Kinetic discrimination of DNA single-base mutations by localized surface plasmon resonance

Advancements in Biosensors for Point-of-Care Testing of Nucleic Acid

Rapid, low-cost and high-specific diagnosis based on nucleic acid detection is pivotal in both detecting and controlling various infectious diseases, effectively curbing their spread. Moreover, the analysis of circulating DNA in whole blood has emerged as a promising noninvasive strategy for cancer diagnosis and monitoring. Although traditional nucleic acid detection methods are reliable, their time-consuming and intricate processes restrict their application in rapid field assays. Consequently, an urgent emphasis on point-of-care testing (POCT) of nucleic acids has arisen. POCT enables timely and efficient detection of specific sequences, acting as a deterrent against infection sources and potential tumor threats. To address this imperative need, it is essential to consolidate key aspects and chart future directions in POCT biosensors development. This review aims to provide an exhaustive and meticulous analysis of recent advancements in POCT devices for nucleic acid diagnosis. It will comprehensively compare these devices across crucial dimensions, encompassing their integrated structures, the synthesized nanomaterials harnessed, and the sophisticated detection principles employed. By conducting a rigorous evaluation of the current research landscape, this review will not only spotlight achievements but also identify limitations, offering valuable insights into the future trajectory of nucleic acid POCT biosensors. Through this comprehensive analysis, the review aspires to serve as an indispensable guide for fostering the development of more potent biosensors, consequently fostering precise and efficient POCT applications for nucleic acids.

LSPR-Based Biosensing Enables the Detection of Antimicrobial Resistance Genes

The development of rapid, simple, and accurate bioassays for the detection of nucleic acids has received increasing demand in recent years. Here, localized surface plasmon resonance (LSPR) spectroscopy for the detection of an antimicrobial resistance gene, sulfhydryl variable β-lactamase (blaSHV), which confers resistance against a broad spectrum of β-lactam antibiotics is used. By performing limit of detection experiments, a 23 nucleotide (nt) long deoxyribonucleic acid (DNA) sequence down to 25 nm was detected, whereby the signal intensity is inversely correlated with sequence length (23, 43, 63, and 100 nt). In addition to endpoint measurements of hybridization events, the setup also allowed to monitor the hybridization events in real-time, and consequently enabled to extract kinetic parameters of the studied binding reaction. Performing LSPR measurements using single nucleotide polymorphism (SNP) variants of blaSHV revealed that these sequences can be distinguished from the fully complementary sequence. The possibility to distinguish such sequences is of utmost importance in clinical environments, as it allows to identify mutations essential for enzyme function and thus, is crucial for the correct treatment with antibiotics. Taken together, this system provides a robust, label-free, and cost-efficient analytical tool for the detection of nucleic acids and will enable the surveillance of antimicrobial resistance determinants.

Plasmonic Nanomaterials for Colorimetric Biosensing: A Review

In the last few decades, plasmonic colorimetric biosensors raised increasing interest in bioanalytics thanks to their cost-effectiveness, responsiveness, and simplicity as compared to conventional laboratory techniques. Potential high-throughput screening and easy-to-use assay procedures make them also suitable for realizing point of care devices. Nevertheless, several challenges such as fabrication complexity, laborious biofunctionalization, and poor sensitivity compromise their technological transfer from research laboratories to industry and, hence, still hamper their adoption on large-scale. However, newly-developing plasmonic colorimetric biosensors boast impressive sensing performance in terms of sensitivity, dynamic range, limit of detection, reliability, and specificity thereby continuously encouraging further researches. In this review, recently reported plasmonic colorimetric biosensors are discussed with a focus on the following categories: (i) on-platform-based (localized surface plasmon resonance, coupled plasmon resonance and surface lattice resonance); (ii) colloid aggregation-based (label-based and label free); (iii) colloid non-aggregation-based (nanozyme, etching-based and growth-based).

Biosensors for circulating tumor cells (CTCs)-biomarker detection in lung and prostate cancer: Trends and prospects

Cancer is one of the leading cause of death worldwide. Lung cancer (LCa) and prostate cancer (PCa) are the two most common ones particularly among men with about 20% of aggressive metastatic form leading to shorter overall survival. In recent years, circulating tumor cells (CTCs) have been investigated extensively for their role in metastatic progression and their involvement in reduced overall survival and treatment responses. Analysis of these cells and their associated biomarkers as "liquid biopsy" can provide valuable real-time information regarding the disease state and can be a potential avenue for early-stage detection and possible selection of personalized treatments. This review focuses on the role of CTCs and their associated biomarkers in lung and prostate cancer, as well as the shortcomings of conventional methods for their isolation and analysis. To overcome these drawbacks, biosensors are an elegant alternative because they are capable of providing valuable multiplexed information in real-time and analyzing biomarkers at lower concentrations. A comparative analysis of different transducing elements specific for the analysis of cancer cell and cancer biomarkers have been compiled in this review.

