Search Results (103)

Magnesium ions (Mg²⁺) play an important role in animal health, with their concentration in the bloodstream serving as a key indicator for hypomagnesemia diagnosis. In this study, a flexible hydrophobic paper-based microfluidic field-effect biosensor was developed for point-of-care Mg²⁺ detection, which integrated flexible hydrophobic paper, semiconducting single-walled carbon nanotubes (SWNTs) and a Mg²⁺-specific RNA-cleaving DNAzyme(RCD)-based DNA nanostructure. Flexible hydrophobic paper was synthesized by using cellulose paper and octadecyltrichlorosilane, improving mechanical strength and decreasing biological interference. To achieve high sensitivity, the Mg²⁺-specific RCD was functionalized with SWNTs, and then repeatedly self-assembled two different Y-shaped DNAs to construct a DNA nanostructure based on a similar DNA origami technique. This proposed biosensor exhibited a linear detection range from 1 μM to 1000 μM, with a detection limit of 0.57 μM, demonstrating its great stability, selectivity, and anti-interference performance. This innovative design offers promising potential for Mg²⁺ monitoring in real applications. Full article

Single-molecule optical signal detection provides high sensitivity and specificity for the detection of biomolecules and chemical substances, which is of significant importance in fields such as biomedicine, environmental monitoring, and materials science. In recent years, DNA-based plasmonic nanostructures have emerged as powerful tools for achieving single-molecule optical signal detection due to their unique self-assembly properties and excellent optical performance. In particular, DNA origami technology enables the precise construction of metallic nanostructures with specific shapes and functions, which can effectively enhance the interaction between light and matter, thereby significantly increasing signal intensity and detection sensitivity. Furthermore, the programmability of DNA not only simplifies the implementation of single-molecule operations but also allows researchers to design and optimize nanostructures according to specific detection requirements. This review will explore the applications of DNA-based plasmonic nanostructures in single-molecule optical signal detection, including surface-enhanced Raman spectroscopy and enhanced fluorescence for single-molecule signal detection. We will analyze their working principles, advantages, current research progress, and future research directions. By summarizing the work in this field, we hope to provide references and insights for researchers, contributing to the advancement of biomedicine and environmental monitoring. Full article

The International CCN Society has been organizing workshops and conferences for the past two decades to advance our understanding of the biology and pathophysiology of the cellular communication network (CCN) proteins. The 12th CCN Workshop broadened the scope of discussions, introducing topics like CCN-dependent and -independent signaling networks involved in brain development, cellular senescence, efferocytosis, neurobiology, and the application of DNA-fabricated origami structures. This expansion proved fruitful and should continue in future events. Fostering collaborations across various fields has created a dynamic environment for innovative ideas, driving substantial progress to tackle both basic scientific questions and clinically relevant challenges. Three standout presentations sparked significant discussions and highlighted key advancements in these areas. These include the work of Li-Jen Lee (Neurobiology and Cognitive Science Center, National Taiwan University) on the involvement of the CCN2 protein in depressive and aggressive behaviors in mice; the studies of Anna Zampetaki (King’s College London British Heart Foundation Centre, School of Cardiovascular & Metabolic Medicine and Sciences) and Brahim Chaqour (University of Pennsylvania, Perelman School of Medicine, Dept of Molecular Ophthalmology) on the metabolome and mechanosensing in iPSC-derived human blood vessel organoids and in the microvasculature of genetically modified mice, and the talk of Björn Högberg (Karolinska Institutet, Department of Medical Biochemistry and Biophysics) on the promises of DNA origami. We believe that these examples illustrate better future directions, as they offer an opportune moment to pursue initiatives that broaden the focus of the CCN Workshops and other projects like ARBIOCOM (website link included below) that support collaboration among research societies, educational institutions, and private biomedical industries, all working together to further our understanding of biosignaling and cellular communication networks for the development of new drug discovery methods and disease treatments. Full article

