DNA origami nanorobot fiber optic genosensor to TMV

Nanomaterial surface modification toolkit: Principles, components, recipes, and applications

Surface-functionalized nanostructures are at the forefront of biotechnology, providing new opportunities for biosensors, drug delivery, therapy, and bioimaging applications. The modification of nanostructures significantly impacts the performance and success of various applications by enabling selective and precise targeting. This review elucidates widely practiced surface modification strategies, including click chemistry, cross-coupling, silanization, aldehyde linkers, active ester chemistry, maleimide chemistry, epoxy linkers, and other protein and DNA-based methodologies. We also delve into the application-focused landscape of the nano-bio interface, emphasizing four key domains: therapeutics, biosensing, environmental monitoring, and point-of-care technologies, by highlighting prominent studies. The insights presented herein pave the way for further innovations at the intersection of nanotechnology and biotechnology, providing a useful handbook for beginners and professionals. The review draws on various sources, including the latest research articles (2018-2023), to provide a comprehensive overview of the field.

The Dual-Response-Single-Amplification Fluorescent Nanomachine for Tumor Imaging and Gastric Cancer Diagnosis

Gastric cancer (GC) is one of the most common tumors worldwide and is the leading cause of tumor-related mortality. Traditional biomarkers and screening methods cannot meet the clinical demands. There is an urgent need for highly sensitive diagnostic markers as well as accurate quantification methods for early gastric cancer (EGC) screening. Here a dual-target cooperatively responsive fluorescent nanomachine by the innovative application of two targets─responsive strand migration system with a single-amplification-cycle element was developed for the simultaneous detection of GC biomarkers miR-5585-5p and PLS3 mRNA, which were selected by next-generation sequencing and RT-qPCR. It was also an RNA extraction-free, PCR-free, and nonenzymatic biosensor to achieve tumor cell imaging and serum diagnosis. Requiring only a 20 μL serum sample and 20 min incubation time, the nanomachine achieved an ultrasensitive detection limit of fM level with a broad linear range from fM to nM. More importantly, a higher AUC value (0.884) compared to the clinically used biomarker CA 72-4 was obtained by the nanomachine to distinguish GC patients successfully. Notably, for the key concerns of diagnosis of EGC patients, the nanomachine also achieved a satisfactory AUC value of 0.859. Taken together, this work has screened and obtained multiple biomarkers and developed a fluorescent nanomachine for combination diagnosis of GC, providing an ingenious design of a functionalized DNA nanomachine and a feasible strategy for the transformation of serum biomarkers into clinical diagnosis.

A review of Optical Point-of-Care devices to Estimate the Technology Transfer of These Cutting-Edge Technologies

Despite the remarkable development related to Point-of-Care devices based on optical technology, their difficulties when used outside of research laboratories are notable. In this sense, it would be interesting to ask ourselves what the degree of transferability of the research work to the market is, for example, by analysing the relation between the scientific work developed and the registered one, through patent. In this work, we provide an overview of the state-of-the-art in the sector of optical Point-of-Care devices, not only in the research area but also regarding their transfer to market. To this end, we explored a methodology for searching articles and patents to obtain an indicator that relates to both. This figure of merit to estimate this transfer is based on classifying the relevant research articles in the area and the patents that have been generated from these ones. To delimit the scope of this study, we researched the results of a large enough number of publications in the period from 2015 to 2020, by using keywords "biosensor", "optic", and "device" to obtain the most representative articles from Web of Science and Scopus. Then, we classified them according to a particular classification of the optical PoC devices. Once we had this sampling frame, we defined a patent search strategy to cross-link the article with a registered patent (by surfing Google Patents) and classified them accordingly to the categories described. Finally, we proposed a relative figure called Index of Technology Transference (IoTT), which estimates to what extent our findings in science materialized in published articles are protected by patent.

Autonomous Bionanorobots via a Cage-Shaped Silsesquioxane Vehicle for In Vivo Heavy Metal Detoxification

Nanorobots hold great promise for integrated drug delivery systems that are responsive to molecular triggers. Herein, we successfully developed an automatic smart bionanorobot that has transport capability and recognizes and removes zinc ions from poisoned cells based on nanoscale polyhedral oligomeric silsesquioxane molecules. This intelligent bionanorobot can easily move inside and outside the cell and find zinc ions owing to its highly selective recognition to zinc ions and high cell permeability, especially the well-combined high penetration and strong binding energy. More importantly, it was also found that this intelligent bionanorobot can restore round HeLa cells to a normal fusiform cell morphology following high-concentration zinc treatment and does not interfere with cell proliferation and division. It was also shown by in vivo experiments that the bionanorobot can inhibit persistent enlargement of the liver caused by zinc ion poisoning.

