DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

In support of the publication "DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access" we share the following datasets and code: AutoCAD drawing of the microfluidic trapping device. Sequences of the DNA used to encode the 25 files used in the current study. FASTQ-files of the sequencing experiments of Figures 5b and d. Python scripts that allow for the reproduction of our sequencing data analysis. The code has been tested on MacOS 13.0.1, Python 3.7.13, samtools 1.16.1 and BWA 0.7.17

Impact of arginine modified SNARE peptides on interactions with phospholipid bilayers and coiled-coil formation: A molecular dynamics study

Membrane fusion plays a vital role in several biological processes such as cellular uptake, communication between cells and RNA delivery. Due to its complexity, model membranes and minimalistic fusion protein models are often used to gain insight into the fusion process. Coiled–coil (CC) peptides, consisting of two to five –helical peptides, are highly advantageous as minimalistic protein models. One of the most common fusion CC complex is formed between the complementary peptides E ((KIAALKE)4) and K ((EIAALEK)4). In this system, K peptides have been suggested to prime the membrane for fusion by causing small lipid protrusions within the membrane, increasing local curvature and membrane dehydration. In this study, we develop a library of peptides based on K peptide sequence by substituting lysine amino acids with arginine at varying heptad locations. By molecular dynamics simulations, we find that increasing the amount of arginine in the peptides results in enhanced affinity to the membrane. With coarse-grained simulations, we show that the interaction of peptides with the membrane triggers increased curvature in the membrane without significantly disrupting the lipid packing. Additionally, we find that all modified peptides retain the capability of forming CC complexes with E peptides. Our results suggest that arginine positioning is critical when designing CC fusion peptides. Peptides with arginines located at the N–terminus (ARG1, ARG6) show greater affinity to the lipid membrane. Our simulations suggest that introducing arginine into CC peptide sequences can enhance the binding affinity to the membrane via hydrogen bonds and may lead to more effective CC fusion peptides than E–K complexes

Bioinspired Scaffolding by Supramolecular Amines Allows the Formation of One- and Two-Dimensional Silica Superstructures

Silica materials attract an increasing amount of interest in (fundamental) research, and find applications in, for example, sensing, catalysis, and drug delivery. As the properties of these (nano)materials not only depend on their chemistry but also their size, shape, and surface area, the controllable synthesis of silica is essential for tailoring the materials to specific applications. Advantageously, bioinspired routes for silica production are environmentally friendly and straightforward since the formation process is spontaneous and proceeds under mild conditions. These strategies mostly employ amine-bearing phosphorylated (bio)polymers. In this work, we expand this principle to supramolecular polymers based on the water-soluble cationic cyanine dye Pinacyanol acetate. Upon assembly in water, these dye molecules form large, polyaminated, supramolecular fibers. The surfaces of these fibers can be used as a scaffold for the condensation of silicic acid. Control over the ionic strength, dye concentration, and silicic acid saturation yielded silica fibers with a diameter of 25 nm and a single, 4 nm pore. Unexpectedly, other unusual superstructures, namely, nummulites and spherulites, are also observed depending on the ionic strength and dye concentration. Transmission and scanning electron microscopy (TEM and SEM) showed that these superstructures are formed by aligned silica fibers. Close examination of the dye scaffold prior silicification using small-angle X-ray scattering (SAXS), and UV/Vis spectroscopy revealed minor influence of the ionic strength and dye concentration on the morphology of the supramolecular scaffold. Total internal reflection fluorescence (TIRF) during silicification unraveled that if the reaction is kept under static conditions, only silica fibers are obtained. Experiments performed on the dye scaffold and silica superstructures evidenced that the marked structural diversity originates from the arrangement of silica/dye fibers. Under these mild conditions, external force fields can profoundly influence the morphology of the produced silica

Impact of poly(ethylene glycol) functionalized lipids on ordering and fluidity of colloid supported lipid bilayers

