Angle-dependent effects in Dynamic Light Scattering measurements of polydisperse particles

Dynamic light scattering (DLS) is widely used for analyzing biological polymers and colloids. Its application to nanoparticles in medicine is becoming increasingly important with the recent emergence of prominent lipid nanoparticle-(LNP)based products, such as the SARS-CoV-2 vaccines from Pfizer, Inc.-BioNTech (BNT162b2) and Moderna, Inc. (mRNA-1273). DLS plays an important role in the characterization and quality control of nanoparticle-based therapeutics and vaccines. However, most DLS instruments have a single detection angle ,and the amplitude of the scattering vector, q, varies among them according to the relationship q=(n/sin(/2) where 0 is the laser wavelength. Results for identical, polydisperse samples among instruments of varying q yield different hydrodynamic diameters, because, as particles become larger they scatter less light at higher angles, so that higher-q instruments will under-sample large particles in polydisperse populations, and report higher z-average diffusion coefficients, and hence smaller effective hydrodynamic diameters than lower-q instruments. As particle size reaches the Mie regime the scattering envelope manifests angular maxima and minima, and the monotonic decrease of average size versus q is lost. This work examines results for different q-value instruments, using mixtures of monodisperse latex sphere standards, for which experimental measurements agree well with computations, and also polydisperse solutions of LNP, for which results follow expected trends. Mie effects on broad unimodal populations are also considered. There is no way to predict results between two instruments with different q for samples of unknown particle size distributions.

Evaluating RNA Structural Flexibility: Viruses Lead the Way

Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked.

3. The chemical nature of enzymes

‘The chemical nature of enzymes’ evaluates the chemical nature of enzymes. To discover the chemical nature of enzymes, it was essential to obtain them in a pure form. To this end, the early biochemists devised various procedures, including fractionation and column chromatography. However, purification of enzymes led to controversy, which ultimately revealed that enzymes are proteins. Proteins are biological polymers, that is, they are built of similar units joined end to end to form very large molecules. Chemically, a protein molecule is a linear polypeptide.

Tools for generating and analyzing glycan microarray data

Glycans are one of the major biological polymers found in the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions. In this review, we describe the intricacies of the generation of glycan microarray data and the experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics tools.

Complex DNA knots detected with a nanopore sensor

Equilibrium knots are common in biological polymers—their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.

Cyclophospholipids Increase Protocellular Stability to Metal Ions

<p>Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and life as we know it is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here we show that prebiotically plausible monoacyl cyclophospholipids form robust vesicles that survive a broad range of pH and high concentrations of Mg2+, Ca2+, and Na+. Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+. These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.</p>

Cyclophospholipids Increase Protocellular Stability to Metal Ions

<p>Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and life as we know it is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here we show that prebiotically plausible monoacyl cyclophospholipids form robust vesicles that survive a broad range of pH and high concentrations of Mg2+, Ca2+, and Na+. Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+. These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.</p>