Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms

Recent Progress in Single-Nucleotide Polymorphism Biosensors

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

The Promise of Nanotechnology in Personalized Medicine

Both personalized medicine and nanomedicine are new to medical practice. Nanomedicine is an application of the advances of nanotechnology in medicine and is being integrated into diagnostic and therapeutic tools to manage an array of medical conditions. On the other hand, personalized medicine, which is also referred to as precision medicine, is a novel concept that aims to individualize/customize therapeutic management based on the personal attributes of the patient to overcome blanket treatment that is only efficient in a subset of patients, leaving others with either ineffective treatment or treatment that results in significant toxicity. Novel nanomedicines have been employed in the treatment of several diseases, which can be adapted to each patient-specific case according to their genetic profiles. In this review, we discuss both areas and the intersection between the two emerging scientific domains. The review focuses on the current situation in personalized medicine, the advantages that can be offered by nanomedicine to personalized medicine, and the application of nanoconstructs in the diagnosis of genetic variability that can identify the right drug for the right patient. Finally, we touch upon the challenges in both fields towards the translation of nano-personalized medicine.

Thinking outside the shell: novel sensors designed from plasmon-enhanced fluorescent concentric nanoparticles

The alteration of photophysical properties of fluorophores in the vicinity of a metallic nanostructure, a phenomenon termed plasmon- or metal-enhanced fluorescence (MEF), has been investigated extensively and used in a variety of proof-of-concept demonstrations over the years. A particularly active area of development in this regard has been the design of nanostructures where fluorophore and metallic core are held in a stable geometry that imparts improved luminosity and photostability to a plethora of organic fluorophores. This minireview presents an overview of MEF-based concentric core-shell sensors developed in the past few years. These architectures expand the range of applications of nanoparticles (NPs) beyond the uses possible with fluorescent molecules. Design aspects that are being described include the influence of the nanocomposite structure on MEF, notably the dependence of fluorescence intensity and lifetime on the distance to the plasmonic core. The chemical composition of nanocomposites as a design feature is also discussed, taking as an example the use of non-noble plasmonic metals such as indium as core materials to enhance multiple fluorophores throughout the UV-Vis range and tune the sensitivity of halide-sensing fluorophores operating on the principle of collisional quenching. Finally, the paper describes how various solid substrates can be functionalized with MEF-based nanosensors to bestow them with intense and photostable pH-sensitive properties for use in fields such as medical therapy and diagnostics, dentistry, biochemistry and microfluidics.

Application of magnetic nanoparticles in nucleic acid detection

Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.

An aptamer based fluorometric assay for amyloid-β oligomers using a metal-organic framework of type Ru@MIL-101(Al) and enzyme-assisted recycling

Amyloid-beta (Aβ) oligomers causing neuron damage are regarded as potential therapeutic targets and diagnostic markers for Alzheimer's disease (AD). A homogeneous turn-on fluorometric aptasensor is described for Aβ oligomers. It is highly selective and non-invasive and based on (a) the use of a luminescent metal-organic framework carrying aptamer-modified AuNPs (L-MOF/Apt-Au) as tracking agent, and (b) enzyme-assisted target recycling signal amplification. The tracking agent does not emit fluoresce by fluorescence resonance energy transfer (FRET) between the luminescent MOF as donor and Apt-Au as the acceptor under the excitation wavelength of 466 nm. When Aβ oligomers are added to the tracking agent solution, the Apt-Au on tracking agent can preferentially bind with Aβ oligomers and then be released. This turns the "off" signal of the luminescent MOF tracer to the "on" state. The enzyme (Rec Jf exonuclease) added into the supernatant further improves sensitivity due to enzyme-assisted target-recycling signal amplification. The assay has an excellent linear response to Aβ oligomers from 1.0 pM to 10 nM, with a detection limit of 0.3 pM. This homogeneous turn-on fluorometric method is expected to have potential and applications in clinical diagnosis. Graphical abstractSchematic representation of fluorometric assay for amyloid-β oligomers based on luminescence metal-organic framework nanocomposites as tracking agent with exonuclease-assisted target recycling.

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.

Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence

Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes.

Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors

Current diagnostic tools for Mycobacterium tuberculosis (Mtb) have many disadvantages including low sensitivity, slow turnaround times, or high cost. Accurate, easy to use, and inexpensive point of care molecular diagnostic tests are urgently needed for the analysis of multidrug resistant (MDR) and extensively drug resistant (XDR) Mtb strains that emerge globally as a public health threat. In this study, we established proof-of-concept for a novel diagnostic platform (TB-DzT) for Mtb detection and the identification of drug resistant mutants using binary deoxyribozyme sensors (BiDz). TB-DzT combines a multiplex PCR with single nucleotide polymorphism (SNP) detection using highly selective BiDz sensors targeting loci associated with species typing and resistance to rifampin, isoniazid and fluoroquinolone antibiotics. Using the TB-DzT assay, we demonstrated accurate detection of Mtb and 5 mutations associated with resistance to three anti-TB drugs in clinical isolates. The assay also enables detection of a minority population of drug resistant Mtb, a clinically relevant scenario referred to as heteroresistance. Additionally, we show that TB-DzT can detect the presence of unknown mutations at target loci using combinatorial BiDz sensors. This diagnostic platform provides the foundation for the development of cost-effective, accurate and sensitive alternatives for molecular diagnostics of MDR- and XDR-TB.

DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection

The Nobel prize in chemistry in 2016 was awarded for 'the design and synthesis of molecular machines'. Here we designed and assembled a molecular machine for the detection of specific RNA molecules. An association of several DNA strands, named multifunctional DNA machine for RNA analysis (MDMR1), was designed to (i) unwind RNA with the help of RNA-binding arms, (ii) selectively recognize a targeted RNA fragment, (iii) attract a signal-producing substrate and (iv) amplify the fluorescent signal by catalysis. MDMR1 enabled detection of 16S rRNA at concentrations ∼24 times lower than that by a traditional deoxyribozyme probe.