Colloid supported lipid bilayers (CSLBs) are highly appealing building blocks for functional colloids. In this contribution, we critically evaluate the impact on lipid ordering and CSLB fluidity of inserted additives. We focus on poly(ethylene glycol) (PEG) bearing lipids, which are commonly introduced to promote colloidal stability. We investigate whether their effect on the CSLB is related to the incorporated amount and chemical nature of the lipid anchor. To this end, CSLBs were prepared from lipids with a low or high melting temperature (Tm), DOPC, and DPPC, respectively. Samples were supplemented with either 0, 5 or 10 mol% of either a low or high Tm PEGylated lipid, DOPE-PEG2000 or DSPE-PEG2000, respectively. Lipid ordering was probed via differential scanning calorimetry and fluidity by fluorescence recovery after photobleaching. We find that up to 5 mol% of either PEGylated lipids could be incorporated into both membranes without any pronounced effects. However, the fluorescence recovery of the liquid-like DOPC membrane was markedly decelerated upon incorporating 10 mol% of either PEGylated lipids, whilst insertion of the anchoring lipids (DOPE and DSPE without PEG2000) had no detectable impact. Therefore, we conclude that the amount of incorporated PEG stabilizer, not the chemical nature of the lipid anchor, should be tuned carefully to achieve sufficient colloidal stability without compromising the membrane dynamics. These findings offer guidance for the experimental design of studies using CSLBs, such as those focusing on the consequences of intra- and inter-particle inhomogeneities for multivalent binding and the impact of additive mobility on superselectivity. Graphical abstract: Impact of poly(ethylene glycol) functionalized lipids on ordering and fluidity of colloid supported lipid bilayer

Fractal-like R5 assembly promote the condensation of silicic acid into silica particles

HYPOTHESIS: Despite advances in understanding the R5 (SSKKSGSYSGKSGSKRRIL) peptide-driven bio-silica process, there remains significant discrepancies regarding the physicochemical characterization and the self-assembling mechanistic driving forces of the supramolecular R5 template. This paper investigates the self-assembly of R5 as a function of monovalent (sodium chloride) and multivalent salt (phosphate) to determine if assembly is phosphate ion concentration dependent. Additionally, we hypothesize that the assembled R5 aggregates do not resemble a micelle or unimer structure as proposed in current literature. EXPERIMENTS: R5 peptides were synthesized, and aggregates evaluated for their size, morphology, and association state as a function of salt and ionic strength concentration via dynamic and static light scattering, small angle X-ray and neutron scattering and cryogenic transmission electron microscopy. Furthermore, we compare the proposed R5 template to precipitated silica by scanning electron microscopy. FINDINGS: R5 peptides assemble into large aggregates due to multivalence bridging and the decrease in electrostatic repulsion due to ionic strength. We elucidate the structure of R5 aggregates as mass-fractals composed of small spherical aggregates. Moreover, we discover that phosphate ions not only have a significant role in driving the growth of the R5 scaffold, but additionally in driving the polycondensation of silicic acid during the bio-silification process via electrostatic interactions

Bioinspired Scaffolding by Supramolecular Amines Allows the Formation of One‐ and Two‐Dimensional Silica Superstructures

Silica materials attract an increasing amount of interest in (fundamental) research, and find applications in, for example, sensing, catalysis, and drug delivery. As the properties of these (nano)materials not only depend on their chemistry but also their size, shape, and surface area, the controllable synthesis of silica is essential for tailoring the materials to specific applications. Advantageously, bioinspired routes for silica production are environmentally friendly and straightforward since the formation process is spontaneous and proceeds under mild conditions. These strategies mostly employ amine-bearing phosphorylated (bio)polymers. In this work, we expand this principle to supramolecular polymers based on the water-soluble cationic cyanine dye Pinacyanol acetate. Upon assembly in water, these dye molecules form large, polyaminated, supramolecular fibers. The surfaces of these fibers can be used as a scaffold for the condensation of silicic acid. Control over the ionic strength, dye concentration, and silicic acid saturation yielded silica fibers with a diameter of 25 nm and a single, 4 nm pore. Unexpectedly, other unusual superstructures, namely, nummulites and spherulites, are also observed depending on the ionic strength and dye concentration. Transmission and scanning electron microscopy (TEM and SEM) showed that these superstructures are formed by aligned silica fibers. Close examination of the dye scaffold prior silicification using small-angle X-ray scattering (SAXS), and UV/Vis spectroscopy revealed minor influence of the ionic strength and dye concentration on the morphology of the supramolecular scaffold. Total internal reflection fluorescence (TIRF) during silicification unraveled that if the reaction is kept under static conditions, only silica fibers are obtained. Experiments performed on the dye scaffold and silica superstructures evidenced that the marked structural diversity originates from the arrangement of silica/dye fibers. Under these mild conditions, external force fields can profoundly influence the morphology of the produced silica