Advanced biosensing and bioanalysis techniques

This study investigates how dense DNA packing on polymeric nanoparticles enhances duplex stability and hybridization specificity for nucleic acid sensing.

The paper uses molecular dynamics simulations to study how ligation patterns affect the mechanical properties of DNA crystals.

This study uses plasmon-enhanced fluorescence to analyze the kinetics and dynamics of single-molecule multivalent interactions, revealing how spacer length and flexibility affect binding strength and dynamics.

This paper develops an optical nanosensor using carbon nanotubes to rapidly detect estrogen receptor status in breast cancer biopsies with high accuracy.

This paper develops a small-molecule approach to detect reactive inorganic targets using pre-ligands and the Baby Spinach aptamer, bypassing in vitro selection and enabling cell-based sensing.

The paper quantifies cargo on DNA origami nanoparticles using gel-based and fluorescence-based methods for therapeutic applications.

This study selects DNA aptamers targeting Streptococcus mutans GbpC to inhibit biofilm formation, showing 30% reduction in wild-type strains and no effect on GbpC-deficient strains.

The paper establishes design principles for accurate DNA origami folding using thermodynamic modeling and graph-based routing, validated through experimental analysis.

The paper demonstrates the feasibility of identifying biologically active DNA aptamers that modulate the activity of human SH-SY5Y neuroblastoma cells.

This study develops a method to study DNA and DNA-protein interactions with high spatial and temporal resolution using graphene and energy transfer.

This paper introduces modular and tunable single-molecule sensors using DNA origami scaffolds to detect biomolecules with adjustable response windows and specificity.

This paper demonstrates the localization of nucleic-acid cleaving enzyme activity within DNA-based membrane-less compartments, enabling spatially organized enzymatic reactions and dynamic pattern formation.

This paper develops an amplification-free method to quantify DNA methylation at the BCAT1 promoter with high sensitivity and specificity, enabling improved early detection of methylated cancer DNA biomarkers.

The paper introduces xPlex, a method for multiplexed and quantitative detection of small-molecule analytes using aptamer switches and UV-crosslinkable strands, demonstrating its effectiveness with dopamine and glucose.

The paper designs and characterizes artificial nucleic acid condensates that recruit and concentrate proteins in vitro, demonstrating control over condensation and protein recruitment through UV irradiation and RNA transcription.

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.

The paper develops a modular biosensing platform using aptamer-regulated transcription to detect proteins with tunable detection ranges and diverse output responses.

The paper describes a DNA origami-based biosensor that detects lipid vesicles through smFRET and enables targeted cargo transfer to vesicles.

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.

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.

This study develops DNA origami tension sensors (DOTS) to measure TCR mechanotransduction at immune cell junctions, revealing forces between 5-10 pN and dependencies on cell state and antigen properties.

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 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.