Mapping multiple RNA modifications simultaneously by proximity barcode sequencing.

RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (mA) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns.

Sequencing by avidity enables high accuracy with low reagent consumption.

We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates.

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information.

Magnetic relaxometry as applied to sensitive cancer detection and localization.

Background: Here we describe superparamagnetic relaxometry (SPMR), a technology that utilizes highly sensitive magnetic sensors and superparamagnetic nanoparticles for cancer detection. Using SPMR, we sensitively and specifically detect nanoparticles conjugated to biomarkers for various types of cancer. SPMR offers high contrast in vivo, as there is no superparamagnetic background, and bones and tissue are transparent to the magnetic fields.

Poly(N-isopropylacrylamide) surfactant-functionalized responsive silver nanoparticles and superlattices.

Metal nanoparticles exhibit unique optical characteristics in visible spectra produced by local surface plasmon resonance (SPR) for a wide range of optical and electronic applications. We report the synthesis of poly(N-isopropylacrylamide) surfactant (PNIPAM-C18)-functionalized metal nanoparticles and ordered superlattice arrays through an interfacial self-assembly process. The method is simple and reliable without using complex chemistry.

Triggered cargo release by encapsulated enzymatic catalysis in capsosomes.

We report the coencapsulation of glutathione reductase and disulfide-linked polymer-oligopeptide conjugates into capsosomes, polymer carrier capsules containing liposomal subcompartments. The architecture of the capsosomes enables a temperature-triggered conversion of oxidized glutathione to its reduced sulfhydryl form by the encapsulated glutathione reductase. The reduced glutathione subsequently induces the release of the encapsulated oligopeptides from the capsosomes by reducing the disulfide linkages of the conjugates.

Poly(methacrylic acid) polymer hydrogel capsules: drug carriers, sub-compartmentalized microreactors, artificial organelles.

Multilayered polymer capsules attract significant research attention and are proposed as candidate materials for diverse biomedical applications, from targeted drug delivery to microencapsulated catalysis and sensors. Despite tremendous efforts, the studies which extend beyond proof of concept and report on the use of polymer capsules in drug delivery are few, as are the developments in encapsulated catalysis with the use of these carriers. In this Concept article, the recent successes of poly(methacrylic acid) hydrogel capsules as carrier vessels for delivery of therapeutic cargo, creation of microreactors, and assembly of sub-compartmentalized cell mimics are discussed.

Polymer hydrogel capsules: en route toward synthetic cellular systems.

Engineered synthetic cellular systems are expected to become a powerful biomedical platform for the development of next-generation therapeutic carrier vehicles. In this mini-review, we discuss the potential of polymer capsules derived by the layer-by-layer assembly as a platform system for the construction of artificial cells and organelles. We outline the characteristics of polymer capsules that make them unique for these applications, and we describe several successful examples of microencapsulated catalysis, including biologically relevant enzymatic reactions.

Subcompartmentalized polymer hydrogel capsules with selectively degradable carriers and subunits.

Subcompartmentalized hydrogel capsules (SHCs) with selectively degradable carriers and subunits are designed for potential applications in drug delivery and microencapsulated biocatalysis. Thiolated poly(methacrylic acid) and poly(N-vinyl pyrrolidone) are used to assemble 3-microm-diameter carrier capsules and 300-nm-diameter subunits, independently stabilized by a diverse range of covalent linkages. This paper presents examples of SHCs with tens of subcompartments and their successful drug loading, as well as selective degradation of the SHC carrier and/or subunits in response to multiple chemical stimuli.

A microreactor with thousands of subcompartments: enzyme-loaded liposomes within polymer capsules.

Fully loaded: Noncovalent anchoring of liposomes into polymer multilayered films with cholesterol-modified polymers allows the preparation of capsosomes-liposome-compartmentalized polymer capsules (see picture). A quantitative enzymatic reaction confirmed the presence of active cargo within the capsosomes and was used to determine the number of subcompartments within this novel biomedical carrier system.

DNA hybridization-induced reorientation of liquid crystal anchoring at the nematic liquid crystal/aqueous interface.

Interactions between DNA and an adsorbed cationic surfactant at the nematic liquid crystal (LC)/aqueous interface were investigated using polarized and fluorescence microscopy. The adsorption of octadecyltrimethylammonium bromide (OTAB) surfactant to the LC/aqueous interface resulted in homeotropic (untilted) LC alignment. Subsequent adsorption of single-stranded DNA (ssDNA) to the surfactant-laden interface modified the interfacial structure, resulting in a reorientation of the LC from homeotropic alignment to an intermediate tilt angle.

Fatty-acid monolayers at the nematic/water interface: phases and liquid-crystal alignment.

The two-dimensional (2D) phases of fatty-acid monolayers (hexadecanoic, octadecanoic, eicosanoic, and docosanoic acids) have been studied at the interface of a nematic liquid crystal (LC) and water. When observed between crossed polarizers, the LC responds to monolayer structure owing to mesoscopic alignment of the LC by the adsorbed molecules. Similar to Langmuir monolayers at the air/water interface, the adsorbed monolayer at the nematic/water interface displays distinct thermodynamic phases.

Anchoring of a nematic liquid crystal on a wettability gradient.

We have studied the anchoring of the nematic liquid crystal 5CB (4'-n-pentyl-4-cyanobiphenyl) as a function of the surface wettability, thickness of the liquid crystal layer, and temperature by measuring the birefringence of a hybrid aligned nematic cell where the nematic material was confined between octadecyltriethoxysilane-treated glass surfaces, with one surface linearly varying in its hydrophobicity. A homeotropic-to-tilted anchoring transition was observed as a function of the lateral distance along the hydrophobicity gradient, typically in a region corresponding to a water contact angle of approximately 64 degrees. The effect of the nematic layer thickness was measured simultaneously by preparing a wedge cell where the thickness varied along the direction perpendicular to the wettability.