Fast, accurate, point-of-care COVID-19 pandemic diagnosis enabled through advanced lab-on-chip optical biosensors: Opportunities and challenges

The sudden rise of the worldwide severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in early 2020 has called into drastic action measures to perform instant detection and reduce the rate of spread. Common clinical and nonclinical diagnostic testing methods have been partially effective in satisfying the increasing demand for fast detection point-of-care (POC) methods to slow down further spread. However, accurate point-of-risk diagnosis of this emerging viral infection is paramount as the need for simultaneous standard operating procedures and symptom management of SARS-CoV-2 will be the norm for years to come. A sensitive, cost-effective biosensor with mass production capability is crucial until a universal vaccination becomes available. Optical biosensors can provide a noninvasive, extremely sensitive rapid detection platform with sensitivity down to ∼67 fg/ml (1 fM) concentration in a few minutes. These biosensors can be manufactured on a mass scale (millions) to detect the COVID-19 viral load in nasal, saliva, urine, and serological samples, even if the infected person is asymptotic. Methods investigated here are the most advanced available platforms for biosensing optical devices that have resulted from the integration of state-of-the-art designs and materials. These approaches include, but are not limited to, integrated optical devices, plasmonic resonance, and emerging nanomaterial biosensors. The lab-on-chip platforms examined here are suitable not only for SARS-CoV-2 spike protein detection but also for other contagious virions such as influenza and Middle East respiratory syndrome (MERS).

Plasmonic Biosensors for Single-Molecule Biomedical Analysis

The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewed.

Recent Progress in Optical Sensors for Biomedical Diagnostics

In recent years, several types of optical sensors have been probed for their aptitude in healthcare biosensing, making their applications in biomedical diagnostics a rapidly evolving subject. Optical sensors show versatility amongst different receptor types and even permit the integration of different detection mechanisms. Such conjugated sensing platforms facilitate the exploitation of their neoteric synergistic characteristics for sensor fabrication. This paper covers nearly 250 research articles since 2016 representing the emerging interest in rapid, reproducible and ultrasensitive assays in clinical analysis. Therefore, we present an elaborate review of biomedical diagnostics with the help of optical sensors working on varied principles such as surface plasmon resonance, localised surface plasmon resonance, evanescent wave fluorescence, bioluminescence and several others. These sensors are capable of investigating toxins, proteins, pathogens, disease biomarkers and whole cells in varied sensing media ranging from water to buffer to more complex environments such as serum, blood or urine. Hence, the recent trends discussed in this review hold enormous potential for the widespread use of optical sensors in early-stage disease prediction and point-of-care testing devices.

Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective

Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.

Enhancing the Performance of DNA Surface-Hybridization Biosensors through Target Depletion

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large, and they have high affinity for the target, the DNA in solution may become depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration c₂) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration c₁ ≫ c₂). We show that depletion can give rise to a strongly enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations c₂/c₁ that are up to 3 orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich and exhibits a nonmonotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.

Gold-decorated magnetic nanoparticles modified with hairpin-shaped DNA for fluorometric discrimination of single-base mismatch DNA

The authors describe the use of gold-decorated magnetic nanoparticles (Au/MNPs) in discriminating DNA sequences with a single-base (guanine) mismatch. The Au/MNPs were characterized through dynamic light scattering, X-ray diffraction, superconducting quantum interference device, and UV/visible spectroscopy. They were then conjugated to a probe oligomer consisting of a hairpin-shaped DNA sequence carrying two signalling fluorophores: fluorescein at its 3' end and pyrene in the loop region. When interacting with the target DNA sequences, the hybridized probe-target duplex renders the pyrene signal (at excitation/emission wavelengths of 345/375 nm) either quenched or unquenched. Quenching (or nonquenching) of the pyrene fluorescence depends on the presence of a guanine (or a nonguanine) nucleotide at the designated polymorphic site. The linear range of hybridization in these Au/MNPs is from 0.1 nM to 1.0 μM of ssDNA. Conceivably, this system may serve as a single-nucleotide polymorphism probe. Graphical Abstract Schematic presentation of probe-conjugated Au/MNP preparation (upper panel) and working principle to discriminate DNA with or without single-base (guanine) mismatch sequences at the polymorphic sites (lower panel). Py denotes pyrene-hooked pyrrolocytidine; F denotes fluorescein.

Magnetic beads assay based on Zip nucleic acid for electrochemical detection of Factor V Leiden mutation

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among people. Development of reliable methods for the detection of SNP is crucial in aspects of molecular diagnosis and personalized medicine. In our study, a genomagnetic assay in combination with zip nucleic acid (ZNA) for electrochemical detection of SNP related to Factor V Leiden mutation. For the first time in the literature, a new generation nucleic acid; ZNA was applied herein for electrochemical monitoring of nucleic acid hybridization. Streptavidin coated magnetic beads (MBs) were used for preparation of samples containing ZNA-DNA hybrid and accordingly, the guanine signal was measured as a response of hybridization related to Factor V Leiden mutation by carbon nanofibers (CNF) modified screen printed electrodes (SPE) and multi-channel screen printed array of electrodes (CNF-MULTI SPEx8). The detection limit (DL) was found to be 3.79 μg/mL (376 nM) and, 11.63 μg/mL (1.624 μM), respectively by CNF-SPE and CNF-MULTI SPEx8. The selectivity of ZNA probe to mutation-free DNA sequences was also investigated in contrast to DNA probe. The applicability of ZNA based magnetic beads assay to sequence selective hybridization related to Factor V Leiden was also tested in synthetic PCR samples.

