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 (m6A) 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. However, convenient methods that enable the simultaneous mapping of multiple different RNA marks within the same sample are generally lacking. Here we present EpiPlex RNA modification profiling, a bead-based proximity barcoding assay with sequencing readout that expands the scope of molecular recognition-based RNA modification detection to multiple targets, while providing relative quantification and enabling low RNA input. Measuring signal intensity against spike-in controls provides relative quantification, indicative of the RNA mod abundance at each locus. We report on changes in the modification status of HEK293T cells upon treatment with pharmacological inhibitors separately targeting METTL3, the dominant m6A writer enzyme, and the EIF4A3 component of the exon junction complex (EJC). The treatments resulted in decreased or increased m6A levels, respectively, without effect on inosine levels. Inhibiting the helicase activity of EIF4A3 and EIF4A3 knockdown both cause a significant increase of m6A sites near exon junctions, consistent with the previously reported role of EIF4A3 in shaping the m6A landscape. Thus, EpiPlex offers a reliable and convenient method for simultaneous mapping of multiple RNA modifications to facilitate epitranscriptome studies.

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. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer.

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. This study highlights the potential of capsosomes to continuously generate a potent antioxidant while simultaneously releasing small molecule therapeutics.

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. The developed technologies are outlined, successful applications of these capsules are highlighted, capsules properties which contribute to their performance in diverse applications are discussed, and further directions and plausible developments in the field are suggested.

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. Exposure of the ssDNA/OTAB interfacial complex to its ssDNA complement induced a second change in the interfacial structure characterized by the nucleation, growth, and coalescence of lateral regions that induced homeotropic LC alignment. Fluorescence microscopy showed explicitly that the complement was colocalized in the same regions as the homeotropic domains. Exposure to noncomplementary ssDNA caused no such response, suggesting that the homeotropic regions were due to DNA hybridization. This hybridization occurred in the vicinity of the interface despite the fact that the conditions in bulk solution were such that hybridization did not occur (high stringency), suggesting that the presence of the cationic surfactant neutralized electrostatic repulsion and allowed for hydrogen bonding between DNA complements. This system has potential for label-less and portable DNA detection. Indeed, LC response to ssDNA target was detected with a lower limit of approximately 50 fmol of complement and was sufficiently selective to differentiate a one-base-pair mismatch in a 16-mer target.

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. Observed are a 2D gas, isotropic liquid, and two condensed mesophases, each with a characteristic anchoring of the LC zenithal tilt and azimuth. By varying the monolayer temperature and surface concentration we observe reversible first-order phase transitions from vapor to liquid and from liquid to condensed. A temperature-dependent transition between two condensed phases appears to be a reversible swiveling transition in the tilt azimuth of the monolayer. Similar to monolayers at the air/water interface, the temperature of the gas/liquid/condensed triple-point temperature increased by about 10 degrees C for a two methylene group increase in chain length. However, the absolute value of the triple-point temperatures are depressed by about 40 degrees C compared to those of analogous monolayers at the air/water interface. We also observe a direct influence by the LC layer on the mesoscopic and macroscopic structure of the monolayer by analyzing the shapes and internal textures of gas domains in coexistence with a 2D liquid. An effective anisotropic line tension arises from elastic forces owing to deformation of the nematic director across phase boundaries. This results in the deformation of the domain from circular to elongated, with a distinct singularity. The LC elastic energy also gives rise to transition zones displaying mesoscopic realignment of the director tilt or azimuth between adjacent regions with a sudden change in anchoring.

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. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.

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. METHODS: In SPMR measurements, a brief magnetizing pulse is used to align superparamagnetic nanoparticles of a discrete size. Following the pulse, an array of superconducting quantum interference detectors (SQUID) sensors detect the decaying magnetization field. NP size is chosen so that, when bound, the induced field decays in seconds. They are functionalized with specific biomarkers and incubated with cancer cells in vitro to determine specificity and cell binding. For in vivo experiments, functionalized NPs are injected into mice with xenograft tumors, and field maps are generated to localize tumor sites. RESULTS: Superparamagnetic NPs developed here have small size dispersion. Cell incubation studies measure specificity for different cell lines and antibodies with very high contrast. In vivo animal measurements verify SPMR localization of tumors. Our results indicate that SPMR possesses sensitivity more than 2 orders of magnitude better than previously reported.

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. The PNIPAM-C18-functionalized metal nanoparticles and ordered superlattices exhibit responsive behavior modulated by external temperature and relative humidity (RH). In situ grazing-incidence small-angle X-ray scattering studies confirmed that the superlattice structure of PNIPAM-C18 surfactant-functionalized nanoparticle arrays shrink and spring back reversibly based on external thermal and RH conditions, which allow flexible manipulation of interparticle spacing for tunable SPR. PNIPAM-C18 surfactants play a key role in accomplishing this responsive property. The ease of fabrication of the responsive nanostructure facilitates investigation of nanoparticle coupling that depends on interparticle separation for potential applications in chemical and biological sensors as well as energy storage devices.

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. We also provide examples of subcompartmentalized polymer capsules, which represent a major step toward the creation of synthetic cells.

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. The detailed behavior of the onset of birefringence was found to be consistent with a dual-easy-axis model that predicts a discontinuous anchoring transition from homeotropic to planar. The anchoring was independent of temperature, except within 1 degrees C of the nematic-to-isotropic transition temperature (T(NI)). As the temperature approached T(NI), the tendency for planar anchoring gradually increased relative to that for homeotropic anchoring.