Advanced biosensing and bioanalysis techniques

A spring-loaded and leakage-tolerant synthetic gene switch for in-vitro detection of DNA and RNA

This paper introduces a synthetic gene switch that detects DNA and RNA with high sensitivity and zero background, using a TMSD cascade and fluorescent aptamer output.

Selection of antibody-binding covalent aptamers

This paper develops covalent aptamers that bind mouse monoclonal antibodies and uses them to create antibody-oligonucleotide conjugates for HIV detection and imaging.

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

The paper introduces SCOPE, an optics-free method to reconstruct 2D and 3D shapes using DNA barcode proximity graphs from sequencing data.

Designer DNA Strand Displacement Reaction toward Controlled Release of Cargos

This study investigates how mismatched bases in trigger strands affect TMSDR displacement parameters, enabling finer control of cargo release for biomedical applications.

Advancing Early Diagnosis of Alzheimers Disease: A Paper-Based Aptasensor for Detecting Amyloid Beta(1-42) and p-tau181 from Plasma Using CdTe Quantum Dots

AptaGPT: Advancing aptamer design with a generative pre-trained language model

AptaGPT uses a generative pre-trained transformer to design aptamers, generating high-affinity sequences faster than traditional methods.

Impedance-based assay for pan-cancer early and rapid detection of cell-free DNA

This paper introduces an impedance-based biosensor for rapid, label-free detection of cancer-associated cfDNA with high sensitivity and specificity across multiple cancer types.

High-throughput evolution of near-infrared oxytocin nanosensors enables oxytocin imaging in mice and prairie voles

The paper develops a high-throughput method to evolve near-infrared oxytocin nanosensors for live imaging of oxytocin release in mice and prairie voles.

2D MXene-DNA Hybrid Hydrogel for Thrombin Detection: A Versatile Approach for Biomedical Sensing

This paper develops a 2D MXene-DNA hybrid hydrogel for thrombin detection, achieving 90-92% accuracy in artificial samples by monitoring resistance changes upon thrombin binding.

Developmental assembly of multi-component polymer systems through interconnected gene networks in vitro

This paper demonstrates a method to control the self-assembly of DNA-based polymers using synthetic gene networks, achieving spatial and temporal control over polymer formation and dissolution.

Reconfigurable multi-component nanostructures built from DNA origami voxels

This paper develops a modular DNA origami voxel system capable of assembling into diverse 3D structures with high yield and reversible reconfiguration.

Passivating blunt-ended helices to control monodispersity and multi-subunit assembly of DNA origami structures

This study evaluates methods to prevent aggregation and control multi-subunit assembly in DNA origami by comparing scaffold loops, poly-nucleotide brushes, and orthogonal DNA helices.

Arktos: a simple tool for the design of polyhedral DNA nanostructures

Arktos is an algorithm that designs DNA polyhedra without DNA origami, validated by experimental testing of a DNA tetrahedron.

Multiplex, quantitative, high-resolution imaging of protein:protein complexes via hybridization chain reaction

This paper develops a method to image protein:protein complexes with high resolution and quantitation using hybridization chain reaction, demonstrating its effectiveness in various biological samples.

Stacking effects on mutation detection by T4 DNA ligation within dimeric DNA origami triangle barcodes for single-molecule nanopore analysis

This paper develops a method using DNA origami barcodes and T4 DNA ligation to detect DNA point mutations with nanopore analysis, showing enhanced stacking effects that influence ligation efficiency.

Strong sequence dependence in RNA/DNA hybrid strand displacement kinetics

The paper characterizes RNA/DNA hybrid strand displacement kinetics, finding strong sequence dependence and large rate differences between RNA-DNA hybrids and DNA-DNA duplexes.

Engineering ssRNA tile filaments for (dis)assembly and membrane binding

This paper engineers ssRNA tiles to create cytoskeletal-like filaments with programmable assembly, disassembly, stiffness, membrane binding, and protein attachment capabilities.

Design and synthesis of DNA origami nanostructures to control TNF receptor activation

The paper designs and characterizes DNA origami nanostructures decorated with SC-TRAIL complexes to enhance TNFR activation and cell killing in Jurkat cells.

Design of a Biohybrid Materials Circuit with Binary Decoder Functionality

The paper designs a biohybrid materials circuit with binary decoder functionality using protease-based modules to detect small molecules and produce regulated protease outputs.

AptaBERT: Predicting aptamer binding interactions

AptaBERT predicts aptamer binding interactions with proteins and small molecules, achieving high ROC-AUC scores and outperforming existing models.

Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription

The paper develops a chromatography-free assay to quantify all 12 canonical ribonucleotides in biological samples using real-time fluorogenic detection during in vitro transcription.

Engineering Ca2+-dependent DNA polymerase activity

This paper engineers DNA polymerase activity to respond to Ca2+ by modifying the Pol δ complex in yeast, enabling Ca2+-dependent biosensing.

Signal-amplification for cell-free biosensors, an analog-to-digital converter

The paper introduces a signal-amplification circuit that reduces leakage and improves sensitivity in toehold switches for RNA detection.

An ultrasensitive method for detecting mutations from short and rare cell-free DNA

This paper introduces OPERA, a method for detecting low-frequency mutations in short and rare cell-free DNA, achieving higher sensitivity than existing methods.

C2CAplus: a one-pot isothermal circle-to-circle DNA amplification system

The paper introduces C2CAplus, a one-pot isothermal DNA amplification method that improves upon C2CA by simplifying the process and increasing yield.

Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus

The paper uses DNA-nanomotifs to mimic transcriptional cluster dispersal in stem cells, showing that amphiphilic effects control droplet size and shape.

origamiFISH allows universal, label-free, single molecule visualization of DNA origami nanodevices across biological samples

origamiFISH enables label-free, single-molecule detection of DNA origami nanostructures in cells and tissues, revealing cell-type and shape-specific uptake patterns at low concentrations.

A novel platform for metabolomics using barcoded structure-switching aptamers

This paper introduces a novel metabolomics platform using barcoded structure-switching aptamers for high-sensitivity, multiplexed detection of metabolites and drugs.

Self-assembly of DNA nanostructures in different cations

This study investigates DNA nanostructure assembly in various cations, showing successful assembly in Ca2+, Ba2+, Na+, K+, and Li+ with improved nuclease resistance in monovalent ions.

Identification of post-transcriptional modifications in nucleic acid sequences using purpose-designed molecular beacons

The paper introduces a method using molecular beacons to directly detect miRNAs and isomiRs in cells and extracellular vesicles without RNA isolation, leveraging electrophoretic mobility and computational design for m6A modifications.