Polymerase Chain Reaction on a Viral Nanoparticle

Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials

Controlling the assembly of high-order structures is central to soft-matter and biomaterial engineering. Angle-resolved linear dichroism can probe the ordering of chiral collagen molecules in the dense state. Collagen triple helices were aligned by solvent evaporation. Their ordering gives a strong linear dichroism (LD) that changes sign and intensity with varying sample orientations with respect to the beam linear polarization. Being complementary to circular dichroism, which probes the structure of chiral (bio)molecules, LD can shift from the molecular to the supramolecular scale and from the investigation of the conformation to interactions. Supported by multiphoton microscopy and X-ray scattering, we show that LD provides a straightforward route to probe collagen alignment, determine the packing density, and monitor denaturation. This approach could be adapted to any assembly of chiral (bio)macromolecules, with key advantages in detecting large-scale assemblies with high specificity to aligned and chiral molecules and improved sensitivity compared to conventional techniques.

A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy

A plug-and-play sandwich assay platform for the aptamer-based detection of molecular targets using linear dichroism (LD) spectroscopy as a read-out method has been demonstrated. A 21-mer DNA strand comprising the plug-and-play linker was bioconjugated onto the backbone of the filamentous bacteriophage M13, which gives a strong LD signal due to its ready alignment in linear flow. Extended DNA strands containing aptamer sequences that bind the protein thrombin, TBA and HD22, were then bound to the plug-and-play linker strand via complementary base pairing to generate aptamer-functionalised M13 bacteriophages. The secondary structure of the extended aptameric sequences required to bind to thrombin was checked using circular dichroism spectroscopy, with the binding confirmed using fluorescence anisotropy measurements. LD studies revealed that this sandwich sensor design is very effective at detecting thrombin down to pM levels, indicating the potential of this plug-and-play assay system as a new label-free homogenous detection system based on aptamer recognition.

Hydrophilic-Hydrophobic Nanohybrids of AuNP-Immobilized Two-Dimensional Nanomica Platelets as Flexible Substrates for High-Efficiency and High-Selectivity Surface-Enhanced Raman Scattering Microbe Detection

A flexible hybrid substrate was developed by affixing gold nanoparticles (AuNPs) onto the surface of two-dimensional nanomica platelets (NMPs). The substrate was successfully used in biosensors with high efficiency and high selectivity through surface-enhanced Raman scattering (SERS). By controlling the amphiphilicity of the hybrid substrate, the flexible substrate was made highly selective toward biomolecules. Four different SERS substrate systems were constructed, including intercalated mica, exfoliated NMPs, hydrophilic exfoliated NMPs, and hydrophobic exfoliated NMPs. NMPs were only 1 nm thick. AuNPs adsorbed on both sides of NMPs and thus created excellent three-dimensional hot junction effects in the z-axis direction. For the detection of adenine in DNA, a satisfactory Raman enhancement factor (EF) of up to 8.9 × 10⁶ was achieved with the detection limit as low as 10^-8 M. Subsequently, the AuNP/NMP hybrids were adopted to rapidly detect hydrophilic Staphylococcus hominis and hydrophobic Escherichia coli. The AuNP/PIB-POE-PIB/NMP nanohybrid was concurrently hydrophilic and hydrophobic. This amphiphilic property greatly enhanced the detection selectivity and signal intensity for hydrophilic or hydrophobic bacteria. Overall, AuNPs/PIB-POE-PIB/NMPs developed as SERS substrates enable rapid, sensitive biodetection.

Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers

Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.

Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay

Nucleic acid detection is an important part of our bio-detection arsenal, with the COVID-19 pandemic clearly demonstrating the importance to healthcare of rapid and efficient detection of specific pathogenic sequences. As part of the drive to establish new DNA detection methodologies and signal read-outs, here we show how linear dichroism (LD) spectroscopy can be used to produce a rapid and modular detection system for detecting quantities of DNA from both bacterial and viral pathogens. The LD sensing method exploits changes in fluid alignment of bionanoparticles (bacteriophage M13) engineered with DNA stands covalently attached to their surfaces, with the read-out signal induced by the formation of complementary duplexes between DNA targets and two M13 bionanoparticles. This new sandwich assay can detect pathogenic material down to picomolar levels in under 1 minute without amplification, as demonstrated by the successful sensing of DNA sequences from a plant virus (Potato virus Y) and an ampicillin resistance gene, ampR.

A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.

Model-based image analysis of a tethered Brownian fibre for shear stress sensing

The measurement of fluid dynamic shear stress acting on a biologically relevant surface is a challenging problem, particularly in the complex environment of, for example, the vasculature. While an experimental method for the direct detection of wall shear stress via the imaging of a synthetic biology nanorod has recently been developed, the data interpretation so far has been limited to phenomenological random walk modelling, small-angle approximation, and image analysis techniques which do not take into account the production of an image from a three-dimensional subject. In this report, we develop a mathematical and statistical framework to estimate shear stress from rapid imaging sequences based firstly on stochastic modelling of the dynamics of a tethered Brownian fibre in shear flow, and secondly on a novel model-based image analysis, which reconstructs fibre positions by solving the inverse problem of image formation. This framework is tested on experimental data, providing the first mechanistically rational analysis of the novel assay. What follows further develops the established theory for an untethered particle in a semi-dilute suspension, which is of relevance to, for example, the study of Brownian nanowires without flow, and presents new ideas in the field of multi-disciplinary image analysis.