Biology subjects

Walti, C.

Publications and source records attributed to Walti, C..

3 recordsLinked to original sources

bioRxiv2023

Automated Purification of DNA Origami with SPRI Beads

DNA origami synthesis is a well-established technique and has been employed in various applications. The synthesised origami must be purified to eliminate the excess materials such as DNA oligos and other molecules. While several purification techniques are routinely used, they all have limitations, and none can be automated to simultaneously handle large numbers and quantities of samples. Here we introduce the use of solid-phase immobilisation (SPRI) beads as an easy-to-adopt, scalable, high-throughput and automation-compatible method to purify DNA origami. Not only can this method remove excess oligos and biomolecules with comparable yield to existing methods while maintaining high structural integrity of the origami, but it also allows an automated workflow to simultaneously purify large numbers of samples within a limited time. We envision that the SPRI beads purification approach will improve the scalability of DNA nanostructures synthesis both for research and commercial applications.

biophysics↗

bioRxiv2023

Nanopore Sensors for Enhanced Detection of Nanoparticles

Nanopore sensing is a technique based on the Coulter principle to analyze and characterize nanoscale materials with single entity resolution. However, its use in nanoparticle characterization has been constrained by the need to tailor the nanopore aperture size to the size of the analyte, precluding the analysis of heterogenous samples. Additionally, nanopore sensors often require the use of high salt concentrations to improve the signal-to-noise ratio, which further limits their ability to study a wide range of nanoparticles that are unstable at high ionic strength. Here, we report the development of nanopore sensors enhanced by a polymer electrolyte system, enabling the analysis of heterogenous nanoparticle mixtures at low ionic strength. We present a finite element model to explain the anomalous conductive/resistive pulse signals observed and compare these results with experiments. Furthermore, we demonstrate the wide applicability of the method by characterizing metallic nanospheres of varied sizes, plasmonic nanostars with various degrees of branching, and protein-based spherical nucleic acids with different oligonucleotide loadings. Our system will complement the toolbox of nanomaterials characterization techniques and will enable real-time optimization workflow for engineering a wide range of nanomaterials.

biophysics↗

bioRxiv2022

Nanopore Fingerprinting of Supramolecular DNA Nanostructures

DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilising the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale complex multi-tile arrays. These DNA nanostructures have enabled new applications in biosensing, drug delivery and other multifunctional materials. In this study, we demonstrate real-time, non-destructive and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures using solid-state nanopores. Using this approach, we quantify the assembly yields for each DNA origami nanostructure with single-entity resolution using the nanostructure-induced charge introduced in the nanopore as a discriminant. We compare the assembly yield of the supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and AFM imaging and demonstrate that the nanopore system can provide enhanced information about the nanostructures. We envision that this nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real-time with single-molecule resolution. STATEMENT OF SIGNIFICANCEWe demonstrate a single molecule high-throughput approach for the analysis of higher-order DNA origami assemblies with a crowded nanopore. The technique enables the characterisation of DNA origami nanostructures at statistically relevant numbers in real-time and at single-molecule resolution while being non-destructive and label-free, and without the requirement of lengthy sample preparations or use of expensive reagents. We exemplify the technique by demonstrating the quantification of the assembly yield of DNA origami nanostructures based on their equivalent charge surplus computed from the ion current signals recorded. Compared to the standard analysis methods of AFM and agarose gel electrophoresis, the nanopore measurements provides enhanced information about the nanostructures.

biophysics↗