Herein, we proposed a versatile G-quadruplex (G4)-tetrahedral DNA framework (G4-TDF) nanostructure functionalized origami microfluidic paper-based device (μPADs) for fluorescence detection of K⁺ by lighting up thioflavin T (ThT). In this work, TDF provided robust structural support for G-rich sequence in well-defined orientation and spacing to ensure high recognition efficiency, enabling sensitive fluorescence sensing on origami μPAD. After introducing ThT, the G-rich sequences extended from TDF vertices formed a parallel G4 structure, showing weak fluorescence signal output. Upon the presence of target K⁺, this parallel G4 structure transitioned to antiparallel G4 structure, leading to a significantly increase in fluorescence signal of ThT. Benefiting from the outstanding fluorescence enhancement characteristic of the G4 structure for ThT and excellent specificity of the G4 structure to K⁺ plus satisfactory recognition efficiency with the aid of TDF, this origami paper-based fluorescence sensing strategy exhibited an impressive detection limit as low as 0.2 mM with a wide range of 0.5–5.5 mM. This innovative G4-TDF fluorescence sensing was applied for the first time on μPAD, providing a simple, effective, and rapid method for K⁺ detection in human serum with significant potential for clinical diagnostics. Full article

DNA origami is a powerful technique for constructing nanoscale structures by folding a single-stranded DNA scaffold with short staple strands. While traditional models assume staples bind to a fixed side of the scaffold, we introduce a side-aware DNA origami framework that incorporates the directional binding of staples to either the left or right side. The graphical representation of DNA origami is described using rectangular basic modules of scaffolds and staples, which we refer to as symbols in side-aware DNA origami words. We further define the concatenation of these symbols to represent side-aware DNA origami words. A set of rewriting rules is introduced to define equivalent words that correspond to the same graphical structure. Finally, we compute the number of possible structures by determining the equivalence classes of these words. Full article

DNA (Deoxyribonucleic Acid) logic circuit systems provide a powerful arithmetic architecture for the development of molecular computations. DNA nanotechnology, particularly DNA origami, provides a nanoscale addressable surface for DNA logic circuit systems. Although molecular computations based on DNA origami surfaces have received significant attention in research, there are still obstacles to constructing localized scalable DNA logic circuit systems. Here, we developed elementary DNA logic circuits on a DNA origami surface by employing the strand displacement reaction (SDR) to realize the localized scalable DNA logic circuit systems. We showed that the constructed elementary logic circuits can be scaled up to the localized DNA logic circuit systems that perform arbitrary digital computing tasks, including square root functions, full adder and full subtractor. We used a 50% reduction in the number of localized DNA logic components, compared to localized logic systems based on the threshold strategy. We further demonstrated that the localized DNA logic circuit systems for three-satisfiability (3-SAT) problem solving and disease classification can be implemented using the constructed elementary DNA logic circuits. We expect our approach to provide a new design paradigm for the development of molecular computations and their applications in complex mathematical problem solving and disease diagnosis. Full article

The A-to-G mutation (FecB) in the BMPR1B gene is strongly linked to fertility in sheep, significantly increasing ovulation rates and litter sizes compared to wild-type populations. The rapid and reliable screening of the FecB gene is therefore critical for advancing sheep breeding programs. This study aimed to develop a fast and accurate method for detecting the FecB mutation and genotyping the gene to enhance sheep reproduction and productivity. To achieve this, we integrated the CRISPR-Cas12a system with an optimized amplification refractory mutation system (ARMS). A similar DNA origami technique-based fluorescence reporter nanotree structure was synthesized using gold nanomagnetic beads as carriers to amplify the fluorescence signal further. The resulting biosensing platform, termed CRISPR-ARMS, demonstrated excellent sensitivity for detecting FecB mutations, with a detection limit as low as 0.02 pmol. Therefore, this innovative approach shows great promise for single-base mutation detection and represents a pioneering tool for high-yield genetic screening. Full article

In the field of chemical biology, DNA origami has been actively researched. This technique, which involves folding DNA strands like origami to assemble them into desired shapes, has made it possible to create complex nanometer-sized structures, marking a major breakthrough in nanotechnology. On the other hand, controlling the folding mechanisms and folded structures of proteins or shorter peptides has been challenging. However, recent advances in techniques such as protein origami, peptide origami, and de novo design peptides have made it possible to construct various nanoscale structures and create functional molecules. These approaches suggest the emergence of new molecular design principles, which can be termed “molecular origami”. In this review, we provide an overview of recent research trends in protein/peptide origami and DNA/RNA origami and explore potential future applications of molecular origami technologies in electrochemical biosensors. Full article