Hydrophobin HGFI assisted immunobiologic sensor based on a cascaded taper integrated ultra-long-period fiber grating

A new type of cascaded taper integrated ultra-long-period fiber grating (ULPFG) based immunobiologic sensor has been developed that benefits from the self-assembled monolayer of class I hydrophobin HGFI. Due to the cascaded arc, discharge tapers constitute an ultra-long-period and circular symmetrical refractive index modulation along fiber axial direction, and by local integration in one period, the mode coupling would generate to the higher harmonic of LP₀₂, LP₀₃ and LP₀₄ modes in the wavelength range from 1300 nm to 1620 nm. The hydrophobic characteristic of the ULPFG surface is modified employing the HGFI, and the antibody molecule probes could be absorbed strongly on the HGFI nano-film, furthermore, the performances of immunobiologic sensing are investigated employing multiple control groups of matched and mismatched antigen molecule targets. The results show that it possesses higher sensing sensitivity of 4.5 nm/(µg/ml), faster response time about of 35 min, lower stability error of 8.8%, and excellent immuno-specificity. Moreover, this proposed ULPFG sensor has the advantages of low cost, simple fabrication and label-free, which is a powerful tool in the trace biomedical detection field.

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

µ-PIV Measurements of Flows Generated by Photolithography-Fabricated Achiral Microswimmers

Robotic micro/nanoswimmers can potentially be used as tools for medical applications, such as drug delivery and noninvasive surgery. Recently, achiral microswimmers have gained significant attention because of their simple structures, which enables high-throughput fabrication and size scalability. Here, microparticle image velocimetry (µ-PIV) was used to study the hydrodynamics of achiral microswimmers near a boundary. The structures of these microswimmers resemble the letter L and were fabricated using photolithography and thin-film deposition. Through µ-PIV measurements, the velocity flow fields of the microswimmers rotating at different frequencies were observed. The results herein yield an understanding of the hydrodynamics of the L-shaped microswimmers, which will be useful in applications such as fluidic manipulation.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

DNA nanostructures: A versatile lab-bench for interrogating biological reactions

At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

A silver(I) doped bud-like DNA nanostructure as a dual-functional nanolabel for voltammetric discrimination of methylated from unmethylated genes

A small DNA structure, referred to as DNA nanobud (NB), was used for the first time to design a dual-functional nanolabel in order to recognize a particular oligonucleotide sequence, generate and amplify the electrochemical analytical signal. NBs containing numerous repetitive desired sequences were prepared through self-assembly of 8-h rolling circle amplification. Then, redox-active silver ions were loaded onto the NBs by over-night incubation with a solution of AgNO₃. The incorporation of Ag⁺ into NBs was confirmed by field emission scanning electron microscopy, dynamic light scattering, UV-Vis spectroscopy, zeta potential measurements, and energy-dispersive X-ray spectroscopy. A DNA sandwich complex was created after hybridization of Ag⁺-NB with target sequence, which was captured by immobilized probe on a gold electrode. Cyclic voltammetry was applied to measure the redox signal of silver ions produced typically at a potential around 0.02 V vs. Ag/AgCl. The label can specifically discriminate fully methylated BMP3 gene from fully unmethylated bisulfate-converted part of the gene. The electrochemical signal produced by DNA sandwich complex of gold/probe/BMP3/Ag⁺-NB was linear toward BMP3 concentration from 100 pM to 100 nM. The method has a 100 pM BMP3 detection limit. Conceivably, this nanolabel can be designed and modified such that it may also be used to detect other sequences with lower detection limits. Graphical abstract Ag⁺-NB as a new nanolabel for genosensing was formed by loading Ag⁺ on a spherical DNA nanostructure, nanobud (NB), synthesized by rolling circle amplification process. By using a gold electrode (AuE), Ag⁺-NB with numerous electroactive cations and binding sites can detect targets and generate amplified electrochemical signals.

Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing

Many challenges in biosensing originate from the fact that the all-important nanoarchitecture of the biosensor surface, including precise density and orientation of bioreceptors, is not entirely comprehended. Here, we introduced a three-dimensional DNA origami as a bioreceptor carrier to functionalize the fiber optic surface plasmon resonance (FO-SPR) sensor with nanoscale precision. Starting from a 24-helix bundle, two distinct DNA origami structures were designed to position thrombin-specific aptamers with different densities and distances (27 and 113 nm) from the FO-SPR surface. The origami-based biosensors not only proved to be capable of reproducible, label-free thrombin detection but revealed also valuable innovative features: (1) a significantly better performance in the absence of backfilling, known as essential in the biosensing field, suggesting improved bioreceptor orientation and accessibility, and (2) a wider linear range compared to previously reported thrombin biosensors. We envisage that our method will be beneficial for both scientists and clinicians looking for new surface (bio)chemistry and improved diagnostics.