Advanced biosensing and bioanalysis techniques

Ultra-sensitive water contaminant detection with transcription factor interfaced microcantilevers

The paper develops a biosensor using transcription factors and microcantilevers to detect water contaminants with high sensitivity and speed.

Tuning the stability of DNA tetrahedra with base-stacking interactions

This study investigates how base-stacking interactions affect the stability of DNA tetrahedra by testing 16 designs, finding that altering a single base stack can change melting temperatures by up to 10°C.

Seek-a-Seq: Optical detection of target nucleic acids with attomolar sensitivity

Seek-a-Seq detects microbial nucleic acids at attomolar concentrations using fluorescent hybridization without PCR or enzymes.

Hairpin-locker mediated CRISPR/Cas tandem system for ultrasensitive detection of DNA without pre-amplification

This paper introduces a CRISPR/Cas tandem biosensing system for ultrasensitive DNA detection without pre-amplification, achieving 1 aM sensitivity and distinguishing cancer mutations in CRC mice.

APV-Sankey: A Comprehensive Toolbox for Aptamer Screening and Visualization

APV-Sankey identifies high-affinity aptamers by visualizing K-mer evolution across SELEX rounds and filtering high-frequency sequences without affinity.

Modular photostable fluorescent DNA blocks dissect the effects of pathogenic mutant kinesin on collective transport

The paper develops a photostable DNA block to study how a pathogenic kinesin mutant affects collective transport with wild-type kinesin, revealing velocity dynamics.

Optimizing DNA origami assembly through selection of scaffold sequences that minimise off-target interactions

This paper develops a computational method to select DNA origami scaffold sequences that minimize off-target interactions, validated through AFM and optical tweezers experiments.

Modular DNA Barcoding of Nanobodies Enables Multiplexed in situ Protein Imaging and High-throughput Biomolecule Detection

This paper introduces MaMBA, a modular DNA barcoding strategy for antibodies, enabling multiplexed in situ protein imaging and high-throughput biomolecule detection.

Mechanism-based design of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins

The paper designs a DNA-nanoparticle motor with improved speed and processivity by optimizing DNA/RNA hybridization rates, achieving performance comparable to motor proteins.

Protein-Formatted Biomarker Enrichment Tag for the Detection of Carcinoembryonic Antigen

The paper introduces a biotin-insensitive antigen enrichment system using barnase and barstar for improved detection of carcinoembryonic antigen with higher sensitivity and specificity.

Selection and characterization of DNA aptamers targeting the surface borrelial protein CspZ with high-throughput cross-over SELEX

This paper selects and characterizes DNA aptamers targeting the Borrelia surface protein CspZ using cross-over SELEX and validates their binding affinity and specificity.

Engineering a cell-free biosensor signal amplification circuit with polymerase strand recycling

The paper introduces a cell-free biosensor signal amplification circuit called polymerase strand recycling (PSR) that enhances biosensor sensitivity for small molecule detection.

Ag+-regulated aptamers to thrombin

This paper modifies thrombin aptamers with specific nucleotides to enhance affinity and introduce Ag+ dependency.

Selection of Fluorinated Aptamer Targeting RNA Element with Different Chirality

This study selects a 2-fluoro modified mirror-image RNA aptamer targeting a viral frameshift element with opposite chirality, showing improved stability and moderate binding affinity.

AI-based Prediction of Protein Corona Composition on DNA Nanostructures

The paper develops a machine-learning model to predict protein corona composition on DNA nanostructures based on design features and protein properties.

Cooperative effects in DNA-functionalized polymeric nanoparticles

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

Understanding Structural Mechanics of Ligated DNA Crystals via Molecular Dynamics Simulation

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

Cargo quantification of functionalized DNA origami for therapeutic application

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

Selection of streptococcal glucan-binding protein C specific DNA aptamers to inhibit biofilm formation

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.

DNA aptamers that modulate biological activity of model neurons

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

Enzyme-Responsive DNA Condensates

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.

A multiplexed and quantitative assay for small-molecule detection via photo-crosslinking of structure switching aptamers

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.

Protein recruitment to dynamic DNA-RNA host condensates

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: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

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

Recycling Materials for Sustainable DNA Origami Manufacturing

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: de novo design and optimization of aptamers based on diffusion models

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

Nanoscale visualization of Drosophila E-cadherin ectodomain fragments and their interactions using DNA origami nanoblocks

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.

Nuclease-Resistant L-DNA Tension Probes Enable Long-TermForce Mapping of Single Cells and Cell Consortia

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

A reproducible approach for the use of aptamer libraries for the identification of Aptamarkers for brain amyloid deposition based on plasma analysis.

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.

Ultrahigh-throughput discovery of modified aptamers as specific and potent enzyme inhibitors

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.