Recent Advances in DNA Nanotechnology for Plasmonic Biosensor Construction

Important applications of DNA nanotechnology combined with CRISPR/Cas systems in biotechnology

DNA nanotechnology leverages the specificity of Watson-Crick base pairing and the inherent attributes of DNA, enabling the exploitation of molecular characteristics, notably self-assembly, in nucleic acids to fabricate novel, controllable nanoscale structures and mechanisms. In the emerging field of DNA nanotechnology, DNA is not only a genetic material, but also a versatile multifunctional polymer, comprising deoxyribonucleotides, and facilitating the construction of precisely dimensioned and precise shaped two-dimensional (2D) and three-dimensional (3D) nanostructures. DNA molecules act as carriers of biological information, with notable advancements in bioimaging, biosensing, showing the profound impact. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated systems (Cas) constitute self-defense mechanisms employed by bacteria and archaea to defend against viral invasion. With the discovery and modification of various functional Cas proteins, coupled with the identification of increasingly designable and programmable CRISPR RNAs (crRNAs), the potential of the CRISPR/Cas system in the field of molecular diagnostics is steadily being realized. Structural DNA nanotechnology provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective. This review explores biosensing detection methods that combine DNA nanotechnology with CRISPR/Cas systems. These techniques are used in biosensors to detect small molecules such as DNA, RNA, and etc. The combination of 2D and 3D DNA nanostructures with the CRISPR/Cas system holds significant value and great development prospects in the detection of important biomarkers, gene editing, and other biological applications in fields like biosensing.

Towards Point-of-Care Single Biomolecule Detection Using Next Generation Portable Nanoplasmonic Biosensors: A Review

Over the past few years, nanoplasmonic biosensors have gained widespread interest for early diagnosis of diseases thanks to their simple design, low detection limit down to the biomolecule level, high sensitivity to even small molecules, cost-effectiveness, and potential for miniaturization, to name but a few benefits. These intrinsic natures of the technology make it the perfect solution for compact and portable designs that combine sampling, analysis, and measurement into a miniaturized chip. This review summarizes applications, theoretical modeling, and research on portable nanoplasmonic biosensor designs. In order to develop portable designs, three basic components have been miniaturized: light sources, plasmonic chips, and photodetectors. There are five types of portable designs: portable SPR, miniaturized components, flexible, wearable SERS-based, and microfluidic. The latter design also reduces diffusion times and allows small amounts of samples to be delivered near plasmonic chips. The properties of nanomaterials and nanostructures are also discussed, which have improved biosensor performance metrics. Researchers have also made progress in improving the reproducibility of these biosensors, which is a major obstacle to their commercialization. Furthermore, future trends will focus on enhancing performance metrics, optimizing biorecognition, addressing practical constraints, considering surface chemistry, and employing emerging technologies. In the foreseeable future, these trends will be merged to result in portable nanoplasmonic biosensors offering detection of even a single biomolecule.

Waveguide-Enhanced Nanoplasmonic Biosensor for Ultrasensitive and Rapid DNA Detection

DNA is fundamental for storing and transmitting genetic information. Analyzing DNA or RNA base sequences enables the identification of genetic disorders, monitoring gene expression, and detecting pathogens. Traditional detection techniques like polymerase chain reaction (PCR) and next-generation sequencing (NGS) have limitations, including complexity, high cost, and the need for advanced computational skills. Therefore, there is a significant demand for enzyme-free and amplification-free strategies for rapid, low-cost, and sensitive DNA detection. DNA biosensors, especially those utilizing plasmonic nanomaterials, offer a promising solution. This study introduces a novel DNA-functionalized waveguide-enhanced nanoplasmonic optofluidic biosensor using a nanogold-linked sorbent assay for enzyme-free and amplification-free DNA detection. Integrating plasmonic gold nanoparticles (AuNPs) with a glass planar waveguide (WG) and a microfluidic channel, fabricated through cost-effective, vacuum-free methods, the biosensor achieves specific detection of complementary target DNA sequences. Utilizing a sandwich architecture, AuNPs labeled with detection DNA probes enhance sensitivity by altering evanescent wave distribution and inducing plasmon resonance modes. The biosensor demonstrated exceptional performance in DNA detection, achieving a limit of detection (LOD) of 33.1 fg/mL (4.36 fM) with a rapid response time of approximately 8 min. This ultrasensitive, rapid, and cost-effective biosensor exhibits minimal background nonspecific adsorption, making it highly suitable for clinical applications and early disease diagnosis. The innovative design and fabrication processes offer significant advantages for mass production, presenting a viable tool for precise disease diagnostics and improved clinical outcomes.

