Programming Fluorogenic DNA Probes for Rapid Detection of Steroids

High-content tailoring strategy to improve the multifunctionality of functional nucleic acids

Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.

Structural Antagonism-Aided Conformational Regulation Enables an Aptamer-Loop G-Quadruplex Modular Sensor of β-Lactoglobulin

A simple, reliable method for identifying β-lactoglobulin (β-LG) in dairy products is needed to protect those with β-LG allergies. A common, practical strategy for target detection is designing simplified nucleic acid nanodevices by integrating functional components. This work presents a label-free modular β-LG aptasensor consisting of an aptamer-loop G-quadruplex (G4), the working conformation of which is regulated by conformational antagonism to ensure respective module functionality and the related signal transduction. The polymorphic conformations of the module-fused sequence are systematically characterized, and the cause is revealed as shifting antagonistic equilibrium. Combined with conformational folding dynamics, this helped regulate functional conformations by fine-tuning the sequences. Furthermore, the principle of specific β-LG detection by parallel G4 topology is examined as binding on the G4 aptamer loop by β-LG to reinforce the G4 topology and fluorescence. Finally, a label-free, assembly-free, succinct, and turn-on fluorescent aptasensor is established, achieving excellent sensitivity across five orders of magnitude, rapidly detecting β-LG within 22-min. This study provides a generalizable approach for the conformational regulation of module-fused G4 sequences and a reference model for creating simplified sensing devices for a variety of targets.

Tip-Enhanced Sub-Femtomolar Steroid Immunosensing via Micropyramidal Flexible Conducting Polymer Electrodes for At-Home Monitoring of Salivary Sex Hormones

Noninvasive testing and continuous monitoring of ultralow-concentration hormones in biofluids have attracted increasing interest for health management and personalized medicine, in which saliva could fulfill the demand. Steroid sex hormones such as progesterone (P4) and β-estradiol (E2) are crucial for female wellness and reproduction; however, their concentrations in saliva can vary down to sub-pM and constantly fluctuate over several orders of magnitude. This remains a major obstacle toward user-friendly and reliable monitoring at home with low-cost flexible biosensors. Herein we introduce a 3D micropyramidal electrode architecture to address such challenges and achieve an ultrasensitive flexible electrochemical immunosensor with sub-fM-level detection capability of salivary sex hormones within a few minutes. This is enabled by micropyramidal electrode arrays consisting of a poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonate) (PEDOT:PSS) thin film as the coating layer and electrochemically decorated gold nanoparticles (AuNPs) to improve the antibody immobilization. The enhanced mass transport around the 3D tips provided by the micropyramidal architecture is discovered to improve the detection limit by 3 orders of magnitude, pushing it to as low as ∼100 aM for P4 and ∼20 aM for E2, along with a wide linear range up to μM. Accordingly, these hormones down to sub-fM in >1000-fold-diluted saliva samples can be accurately measured by the printed soft immunosensors, thus allowing at-home testing through simple saliva dilution to minimize the interfering substances instead of centrifugation. Finally, monitoring of the female ovarian hormone cycle of both P4 and E2 is successfully demonstrated based on the centrifuge-free saliva testing during a period of 4 weeks. This ultrasensitive and soft 3D microarchitected electrode design is believed to provide a universal platform for a diverse variety of applications spanning from accurate clinical diagnostics and counselling and in vivo detection of bioactive species to environmental and food quality tracing.

Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA

The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.

Proximity-Driven DNA Nanosensors

In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.

SENSOR FOR PREDNISOLONE DETECTION IN SPORTS DOPING

ABSTRACT Introduction: Prednisolone causes pro-inflammatory impulses to be inhibited and anti-inflammatory signals to be promoted. As a result, it alters how the body's immune system reacts to certain diseases. The World Anti-Doping Agency, however, has banned SNP and other glucocorticosteroids. An electrochemical sensor can be developed using a gold nanocomposite, polypyrrole nanoparticles and synthesized carbon nanotubes (Au-PPy NPs@CNTs). Objective: Develop an electrochemical sensor to detect prednisolone. Method: Au-PPy NPs@CNTs nanocomposite was chemically synthesized with a modified glassy carbon electrode (GCE) surface. Results: According to SEM data, the nanocomposite was composed of amorphous Au NPs, and PPy NPs deposited in tubes strongly entangled in a CNTs network. The wide linear range and low detection limit of the Au-PPy NPs@CNTs/GCE as prednisolone sensors were attributed to the combined catalytic performance of the Au and PPy NPs@CNTs nanostructures. Conclusion: The results of prednisolone detection in each specimen using the amperometric method indicated good accuracy. The accuracy and precision of Au-PPy NPs@CNTs/GCE for prednisolone detection were explored in blood samples from 5 young athletes aged 20-24 years who used prednisolone tablets (RSD less than 4.25%). In addition to monitoring prednisolone concentrations in athletes’ serum, Au-PPy NPs@CNTs/GCE can be used as a reliable prednisolone sensor. Level of evidence II; Therapeutic studies - investigating treatment outcomes.

