Advanced biosensing and bioanalysis techniques

Rapid Isothermal Detection of Heavy Metals via Transcription-Factor-Gated DNA Strand Synthesis

This paper introduces TONE, a rapid, isothermal biosensing platform for heavy metal detection using transcription-factor-gated DNA strand-displacement amplification, achieving low detection limits for copper and lead.

Programmable assembly of higher-order DNA nanostructures from microbial ssDNA staple libraries

This paper develops a biological nanomanufacturing platform in E. coli to produce programmable ssDNA staples for DNA nanotechnology, achieving high-fidelity synthesis and self-assembly of complex structures.

Solution Phase Protein Adsorption to ss(GT)15-DNA Wrapped Single Walled Carbon Nanotubes

The paper examines protein adsorption to DNA-wrapped SWCNTs by measuring photoluminescence changes, identifying metalloproteins as more effective quenchers than metal-free proteins.

Decoupling Fabrication from Encoding: DNA-Addressable Template Microparticles for Large, User-Defined Optical Barcode Libraries

This paper introduces a method to create large optical barcode libraries using DNA-addressable microparticles, achieving high accuracy and scalability.

Inosine incorporation in DNA nanostructures and 3D DNA crystals

This work demonstrates the use of inosine in DNA nanostructures and shows its ability to form 3D DNA crystals through rationally designed motifs.

Unraveling single-molecule reactions via multiplexed in-situ DNA sequencing

This paper introduces SPIN-Seq, a method that links DNA sequence with functional properties at the single-molecule level, revealing sequence-dependent transcription factor interactions and RNA polymerase behavior.

A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution

This paper develops a high-throughput platform to rapidly adapt DNA aptamers against evolving SARS-CoV-2 variants, identifying mutants with improved binding affinity and specificity.

Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution

This paper introduces dcORBIT, a method that extends DNA rotation tracking during transcription to over 10 minutes at 20 Hz with single base-pair precision.

Fuel-driven catalytic molecular templating

This paper introduces an enzyme-free DNA-based templated dimerization reaction controlled by a fuel strand that displaces product to overcome inhibition, enabling information propagation from templates.

Rationally designed split Lettuce aptamer based on large scale mutational analysis

This paper identifies high-performance split sites in DNA aptamers through large-scale mutational analysis, improving signal-to-background ratio for RNA detection.

In Vivo Selection of anti-glioblastoma DNA aptamer-drug conjugates in an orthotopic patient-derived xenograft model

This study develops and tests DNA aptamer-drug conjugates (ApDCs) for glioblastoma treatment using an in vivo SELEX approach in a patient-derived xenograft model.

A computational framework for designing micron-scale crisscross DNA megastructures

This paper develops a computational framework to design crisscross DNA megastructures, optimizing handle assignment and expanding handle libraries to enable large-scale fabrication.

Optical Spectral Fingerprinting Enables Sensitive Detection of Anthracycline Chemotherapeutics in Synthetic Clinical Biofluids

This paper develops an optical nanosensor array to detect anthracycline chemotherapeutics in synthetic biofluids using machine learning for classification and concentration analysis.

A Nanoscale Jitterbug Transformer from DNA

This paper designs a DNA-based nanoscale Jitterbug transformer that reconfigures its structure in response to chemical and optical signals, maintaining a Poissons ratio of -1.

Programmable Nucleic Acid Sensing in Human Cells Using Circularizable ssDNA

This paper introduces SONAR, a platform for detecting nucleic acids and triggering gene expression in human cells, demonstrating its ability to sense DNA and RNA and express various protein payloads.

Expanding High-Fidelity Multiplexing in Ultrasensitive Single-Molecule Protein Detection via Proximity Barcoding

This paper introduces PRO-MOSAIX, a high-accuracy, ultrasensitive multiplex immunoassay that enables 15-plex detection in human plasma with low femtomolar sensitivity.

Adverse Effects of UV-Exposure on DNA Strand Displacement Reactions

This study identifies UV-shadowing as a source of errors in DNA strand displacement reactions and proposes a UV-free purification protocol to improve circuit performance.

Screening Molecular Recognition Element-Based SWCNT Optical Sensors for the Inflammatory Cytokine TNF-α

This study evaluates aptamer and antibody-based sensors for detecting TNF-α in serum using SWCNT optical sensors, finding that modifications improve sensitivity and selectivity.

Monitoring in vivo transcription with synthetic serum markers

This paper introduces a platform called INTACT that non-invasively monitors specific mRNA levels in vivo by using synthetic serum markers and RNA-based sensors.

A 3D printed mini-gel electrophoresis system for rapid and inexpensive DNA nanoswitch biosensing

This paper presents a 3D-printed mini-gel electrophoresis system for DNA nanoswitch biosensing, achieving rapid, low-cost, and portable detection of target molecules.

Homogeneous antibody-DNA-conjugates using unmodified oligonucleotides and photo-crosslinkable protein G-HUH endonuclease fusion proteins

This paper introduces a method to create homogeneous antibody-DNA conjugates using unmodified oligonucleotides and photo-crosslinkable protein G-HUH endonuclease fusion proteins, achieving 1:1 stoichiometry.

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

This paper optimizes a DNA-based fluorogenic aptamer (D-FAP) using a screening-and-simulation pipeline on a repurposed sequencing platform, achieving improved fluorescence properties.

A critical assessment of aptamer and CRISPR-Cas12a-based biosensors for small molecule detection

This study evaluates the effectiveness of aptamer-Cas12a biosensors for small molecule detection, finding limited success and highlighting the need for aptamer validation.

Global Quantitative Analysis of Ligation Reactions in Self-Assembled DNA Nanostructures at the Single-Nick Level

The paper quantitatively analyzes individual ligation reactions in DNA origami nanostructures using qPCR, revealing edge preference and solvent-dependent behavior.

Probing Molecular Diversity and Ultrastructure of Brain Cells with Fluorescent Aptamers

This paper introduces CAptVE, a method for fluorescent aptamer-based labeling that enables molecular analysis in ultrastructurally reconstructable electron micrographs.

Alpha-tocopherol conjugated DNA tetrahedron with enhanced cellular uptake and selective cytotoxicity for cancer therapeutics

This paper develops a DNA tetrahedron conjugated with alpha-tocopherol to enhance cellular uptake and selectively kill cancer cells through ROS-induced apoptosis.

Clamp the LAMP: a photoelectrochemical platform for KRAS mutation detection via wild-type blocking

This paper introduces a photoelectrochemical platform for KRAS mutation detection that uses molecular suppression of wild-type alleles to enhance sensitivity and specificity.

Visualizing and Quantifying microRNA Induced DNA Origami Separation at the Nanoscale

This paper presents a method using DNA origami disassembly driven by miRNA to detect small RNA, showing robust detection in RNAse-containing environments.

Intracellular Expression of a Fluorogenic DNA Aptamer Using Retron Eco2

This study demonstrates the use of the bacterial retron system Eco2 to express a DNA aptamer intracellularly in E. coli, showing comparable activity to chemically synthesized controls.

Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients

This paper introduces a DNA origami-based sensor (NanoDyn) capable of detecting Na+ ion gradients across multiple spatial scales, demonstrating tunable sensitivity and resolution.