Biosensors are widely used across industries such as healthcare, food safety, and environmental monitoring, offering high stability and sensitivity compared to conventional methods. Recently, origami—the art of folding 2D structures into 3D forms—has emerged as a valuable approach in biosensor development, enabling the creation of shape-changing devices. These origami-based biosensors are particularly useful in precision medicine, rapid diagnostics, and resource-limited settings, offering affordable, highly precise, and portable solutions with diverse applications. Paper and biological substrates like DNA have been integrated with origami techniques to develop biosensors with enhanced functionality. The incorporation of aptamer origami into both paper and DNA biosensors further increases sensitivity and specificity for target detection. The concept of paper-based origami biosensors originated from using paper as a platform for biological assays, leading to significant advancements in design and functionality. These devices employ folding techniques to create channels and wells for manipulating samples and detecting target molecules through reactions with specific reagents. Similarly, DNA origami, introduced in 2006, has revolutionized biosensors by enabling the creation of precise molecular systems with tunable properties. Paper-based and DNA origami biosensors have immense potential to transform biosensing technologies in healthcare, food safety, and environmental monitoring. This review explores diverse origami-based biosensor techniques and their applications, including the role of aptamer origami in paper and DNA biosensors. Full article

Over the past few years, significant progress has been made in DNA origami technology due to the unrivaled self-assembly properties of DNA molecules. As a highly programmable, addressable, and biocompatible nanomaterial, DNA origami has found widespread applications in biomedicine, such as cell scaffold construction, antimicrobial drug delivery, and supramolecular enzyme assembly. To expand the scope of DNA origami application scenarios, researchers have developed DNA origami structures capable of actively identifying and quantitatively reporting targets. Optical DNA origami biosensors are promising due to their fast-to-use, sensitive, and easy implementation. However, the conversion of DNA origami to optical biosensors is still in its infancy stage, and related strategies have not been systematically summarized, increasing the difficulty of guiding subsequent researchers. Therefore, this review focuses on the universal strategies that endow DNA origami with dynamic responsiveness from both de novo design and current DNA origami modification. Various applications of DNA origami biosensors are also discussed. Additionally, we highlight the advantages of DNA origami biosensors, which offer a single-molecule resolution and high signal-to-noise ratio as an alternative to traditional analytical techniques. We believe that over the next decade, researchers will continue to transform DNA origami into optical biosensors and explore their infinite possible uses. Full article

Origami, the art of paper folding, has long fascinated researchers and designers in its potential to replicate and tap the complexity of nature. In this paper, we pursue the crossing of origami engineering structures and biology, the realm of biologically-inspired origami structures categorized by the two biggest taxonomy kingdoms and DNA origami. Given the diversity of life forms that Earth comprises, we pursue an analysis of biomimetic designs that resemble intricate patterns and functionalities occurring in nature. Our research begins by setting out a taxonomic framework for the classification of origami structures based on biologically important kingdoms. From each of these, we explore the engineering structures inspired by morphological features, behaviors, and ecological adaptations of organisms. We also discuss implications in realms such as sustainability, biomaterials development, and bioinspired robotics. Thus, by parlaying the principles found in nature’s design playbook through the art of folding, biologically inspired origami becomes fertile ground for interdisciplinary collaboration and creativity. Through this approach, we aim to inspire readers, researchers, and designers to embark on a journey of discovery in which the boundaries between art, science, and nature are blurred, providing a foundation for innovation to thrive. Full article

