Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.

Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING).

Ionic Strength-Mediated "DNA Corona Defects" for Efficient Arrangement of Single-Walled Carbon Nanotubes.

Single-stranded DNA oligonucleotides wrapping on the surface of single-walled carbon nanotubes (SWCNTs), described as DNA corona, are often used as a dispersing agent for SWCNTs. The uneven distribution of DNA corona along SWCNTs is related to the photoelectric properties and the surface activity of SWCNTs. An ionic strength-mediated "DNA corona defects" (DCDs) strategy is proposed to acquire an exposed surface of SWCNTs (accessible surface) as large as possible while maintaining good dispersibility via modulating the conformation of DNA corona.

The controllable patterning of tannic acid on DNA origami.

Tannic acid-based patterning is crucial for its applications in bioengineering, including multifunctional coatings, biosensors, and biochips. However, tannic acid (TA) patterning is challenging owing to the rapid polymerization kinetics of tannins and their strong adhesion towards most surfaces or objects. Herein, we report a strategy for controllable TA nanopatterning based on DNA origami templates.

Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood.

Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process.

Functions and applications of artificial intelligence in droplet microfluidics.

Droplet microfluidics has emerged as a powerful technology to perform high-throughput experiments, while artificial intelligence (AI) serves as a functional tool to analyze a large set of multiplex data. Their convergence creates new opportunities in autonomous system optimization and control, enabling various innovative functions and applications. In this study, we elucidate the basic principles of AI and elaborate on its main functions.

Microwell array chip-based single-cell analysis.

Single-cell profiling is key to uncover the cellular heterogeneity and drives deep understanding of cell fate. In recent years, microfluidics has become an ideal tool for single-cell profiling owing to its benefits of high throughput and automation. Among various microfluidic platforms, microwell has the advantages of simple operation and easy integration with analysis ability, making it an ideal technique for single-cell studies.

Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging.

Spatial visualization of single-cell transcripts is limited by signal specificity and multiplexing. Here, we report hierarchical DNA branch assembly-encoded fluorescent nanoladders, which achieve denoised and highly multiplexed signal amplification for single-molecule transcript imaging. This method first offers independent RNA-primed rolling circle amplification without nonspecific amplification based on circular DNAzyme.

Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations.

Investigating the spatial information of post-translational modifications (PTMs) in distinct cell subpopulations represents a new direction toward single-cell analysis. The specific capture of cell populations combined with PTM spatial proximity visualization making it practically challenging. Here, we develop branched immunochip-integrated pairwise barcoding amplification, termed biChip-PBA, which can perform the respective capture of cell subpopulations expressing different membrane proteins and successive PBA-based fluorescence imaging of PTM proximities.

Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification.

Nucleic acids are naturally decorated with various chemical modifications at nucleobases. Most nucleic acid modifications (NAMs) do not alter Watson-Crick base pairing but can regulate gene expression known as "epigenetics". Their abundances present a very wide range, approximately 10 to 10 of total bases.

Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology.

Lipid vesicle research is of great significance in the field of biomedicine and great progress has been made in recent years, in which the surface engineering on lipid membranes plays an important role. By introducing new active sites on membrane surface, the physicochemical properties of vesicles are regulated and the biological functions are extended. DNA nanotechnology is an excellent tool for surface engineering of vesicles and has attracted more and more attention.

A bifunctional chemical signature enabling RNA 4-thiouridine enrichment sequencing with single-base resolution.

Both sequence enrichment and base resolution are essential for accurate sequencing analysis of low-abundance RNA. Yet they are hindered by the lack of molecular tools. Here we report a bifunctional chemical signature for RNA 4-thiouridine (4sU) enrichment sequencing with single-base resolution.

Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus.

The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has spread rapidly around the world. Accurate and scalable diagnostics are essential for immediate intervention and control of viral transmission. Currently reported diagnostics are rapid and sensitive, yet most are limited by their principle of single-locus identification and suffer from false-negative results because of the mutation-prone nature of RNA viruses.

Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling.

Dynamic information of intracellular transcripts is essential to understand their functional roles. Routine RNA-sequencing (RNA-seq) methods only measure RNA species at a steady state and do not provide RNA dynamic information. Here, we develop addition-elimination mechanism-activated nucleotide transition sequencing (AENT-seq) for transcriptome-wide profiling of RNA dynamics.