Label-free plasmonic biosensors for point-of-care diagnostics: a review

Introduction: Optical biosensors, particularly those based on nanoplasmonics technology, have emerged in recent decades as a potential solution for disease diagnostics and therapy follow-up at the point-of-care (POC). These biosensor platforms could overcome some of the challenges faced in conventional diagnosis techniques offering label-free assays with immediate results and employing small and user-friendly devices. Areas covered: In this review, we will provide a critical overview of the recent advances in the development of nanoplasmonic biosensors for the POC diagnostics. We focus on those systems with demonstrated capabilities for integration in portable platforms, highlighting some of the most relevant diagnostics applications targeting proteins, nucleic acids, and cells as disease biomarkers. Expert commentary: Despite the attractive features of label-free nanoplasmonic sensors in terms of miniaturization and analytical robustness, the route toward an effective clinical implementation involves the integration of fully automated microfluidic systems for sample processing and analysis, and the optimization of surface biofunctionalization procedures. Additionally, the development of multiplexed sensors for high-throughput analysis and including specific neoantigens and novel biomarkers in detection panels will provide the means for delivering a powerful analytical technology for an accurate and improved medical diagnosis.

Label-free detection of live cancer cells and DNA hybridization using 3D multilayered plasmonic biosensor

Three-dimensional (3D) multilayered plasmonic nanostructures consisting of Au nanosquares on top of SU-8 nanopillars, Au asymmetrical nanostructures in the middle, and Au asymmetrical nanoholes at the bottom were fabricated through reversal nanoimprint technology. Compared with two-dimensional and quasi-3D plasmonic nanostructures, the 3D multilayered plasmonic nanostructures showed higher electromagnetic field intensity, longer plasmon decay length and larger plasmon sensing area, which are desirable for highly sensitive localized surface plasmonic resonance biosensors. The sensitivity and resonance peak wavelength of the 3D multilayered plasmonic nanostructures could be adjusted by varying the offset between the top and bottom SU-8 nanopillars from 31% to 56%, and the highest sensitivity of 382 and 442 nm/refractive index unit were observed for resonance peaks at 581 and 805 nm, respectively. Live lung cancer A549 cells with a low concentration of 5 × 10³ cells ml^-1 and a low sample volume of 2 μl could be detected by the 3D multilayered plasmonic nanostructures integrated in a microfluidic system. The 3D plasmonic biosensors also had the advantages of detecting DNA hybridization by capturing the complementary target DNA in the low concentration range of 10^-14-10^-7 M, and providing a large peak shift of 82 nm for capturing 10^-7 M complementary target DNA without additional signal amplification.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Characterization of G4-G4 Crosstalk in the c-KIT Promoter Region

The proximal promoter of c-KIT contains a peculiar domain that consists of three short G-rich sequences that are close together and can fold into noncanonical DNA secondary structures called G-quadruplexes (G4). Here, we focused on a sequence containing two consecutive G4 (kit2 and kit*). By electrophoretic, surface plasmon resonance, and spectroscopic techniques, we demonstrated that they retain the ability to fold into G4 upon being inserted into the extended sequence. Here, we highlighted the occurrence of crosstalk between the two forming units. This previously unexplored G4-G4 interaction modulates both the conformation and the stability of the overall arrangement of the c-KIT promoter. It is not supported by stacking of single nucleotides but refers to a G4-G4 interaction surface surrounded by a two-nucleotides loop that might represent a reliable unprecedented target for anticancer therapy.

Ionic strength-controlled hybridization and stability of hybrids of KRAS DNA single-nucleotides: A surface plasmon resonance study

The discrimination of a fully matched, unlabeled KRAS wild-type (WT) (C-G) target sample with respect to three of the most frequent KRAS codon mutations (G12 S (C-A), G12 R (C-C), G12C (C-T)) was investigated using an optimized detection strategy involving surface plasmon resonance (SPR), based on optimized probe-surface density and ionic strength control. The changes observed in the SPR signal were always larger for WT compared with the single-mismatch target DNA oligonucleotides, and were aligned with the theoretical energy differences between the base pair C-G, C-T, C-A, C-C. Hybridization rates of ∼10⁶M^-1s^-1 were detected without the introduction of high temperature and labels, usually needed in conventional hybridization methods. One hundred percent mutation discrimination of the matched KRAS wild-type (C-G) sequence with respect to three mismatched G12C (C-T), G12 S (C-A), G12 R (C-C) target sequences was achieved.