Advanced biosensing and bioanalysis techniques

Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing

Generalized strategy for engineering mammalian cell-compatible RNA-based biosensors from random sequence libraries

The paper describes a method to engineer RNA-based biosensors for mammalian cells using random sequence libraries, demonstrating a biosensor for L-dopa detection.

Simple in-vitro single stranded linear and circular DNA preparation and validation via SELEX using phosphor-derived modifications

This paper introduces a simple method for in vitro preparation of single-stranded circular DNA using phosphorylated-phosphorothioated primers and validates it through SELEX for MERS-CoV spike protein aptamers.

Red light-emitting short Mango-based system enables tracking a mycobacterial small noncoding RNA in infected macrophages

Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER

The paper introduces pSABER, a method for amplifying in situ hybridization signals in cellular and histopathological samples, achieving 25-fold amplification over conventional methods.

Bright, fluorogenic and photostable avidity probes for RNA imaging

This study develops bright, photostable RNA imaging probes by combining bivalent rhodamine fluorophores with dimeric FLAPs, enabling single mRNA tracking in living cells.

Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion

The paper estimates success probabilities for generating high-affinity DNA aptamers with unnatural bases and identifies structural factors that improve binding affinity.

The role of size in biostability of DNA tetrahedra

This study examines how the size of DNA tetrahedra affects their biostability, showing nuclease-specific degradation patterns.

Suitability Evaluation of Toehold Switch and EXPAR for Cell-Free MicroRNA Biosensor Development

This paper evaluates the suitability of toehold switch and EXPAR for developing a cell-free miRNA biosensor, finding that EXPAR enhances detection sensitivity and accuracy.

Theoretical Analysis of Divalent Cation Effects on Aptamer Recognition of Neurotransmitter Targets

This study uses molecular dynamics simulations to analyze how divalent cations affect aptamer conformational changes when binding neurotransmitters like dopamine and serotonin.

Reverse Engineering DNA Origami Nanostructure Designs from Raw Scaffold and Staple Sequence Lists

This paper introduces an algorithm to convert raw DNA origami sequences back into schematic designs, enabling easier modification and reuse of existing nanostructures.

Paired aptamer capture and FISH detection of individual virions enables cell-free determination of infectious titer

This paper develops a cell-free method to directly measure infectious viral titer by capturing intact virions with an aptamer and detecting their genomes using FISH.

Computational Design of a New Aflatoxin B1 Aptamer in lieu of SELEX Technique

The paper develops a new aflatoxin B1 aptamer using computational methods to replace the SELEX technique, proposing a new pipeline and identifying a potential aptamer through molecular modeling and docking.

Reaction-diffusion patterning of DNA-based artificial cells

This paper introduces a platform for creating DNA-based artificial cells with localized functionalities using reaction-diffusion waves, demonstrating spatial segregation of RNA synthesis and storage.

Targeting triple-negative breast cancer with β1-integrin binding aptamer

This paper demonstrates that the GreenB1 aptamer specifically targets β1-integrin in triple-negative breast cancer cells and tumors, suggesting its potential for precision diagnosis and therapy.

High-throughput variant detection using a color-mixing strategy

This paper introduces a color-mixing strategy for high-throughput variant detection using fluorescence combinations, enabling simultaneous probing of multiple genetic variants with high specificity and sensitivity.

End-to-end computational approach to the design of RNA biosensors for miRNA biomarkers of cervical cancer

The paper develops an end-to-end computational approach to design RNA biosensors for miRNA biomarkers of cervical cancer, using public data and predictive models to guide sensor design and simulation.

Engineering Protein Activity into Off-the-Shelf DNA Devices

This paper describes the engineering of a DNA-activated protein switch, nLuc-AFF, which can be used as a biosensor for DNA/RNA sequences, serotonin, ATP, and as a computational device processing DNA inputs.

Co-transcriptional RNA strand displacement circuits

This paper introduces co-transcriptional RNA strand displacement circuits that are programmable and scalable for molecular computing in biological systems.

Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor

This paper designs a DNA origami receptor that enables stable complexes with rapid subunit exchange, demonstrating the system's ability to handle both DNA and protein cargo.

Minimal DNA Electron Transfer Catalysts Switched by a Chaotropic Ion

This paper demonstrates a DNA nanodevice that switches between catalytic and non-catalytic electron transfer states using a chaotropic ion.

Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides

This paper designs DNA-based reaction-diffusion waveguides to enable spatiotemporal signal propagation in synthetic biomaterials, allowing for controlled biochemical communication.

Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

This paper develops DNA strand displacement circuits to enhance biosensors by enabling fine-tuning of reaction kinetics and faster response times, creating binary outputs that encode target molecule concentrations.

Functionalizing lipid sponge droplets with DNA

This study shows DNA can functionalize lipid sponge droplets, with size-dependent partitioning and applications for cargo control and signaling.

Multi-micron crisscross structures from combinatorially assembled DNA-origami slats

Crisscross polymerization of DNA-origami slats enables the creation of micron-scale structures with uniquely addressable nanoscale features.

OaAEP1-mediated PNA-protein conjugation enables erasable imaging of membrane protein

This paper introduces a method for site-specific conjugation of proteins to PNA using a strict protein ligase, enabling erasable imaging of membrane proteins.

Measurement of Kinetics of Hammerhead Ribozyme Cleavage Reactions using Toehold Mediated Strand Displacement

This paper introduces a DNA-based probe to measure hammerhead ribozyme cleavage kinetics without radioactive labels, gels, or regular sampling, using fluorescence from strand displacement reactions.

Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization

This paper introduces a method using hybridization chain reaction for multiplexed, quantitative, high-resolution imaging of both proteins and RNA in challenging tissues.

Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

This paper develops a DNA-based recording system using TdT to encode environmental signals with minutes resolution.

Determinants of ligand-functionalized DNA nanostructure-cell interactions

This study investigates how design parameters affect the binding of antibody-functionalized DNA nanostructures to cell surface receptors, finding that nanostructure size and DNA handle location influence receptor binding.