Advanced biosensing and bioanalysis techniques

AptamerRunner clusters aptamers by sequence and structure to create visual networks for selecting high-quality candidates for experimental validation.

This paper introduces methods to recycle DNA components in DNA origami manufacturing, demonstrating the reprogramming of nanostructures and recovery of staple strands to create sustainable, reusable devices.

AptaDiff generates and optimizes aptamers using diffusion models, outperforming existing methods and experimental candidates in binding affinity.

This paper uses DNA origami nanoblocks to visualize DE-cadherin ectodomain interactions and reveal a hinge-like structure involved in mechanical flexibility and adhesion-like processes.

This study uses single-molecule force spectroscopy to analyze the kinetics of toehold-mediated strand displacement, revealing sequence-dependent dynamics and load effects in DNA and RNA interactions.

This paper introduces L-DNA tension probes that resist nuclease degradation, enabling long-term force mapping of single cells and migrating cell populations.

The paper presents a Neomer library approach to identify aptamers for predicting brain amyloid deposition from plasma, achieving 0.88 sensitivity and 0.76 specificity using machine learning.

The paper introduces an ultrahigh-throughput strategy to discover modified aptamers as specific and potent enzyme inhibitors, demonstrating its effectiveness with an inhibitor of SPM-1.

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.

This paper introduces Blocker-SELEX, a structure-guided method to design inhibitory aptamers that disrupt transcription factor interactions, demonstrating efficacy against SCAF4/SCAF8-RNAP2 and WDR5-MYC complexes.

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

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

This paper introduces an automated method to synthesize sequence- and size-defined DNA nanotubes using single-molecule fluorescence imaging and K-means clustering for optimization.

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

This study demonstrates the delivery of DNA origami nanorods into live cell nuclei using an antibody against RNA Polymerase II, showing structural integrity and sub-diffusive motion within the nucleus.

This paper develops an optical cytokine nanosensor using SWCNT and IL-6-specific aptamers to detect macrophage activation by bacterial toxins with high sensitivity and rapid response.

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

The paper uses machine learning to predict serotonin detection by DNA-SWNT sensors across multiple wavelengths, showing DNA sequence's key role and limitations due to dataset size.

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.

This study uses DNA origami nanoshells to neutralize hepatitis B virus in cell culture by trapping the virus and enhancing antibody effectiveness through multivalent binding and physical barriers.

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

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.

This paper develops a portable electrochemical DNA sensor for detecting piconewton-scale cellular forces using CRISPR-Cas12a for enhanced sensitivity and tunable threshold forces.

inSequio is a programmable 3D CAD tool for DNA nanostructure design that combines manual and programmatic editing, enhancing precision, scalability, and efficiency in DNA nanotechnology.

The paper evaluates aptamers for testosterone and analogs detection, identifying TESS1 as the best candidate due to its stability and affinity.

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.

This study shows bacterial ExoIII can cleave single-stranded DNA (ssDNA) via exonuclease and endonuclease activities, revealing new enzymatic functions and implications for biosensor design.

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