Biosensing of DNA through difference in interaction between microparticle and glass plate based on particle dissociation in a coupled acoustic-gravitational field

A novel approach for detecting DNA without labeling the target DNA was developed based on the particle dissociation behavior in a combined acoustic-gravitational field. The particles, which are tethered on a glass plate via intermolecular interactions (Fbind), are dissociated by the resultant force of the acoustic radiation force (Fac), which is a function of the applied voltage (V), and the sedimentation force. In this system, V required for particle dissociation is dependent on Fbind. The differences in Fbind were exploited for detecting the target DNA. A glass plate and polystyrene (PS) particles were respectively modified with anchor and capture DNAs. The target DNA induces immobilization of the PS particles on the glass plate through sandwich hybridization, with a large accompanying Fbind. In the absence of the target DNA, the anchor DNA on the glass plate interacted weakly with the capture DNA on the PS particles via direct binding (small Fbind). The particle dissociation behavior varies based on the concentration of the target DNA due to changes in the ratio of the PS particles tethered through direct binding and sandwich hybridization. Target DNA with a length exceeding 12 base pairs (bps) can be detected on the picomolar scale at concentrations of 10-12 to 10-5 M. This detection scheme was applied to a specific sequence of HIV-2 with 20 bps, achieving a picomolar detection limit.

New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics

Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data. Quantum mechanics has recently emerged as a promising tool for the analysis of biological systems, leading to the development of quantum bioinformatics. This new field employs the principles of quantum mechanics, quantum algorithms, and quantum computing to solve complex problems in molecular biology, drug design, and protein folding. However, the intersection of bioinformatics, biology, and quantum mechanics presents unique challenges. One significant challenge is the possibility of confusion among scientists between quantum bioinformatics and quantum biology, which have similar goals and concepts. Additionally, the diverse calculations in each field make it difficult to establish boundaries and identify purely quantum effects from other factors that may affect biological processes. This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics. We examine the challenges and unique features of this field and propose a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress. By unlocking the full potential of quantum bioinformatics, this review aims to contribute to our understanding of quantum mechanics in biological systems.

Recent Advances in Metallic Nanostructures-assisted Biosensors for Medical Diagnosis and Therapy

The field of nanotechnology has witnessed remarkable progress in recent years, particularly in its application to medical diagnosis and therapy. Metallic nanostructures-assisted biosensors have emerged as a powerful and versatile platform, offering unprecedented opportunities for sensitive, specific, and minimally invasive diagnostic techniques, as well as innovative therapeutic interventions. These biosensors exploit the molecular interactions occurring between biomolecules, such as antibodies, enzymes, aptamers, or nucleic acids, and metallic surfaces to induce observable alterations in multiple physical attributes, encompassing electrical, optical, colorimetric, and electrochemical signals. These interactions yield measurable data concerning the existence and concentration of particular biomolecules. The inherent characteristics of metal nanostructures, such as conductivity, plasmon resonance, and catalytic activity, serve to amplify both sensitivity and specificity in these biosensors. This review provides an in-depth exploration of the latest advancements in metallic nanostructures-assisted biosensors, highlighting their transformative impact on medical science and envisioning their potential in shaping the future of personalized healthcare.

Optical Processes behind Plasmonic Applications

Plasmonics is a revolutionary concept in nanophotonics that combines the properties of both photonics and electronics by confining light energy to a nanometer-scale oscillating field of free electrons, known as a surface plasmon. Generation, processing, routing, and amplification of optical signals at the nanoscale hold promise for optical communications, biophotonics, sensing, chemistry, and medical applications. Surface plasmons manifest themselves as confined oscillations, allowing for optical nanoantennas, ultra-compact optical detectors, state-of-the-art sensors, data storage, and energy harvesting designs. Surface plasmons facilitate both resonant characteristics of nanostructures and guiding and controlling light at the nanoscale. Plasmonics and metamaterials enable the advancement of many photonic designs with unparalleled capabilities, including subwavelength waveguides, optical nanoresonators, super- and hyper-lenses, and light concentrators. Alternative plasmonic materials have been developed to be incorporated in the nanostructures for low losses and controlled optical characteristics along with semiconductor-process compatibility. This review describes optical processes behind a range of plasmonic applications. It pays special attention to the topics of field enhancement and collective effects in nanostructures. The advances in these research topics are expected to transform the domain of nanoscale photonics, optical metamaterials, and their various applications.

Plasmonic Sensors: A New Frontier in Nanotechnology

Plasmonics is the study of surface plasmons formed by the interaction of incident light with electrons to form a surface-bound electromagnetic wave [...].