hydrogels for other biomedical applications.

bioengineering↗

bioRxiv2024

Designer DNA Strand Displacement Reaction toward Controlled Release of Cargos

Dynamic DNA nanotechnology systems are used to design DNA logic circuits, signal amplification mechanisms for biosensing, and smart release system that could potentially be used in several biomedical applications. The toehold-mediated strand displacement reaction (TMSDR) is one of the main methods for designing DNA-based biomolecular logic circuits. However, the reaction behaviour such as the displacement rate and the quantity of strand released are difficult to control and often requires chemically modified strands or addition of enzymes. This makes the TMSDR versatility and specificity limited, and not always adapted for biomedical applications. Therefore, further understanding the sequence design parameters enabling fine tuning of the TMSDR behaviour without the need for complex modification, would enable its broader application. In this study, using a DNA motif developed for multiplexed release, we examine how mismatched base(s) in the trigger strand is affecting the release rate and quantity released and found that both location and type of mismatched base(s) significantly impact the displacement parameters of the TMSDR. This allows for a finer control of the cargo release for the multiplexed release system that could be used for varying biomedical applications and help developing release system mimicking the natural distribution of biomolecules.

bioengineering↗

bioRxiv2022

Size-tunable ICG-based contrast agent platform for targeted near-infrared photoacoustic imaging

Near-infrared photoacoustic imaging (NIR-PAI) combines the advantages of optical and ultrasound imaging to provide anatomical and functional information of tissues with high resolution. Although NIR-PAI is promising, its wide application is hindered by the limited availability of NIR contrast agents. J-aggregates (JA) made of indocyanine green dye (ICG) represents an attractive class of biocompatible contrast agents for PAI. Here, we present a facile synthesis method that combines ICG and ICG-azide dyes for producing contrast agent with tunable size down to 230 nm and direct functionalization with targeting moieties. The ICG-JA platform has a detectable PA signal in vitro that is two times stronger than whole blood and high photostability. The targeting ability of ICG-JA was measured in vitro using HeLa cells. The ICG-JA platform was then injected into mice and in vivo NIR-PAI showed enhanced visualization of liver and spleen for 90 minutes post-injection with a contrast-to-noise ratio of 2.42.

bioengineering↗

bioRxiv2022

DNA Origami Presenting the Receptor Binding Domain of SARS-CoV-2 Elicit Robust Protective Immune Response

Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible of the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases.

bioengineering↗

bioRxiv2020

Role of nanoscale antigen organization on B-cell activation probed using DNA origami

Arraying vaccine immunogens in a multivalent form on the surface of virus-like particles is an important strategy used to enhance the efficacy of subunit vaccines. However, the impacts of antigen valency, spacing, and spatial organization on B cell triggering remain poorly understood. Here, we use DNA origami nanoparticles to create precise nanoscale organizations of a clinically-relevant HIV gp120 immunogen to systematically interrogate their impact on B cell triggering in vitro. We find that antigen dimers elicit monotonically increasing B cell receptor activation as inter-antigen spacing increases up to ~30 nm, and only 5 immunogens arrayed on the surface of a 3D particle are needed to elicit maximal B cell calcium signaling. Our results reveal design principles of viral and immunogen display that drive functional B cell responses.

immunology↗

bioRxiv2017

Enzymatic synthesis of gene-length single-stranded DNA

Single-stranded DNA (ssDNA) increases the likelihood of homology directed repair with reduced cellular toxic ity, yet ssDNA synthesis strategies are limited by the maximum length attainable, as well control over nucleotide composition. Here, we apply purely enzymatic synthesis to generate ssDNA greater than 15 kb using asymmetric PCR, and illustrate the incorporation of diverse modified nucleotides for therapeutic and imaging applications.

bioengineering↗

bioRxiv2017

Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteins

Neuronal synapses contain dozens of protein species whose expression levels and localizations are key determinants of synaptic transmission and plasticity. The spectral properties of fluorophores used in conventional microscopy limit the number of measured proteins to four species within a given sample. The ability to perform high-throughput confocal or super-resolution imaging of many proteins simultaneously without limitation in target number imposed by this spectral limit would enable large-scale characterization of synaptic protein networks in situ. Here, we introduce PRISM: Probe-based Imaging for Sequential Multiplexing, a method that sequentially utilizes either high affinity Locked Nucleic Acid (LNA) or low affinity DNA probes to enable diffraction-limited confocal and PAINT-based super-resolution imaging. High-affinity LNA probes offer high-throughput, confocal-based imaging compared with PAINT, which uses low affinity probes to realize localization-based super-resolution imaging. Simultaneous immunostaining of all targets is performed prior to imaging, followed by sequential LNA/DNA probe exchange that requires only minutes under mild wash conditions. We apply PRISM to quantify the co-expression levels and nanometer-scale organization of one dozen cytoskeletal and synaptic proteins within individual neuronal synapses. Our approach is scalable to dozens of target proteins and is compatible with high-content screening platforms commonly used to interrogate phenotypic changes associated with genetic and drug perturbations in a variety of cell types.

bioengineering↗