Near-Infrared Dye-Aptamer Assay for Small Molecule Detection in Complex Specimens

Aptamers are single-stranded oligonucleotides isolated in vitro that bind specific targets with high affinity and are commonly used as receptors in biosensors. Aptamer-based dye-displacement assays are a promising sensing platform because they are label-free, sensitive, simple, and rapid. However, these assays can exhibit impaired sensitivity in biospecimens, which contain numerous interferents that cause unwanted absorbance, scattering, and fluorescence in the UV-vis region. Here, this problem is overcome by utilizing near-infrared (NIR) signatures of the dye 3,3'-diethylthiadicarbocyanine iodide (Cy5). Cy5 initially complexes with aptamers as monomers and dimers; aptamer-target binding displaces the dye into solution, resulting in the formation of J-aggregates that provide a detectable NIR signal. The generality of our assay is demonstrated by detecting three different small-molecule analytes with their respective DNA aptamers at clinically relevant concentrations in serum and urine. These successful demonstrations show the utility of dye-aptamer NIR biosensors for high-throughput detection of analytes in clinical specimens.

Signal Transduction Strategies for Analyte Detection Using DNA-Based Nanostructures

The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures. The utility of these structures arises both from DNA's inherent ability to selectively recognize and bind a variety of chemical species and from the unique properties observed when DNA is restructured at the nanoscale. In this Minireview, we chronicle the most commonly used signal transduction strategies that have been interfaced with various DNA-based nanostructures. We discuss the types of analytes and the detection scenarios that are sought after, delineate the advantages and disadvantages of each signaling strategy, and outline the key considerations that guide the selection of each signaling method.

Programmable Matter: The Nanoparticle Atom and DNA Bond

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.

Protein transfection via spherical nucleic acids

The efficient transfection of functional proteins into cells can serve as a means for regulating cellular processes toward solving fundamental challenges in biology and medicine. However, the use of proteins as effective intracellular agents is hindered by their low cellular uptake and susceptibility to degradation. Over the past 15 years, our group has been developing spherical nucleic acids (SNAs), nanoparticles functionalized with a dense radially oriented shell of nucleic acids. These structures actively enter cells and have opened new frontiers in chemical sensing, biodiagnostics and therapeutics. Recently, we have shown that proteins can be used as structurally precise and homogeneous nanoparticle cores in SNAs. The resultant protein SNAs (ProSNAs) allow previously cell-impermeable proteins to actively enter cells, exhibit high degrees of stability and activity both in cell culture and in vivo, and show enhanced pharmacokinetics. Consequently, these modular structures constitute a plug-and-play platform in which the protein core and nucleic acid shell can be independently varied to achieve a desired function. Here, we describe the synthesis of ProSNAs through the chemical modification of solvent-accessible surface residues (3-5 d). We also discuss design considerations, strategies for characterization, and applications of ProSNAs in cellular transfection, biological sensing and functional enzyme delivery in vivo.

E2EDNA: Simulation Protocol for DNA Aptamers with Ligands

We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are important to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Existing computational tools used for aptamer design focus on cost-effective secondary structure prediction and motif analysis in the large data sets produced by SELEX experiments. As a rule, they do not offer flexibility with respect to the choice of the theoretical engine or direct access to the simulation platform. Practical aptamer optimization often requires higher accuracy predictions for only a small subset of sequences suggested, e.g., by SELEX experiments, but in the absence of a streamlined procedure, this task is extremely time and expertise intensive. We address this gap by introducing E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy. As a case study, we simulate a DNA-UTP (uridine triphosphate) complex in water using the state-of-the-art AMOEBA polarizable force field. The code is available at https://github.com/InfluenceFunctional/E2EDNA.