Advanced biosensing and bioanalysis techniques

Spatial Proofreading Amplification of in situ Transcript and Protein Signals

The paper introduces an enzyme-free signal amplification method for spatial transcriptomics that achieves over 500-fold signal amplification and enables multiplex readout.

DNA Hanger: Surface Free Single-Molecule Blotting Platform

The paper introduces a surface-free single-molecule blotting platform called DNA Hanger that reduces nonspecific binding and improves sensitivity for detecting sub-picomolar concentrations of fluorophore-conjugated proteins.

Reusing excess staple oligonucleotides for economical production of DNA origami

This paper demonstrates that reusing excess staple oligonucleotides with replenishment can reduce DNA origami production costs by up to 80%.

Controlling DNA-RNA strand displacement kinetics with base distribution

This study shows that base distribution along an invading strand strongly affects DNA-RNA strand displacement kinetics, enabling design of sequences with reaction rates spanning two orders of magnitude.

Realizing Mechanical Frustration at the Nanoscale Using DNA Origami

This paper uses DNA origami to create a nanoscale metastructure that can switch between frustrated and non-frustrated mechanical states, with distinct free energy profiles.

De novo design of protein-binding aptamers through deep reinforcement learning assembly of nucleic acid fragments

This paper introduces AiDTA, a deep reinforcement learning method for de novo design of protein-binding aptamers, achieving high-affinity DNA aptamers for disease-related proteins.

DNA framework array enables ultra-high throughput DNA synthesis

The paper introduces a DNA framework array for high-throughput DNA synthesis with single-molecule control, achieving a 4-order-of-magnitude improvement in synthesis throughput.

Non-enzymatic isothermal strand displacement and amplification (NISDA) does not enable sensitive nucleic acid quantification.

This study attempts to replicate the claimed sensitivity of NISDA but fails to achieve detectable signals except at very high concentrations.

Peptide nucleic acid (PNA) and DNA hybrid three-way junctions and mesojunctions

This study synthesizes and characterizes PNA/DNA hybrid three-way junctions and mesojunctions, showing improved thermal stability and nuclease resistance compared to DNA-only versions.

Sequence programmable nucleic acid coacervates

This study creates programmable DNA and RNA liquids that can be tuned by sequence-specific hybridization to control their material properties.

Discovery of a DNA-based Optical Nanotube Sensor for Glucose Using Clustering and Deep Learning Algorithms

The paper designs a DNA-based optical nanotube sensor for glucose using clustering and deep learning to identify and optimize a responsive DNA sequence.

Computational Assessment of Circularization Impact on Saxitoxin G-quadruplex Aptamer Performance

The paper develops a computational method to guide the cyclization of saxitoxin aptamers, showing that circular aptamers have higher affinity and improved survival in mice.

A purification-free nucleic acid amplification platform for diverse samples

The paper evaluates an enzyme-free nucleic acid amplification method that eliminates purification steps and works in diverse sample matrices, showing robust performance in various conditions.

Cation-controlled assembly, activity, and organisation of biomimetic DNA receptors in synthetic cell membranes

This study develops DNA-based receptors in synthetic membranes that respond to cations, enabling controlled assembly and catalytic activity, mimicking biological signaling mechanisms.

Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Spheroid Model

This study evaluates DNA origami-based nanoagents' ability to induce apoptosis in 3D spheroids, finding that rigid FasL attachment strategies are more effective than flexible ones.

Modulating cell-free transcription electrolytically with switchable DNA triplexes

This paper introduces EDGE, an electrochemical method to modulate gene expression using DNA triplexes, showing that triplexes inhibit gene expression in cell-free systems.

Mechanistic Insights into Crossover-Dependent Stability and Exceptional Resistance of PX/JX Nanostructures to DNase I using Enhanced Sampling

This study uses enhanced sampling to reveal how crossover points in PX/DNA structures enhance nuclease resistance by altering helix topology and reducing DNase I binding affinity.

DNA six-way junction conformations and their use in a 2D square lattice

This paper explores DNA six-way junction conformations, identifies preferred structural isomers, and demonstrates their use in creating a 2D square lattice for DNA nanotechnology.

DNA Origami Signal Amplification in LateralFlow Immunoassays

This paper introduces a DNA origami-based signal amplification method for lateral flow immunoassays, significantly improving sensitivity for cardiac troponin I detection in human serum.

A High-Performance and Recoverable DNA Origami Rotary Motor

This paper develops a DNA origami rotary motor that can perform multiple revolutions and recover from operational errors using microfluidic control and high-resolution imaging.

From Randomness to Recognition: Modeling the Evolution of DNA Sequence Information During SELEX

This paper uses NLP to model DNA sequence evolution during SELEX, showing that latent space representations correlate with binding specificity and can distinguish between enriched libraries for different targets.

Non-invasive diagnosis of early chronic colitis cancerization via amplified sensing of miRNA-21 in NIR-IIb window

This paper develops a non-invasive method to detect early chronic colitis cancerization by amplifying miRNA-21 sensing in the NIR-IIb window, enabling detection up to 4 weeks before biopsy.

DNA-Based Nanoprobes for Fluorescence K+ Sensing in Neural Systems

This paper introduces a DNA-based fluorescent nanoprobe for detecting potassium ion dynamics in neurons, showing linear fluorescence changes in response to electrical stimulation.

Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells

This paper introduces RNA origami cytoskeletons in synthetic cells, demonstrating their self-assembly and functional expression in lipid vesicles.

Design Principles for Polymerase Strand Recycling Circuits

This paper develops design principles for Polymerase Strand Recycling (PSR) circuits to enhance detection of microRNA inputs in cell-free biosensing systems.

Demonstration and structural basis of a therapeutic DNA aptamer for SARS-CoV-2 spike protein detection

This paper develops a rapid, specific, and reusable DNA aptamer-based biosensor for detecting SARS-CoV-2 spike protein, demonstrating high sensitivity and structural insights through cryo-EM.

Influence of metal ions on the isothermal self-assembly of DNA nanostructures

This study shows that metal ions and temperature affect DNA nanostructure self-assembly, with divalent ions enabling assembly at lower temperatures and no adverse effects on cell viability.

Tumbleweed: an artificial motor protein that walks along a DNA track

This paper introduces an artificial protein motor called Tumbleweed that walks directionally along a DNA track in response to ligand inputs.

Designer DX-tile DNAns hydrogels

This study introduces DX-tile motifs to enhance the mechanical properties and functionalization of DNA hydrogels, enabling tunable viscoelasticity and printability for biomedical applications.

Using Aptamers for Protein Scale-up

This study develops a method using DNA aptamers to purify proteins, showing 20.7% recovery of BSA and demonstrating specific binding to domains I and III of BSA.