Water is indispensable for life, yet many lack access to clean drinking water, resulting in fatalities from waterborne bacterial infections. Precise assessment of microbial abundance and viability in natural aquatic environments is vital. Adenosine triphosphate (ATP) serves as a parameter for viability assessments due to its presence in viable bacterial cells as an energy carrier. Traditional ATP detection methods involve chemical or enzymatic extraction, followed by measurement of light emission via the Luciferin–Luciferase complex. However, these methods are costly, present a low stability, require specialized equipment, and entail complex sample pretreatment. To overcome these limitations, we developed a biosensor based on aptamers, nucleic acid sequences with specific target-molecule-binding capabilities. Aptamers offer advantages such as an enhanced stability, a lower cost, and ease of design compared to antibodies. Recently, ATP has been used for aptamer selection testing. Our proposed biosensor utilizes a structure-switching ATP-binding DNA nanoswitch with two functional domains: a catalytic DNA-zyme domain and an ATP-binding aptamer domain. In the presence of ATP, its binding to the aptamer domain triggers the activation of the DNA-zyme domain, which is exploited for chemiluminescence (CL) detection. Integrating functional DNA biosensors with microfluidic paper-based analytical devices (µPADs) holds promise for point-of-care (POC) applications. However, achieving proper DNA binding on paper remains challenging, often requiring solution-based assay protocols, leaving µPADs for final signal readout. Here, we introduce an origami µPAD with preloaded dried reagents, allowing for on-paper assay execution upon sample addition and proper folding. Paper functionalization strategies and assay protocols were optimized to ensure simple and straightforward detection of ATP, employing a portable charge-coupled device (CCD) camera for CL detection. Calibration curves plotted against the logarithm of ATP concentration in the range of 1 to 500 µM facilitated determination of the assay’s limit of detection (LOD), which was found to be 3 µM. Full article

To assist in the speed and accuracy of designing brick-based DNA nanostructures, we introduce a lightweight software suite 3DNA that can be used to generate complex structures. Currently, implementation of this fabrication strategy involves working with generalized, typically commercial CAD software, ad-hoc sequence-generating scripts, and visualization software, which must often be integrated together with an experimental lab setup for handling the hundreds or thousands of constituent DNA sequences. 3DNA encapsulates the solutions to these challenges in one package by providing a customized, easy-to-use molecular canvas and back-end functionality to assist in both visualization and sequence design. The primary motivation behind this software is enabling broader use of the brick-based method for constructing rigid, 3D DNA-based nanostructures, first introduced in 2012. 3DNA is developed to provide a streamlined, real-time workflow for designing and implementing this type of 3D nanostructure by integrating different visualization and design modules. Due to its cross-platform nature, it can be used on the most popular desktop environments, i.e., Windows, Mac OS X, and various flavors of Linux. 3DNA utilizes toolbar-based navigation to create a user-friendly GUI and includes a customized feature to analyze the constituent DNA sequences. Finally, the oligonucleotide sequences themselves can either be created on the fly by a random sequence generator, or selected from a pre-existing set of sequences making up a larger molecular canvas. Full article

The DNA origami method has revolutionized the field of DNA nanotechnology since its introduction. These nanostructures, with their customizable shape and size, addressability, nontoxicity, and capacity to carry bioactive molecules, are promising vehicles for therapeutic delivery. Different approaches have been developed for manipulating and folding DNA origami, resulting in compact lattice-based and wireframe designs. Platinum-based complexes, such as cisplatin and phenanthriplatin, have gained attention for their potential in cancer and antiviral treatments. Phenanthriplatin, in particular, has shown significant antitumor properties by binding to DNA at a single site and inhibiting transcription. The present work aims to study wireframe DNA origami nanostructures as possible carriers for platinum compounds in cancer therapy, employing both cisplatin and phenanthriplatin as model compounds. This research explores the assembly, platinum loading capacity, stability, and modulation of cytotoxicity in cancer cell lines. The findings indicate that nanomolar quantities of the ball-like origami nanostructure, obtained in the presence of phenanthriplatin and therefore loaded with that specific drug, reduced cell viability in MCF-7 (cisplatin-resistant breast adenocarcinoma cell line) to 33%, while being ineffective on the other tested cancer cell lines. The overall results provide valuable insights into using wireframe DNA origami as a highly stable possible carrier of Pt species for very long time-release purposes. Full article

DNA code design is a challenging problem, and it has received great attention in the literature due to its applications in DNA data storage, DNA origami, and DNA computing. The primary focus of this paper is in constructing new DNA codes using the cosets of linear codes over the ring ${\mathbb{Z}}_4$. The Hamming distance constraint, GC-content constraint, and homopolymers constraint are all considered. In this study, we consider the cosets of Simplex alpha code, Kerdock code, Preparata code, and Hadamard code. New DNA codes of lengths four, eight, sixteen, and thirty-two are constructed using a combination of an algebraic coding approach and a variable neighborhood search approach. In addition, good lower bounds for DNA codes that satisfy important constraints have been successfully established using Magma software V2.24-4 and Python 3.10 programming in our comprehensive methodology. Full article