Advanced biosensing and bioanalysis techniques

This paper evaluates the suitability of toehold switch and EXPAR for developing a cell-free miRNA biosensor, finding that EXPAR enhances detection sensitivity and accuracy.

This study uses molecular dynamics simulations to analyze how divalent cations affect aptamer conformational changes when binding neurotransmitters like dopamine and serotonin.

This paper introduces an algorithm to convert raw DNA origami sequences back into schematic designs, enabling easier modification and reuse of existing nanostructures.

This paper develops a cell-free method to directly measure infectious viral titer by capturing intact virions with an aptamer and detecting their genomes using FISH.

The paper develops a new aflatoxin B1 aptamer using computational methods to replace the SELEX technique, proposing a new pipeline and identifying a potential aptamer through molecular modeling and docking.

This paper introduces a platform for creating DNA-based artificial cells with localized functionalities using reaction-diffusion waves, demonstrating spatial segregation of RNA synthesis and storage.

This paper demonstrates that the GreenB1 aptamer specifically targets β1-integrin in triple-negative breast cancer cells and tumors, suggesting its potential for precision diagnosis and therapy.

This paper introduces a color-mixing strategy for high-throughput variant detection using fluorescence combinations, enabling simultaneous probing of multiple genetic variants with high specificity and sensitivity.

The paper develops an end-to-end computational approach to design RNA biosensors for miRNA biomarkers of cervical cancer, using public data and predictive models to guide sensor design and simulation.

This paper describes the engineering of a DNA-activated protein switch, nLuc-AFF, which can be used as a biosensor for DNA/RNA sequences, serotonin, ATP, and as a computational device processing DNA inputs.

This paper introduces co-transcriptional RNA strand displacement circuits that are programmable and scalable for molecular computing in biological systems.

This paper designs a DNA origami receptor that enables stable complexes with rapid subunit exchange, demonstrating the system's ability to handle both DNA and protein cargo.

This paper demonstrates a DNA nanodevice that switches between catalytic and non-catalytic electron transfer states using a chaotropic ion.

This paper designs DNA-based reaction-diffusion waveguides to enable spatiotemporal signal propagation in synthetic biomaterials, allowing for controlled biochemical communication.

This paper develops DNA strand displacement circuits to enhance biosensors by enabling fine-tuning of reaction kinetics and faster response times, creating binary outputs that encode target molecule concentrations.

This study shows DNA can functionalize lipid sponge droplets, with size-dependent partitioning and applications for cargo control and signaling.

Crisscross polymerization of DNA-origami slats enables the creation of micron-scale structures with uniquely addressable nanoscale features.

This paper introduces a method for site-specific conjugation of proteins to PNA using a strict protein ligase, enabling erasable imaging of membrane proteins.

This paper introduces a DNA-based probe to measure hammerhead ribozyme cleavage kinetics without radioactive labels, gels, or regular sampling, using fluorescence from strand displacement reactions.

This paper introduces a method using hybridization chain reaction for multiplexed, quantitative, high-resolution imaging of both proteins and RNA in challenging tissues.

This paper develops a DNA-based recording system using TdT to encode environmental signals with minutes resolution.

This study investigates how design parameters affect the binding of antibody-functionalized DNA nanostructures to cell surface receptors, finding that nanostructure size and DNA handle location influence receptor binding.

This paper demonstrates programmable aggregation of synthetic cells using DNA signals, showing controlled assembly and disassembly of artificial cells.

This study develops RNA beacons to detect the testis-determining factor (TDF) using in vitro evolved aptamers and shows their binding kinetics and structural interactions.

This paper introduces a method for robust nucleation control in DNA-based self-assembly using crisscross polymerization, achieving strictly seed-initiated growth without spontaneous nucleation.

This paper describes a method to generate RNA complexes in situ using self-cleaving ribozymes for synthetic molecular circuits.

The paper develops DNA-encoded sender-receiver architectures using microfluidic trapping arrays and light-activated DNA strand displacement to study diffusion-based signaling and spatial integration of chemical communication.

This study uses DNA origami and fast-scan atomic force microscopy to visualize PKA activation at the single-molecule level by observing cAMP-induced dissociation of catalytic subunits.

This paper introduces a methanol-responsive polymer (MeRPy) that selectively binds and releases DNA targets, improving NGS library quality by depleting unwanted transcripts.

This paper introduces a method using DNA nanoswitches to purify specific RNA species and validates its effectiveness with microRNA, rRNA, and mRNA fragments.