Development of pH-responsive nanocomposites with remarkably synergistic antibiofilm activities based on ultrasmall silver nanoparticles in combination with aminoglycoside antibiotics.

Bacterial biofilms are responsible for many chronic infections because antibacterial agents exhibit poor penetration into the dense matrix barrier and cannot easily reach the internal bacteria. Herein, we reported pH-responsive nanocomposites (PDA@Kana-AgNPs) that could penetrate and disperse biofilms, which were synthesized by the combination of ultrasmall silver nanoparticles (AgNPs) and kanamycin, and then coating with polydopamine. Confocal fluorescence imaging indicated that PDA@Kana-AgNPs could respond to the acidic microenvironment of biofilms, leading to biofilm-triggered on- demand drug release in situ.

Construction of a Mesoporous Ceria Hollow Sphere/Enzyme Nanoreactor for Enhanced Cascade Catalytic Antibacterial Therapy.

Nanozyme has been regarded as one of the antibacterial agents to kill bacteria via a Fenton-like reaction in the presence of HO. However, it still suffers drawbacks such as insufficient catalytic activity in near-neutral conditions and the requirement of high HO levels, which would minimize the side effects to healthy tissues. Herein, a mesoporous ceria hollow sphere/enzyme nanoreactor is constructed by loading glucose oxidase in the mesoporous ceria hollow sphere nanozyme.

Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines.

Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells.

Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.

Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications.

Controllable synthesis of iron-polyphenol colloidal nanoparticles with composition-dependent photothermal performance.

Iron-polyphenol nanoparticles are usually prepared with nontoxic plant polyphenols as a main building block, which are an emerging photothermal agent for photothermal therapy. However, till now, few works have been made on the controllable synthesis of iron-polyphenol nanoparticles with tunable composition, as well as investigation of the relationship between material composition and photothermal property. In the present study, iron-polyphenol colloidal nanoparticles with tunable diameter (21-303 nm) and ion content (9.

Aptamer-Functionalized Microdevices for Bioanalysis.

Aptamers have drawn great attention in the field of biological research and disease diagnosis for the remarkable advantages as recognition elements. They show unique superiority for facile selection, desirable thermal stability, flexible engineering, and low immunogenicity, complementing the use of conventional antibodies. Aptamer-functionalized microdevices offer promising properties for bioanalysis applications because of the compact sizes, minimal reaction volume, high throughput, operational feasibility, and controlled preciseness.

Pairwise Proximity-Differentiated Visualization of Single-Cell DNA Epigenetic Marks.

Spatial positioning and proximity of relevant biomolecules such as DNA epigenetic marks are fundamental to a deeper understanding of life. However, it remains poorly explored and technically challenging. Here we report the pairwise proximity-differentiated visualization of single-cell 5-formylcytosine (5fC) and 5-hydroxymethylcytosine (5hmC).

Sol-Gel Synthesis of Spherical Mesoporous High-Entropy Oxides.

High-entropy oxides (HEOs) have attracted increasing interest owing to their unique structures and fascinating physicochemical properties. Spherical mesoporous HEOs further inherit the advantages of spherical mesoporous materials including high surface area and tunable pore size. However, it is still a huge challenge to construct HEOs with uniform spheres and a mesoporous framework.

RNA-Primed Amplification for Noise-Suppressed Visualization of Single-Cell Splice Variants.

Splice variants visualization is pivotal for a deeper understanding of cell growth and development. However, it remains technically challenging due to short lengths, similar sequences, and low abundance. The existing single-cell imaging strategies suffer from nonspecific amplification that causes considerable noise during visualization of the splice variants.

Visualizing Newly Synthesized RNA by Bioorthogonal Labeling-Primed DNA Amplification.

Monitoring RNA synthesis and spatial distribution can help to understand its role in physiology and diseases. However, visualizing newly synthesized RNA in single cells remains a great challenge. Here, we developed a bioorthogonal labeling-primed DNA amplification strategy to visualize newly synthesized RNA in single cells.

Intracellular Entropy-Driven Multi-Bit DNA Computing for Tumor Progression Discrimination.

Tumor progressions such as metastasis are complicated events that involve abnormal expression of different miRNAs and enzymes. Monitoring these biomolecules in live cells with computational DNA nanotechnology may enable discrimination of tumor progression via digital outputs. Herein, we report intracellular entropy-driven multivalent DNA circuits to implement multi-bit computing for simultaneous analysis of intracellular telomerase and microRNAs including miR-21 and miR-31.