Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

Loop-Mediated Isothermal Amplification-Based Microfluidic Platforms for the Detection of Viral Infections

Purpose of Review

Easy-to-use, fast, and accurate virus detection method is essential for patient management and epidemic surveillance, especially during severe pandemics. Loop-mediated isothermal amplification (LAMP) on a microfluidic platform is suitable for detecting infectious viruses, regardless of the availability of medical resources. The purpose of this review is to introduce LAMP-based microfluidic devices for virus detection, including their detection principles, methods, and application.

Recent Findings

Facing the uncontrolled spread of viruses, the large-scale deployment of LAMP-based microfluidic platforms at the grassroots level can help expand the coverage of nucleic acid testing and shorten the time to obtain test reports. Microfluidic chip technology is highly integrated and miniaturized, enabling precise fluid control for effective virus detection. Performing LAMP on miniaturized systems can reduce analysis time, reagent consumption and risk of sample contamination, and improve analytical performance.

Summary

Compared to traditional benchtop protocols, LAMP-based microfluidic devices reduce the testing time, reagent consumption, and the risk of sample contamination. In addition to simultaneous detection of multiple target genes by special channel design, microfluidic chips can also integrate digital LAMP to achieve absolute quantification of target genes.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Polariton-assisted manipulation of energy relaxation pathways: donor-acceptor role reversal in a tuneable microcavity

Resonant interaction between excitonic transitions of molecules and localized electromagnetic field allows the formation of hybrid light-matter polaritonic states. This hybridization of the light and the matter states has been shown to significantly alter the intrinsic properties of molecular ensembles placed inside the optical cavity. Here, we have observed strong coupling of excitonic transition in a pair of closely located organic dye molecules demonstrating an efficient donor-to-acceptor resonance energy transfer with the mode of a tuneable open-access cavity. Analysing the dependence of the relaxation pathways between energy states in this system on the cavity detuning, we have demonstrated that predominant strong coupling of the cavity photon to the exciton transition in the donor dye molecule can lead not only to an increase in the donor-acceptor energy transfer, but also to an energy shift large enough to cause inversion between the energy states of the acceptor and the mainly donor lower polariton energy state. Furthermore, we have shown that the polariton-assisted donor-acceptor chromophores' role reversal or "carnival effect" not only changes the relative energy levels of the donor-acceptor pair, but also makes it possible to manipulate the energy flow in the systems with resonant dipole-dipole interaction and direct energy transfer from the acceptor to the mainly donor lower polariton state. Our experimental data are the first confirmation of the theoretically predicted possibility of polariton-assisted energy transfer reversal in FRET systems, thus paving the way to new avenues in FRET-imaging, remote-controlled chemistry, and all-optical switching.

Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay

Two types of clinically important nucleic acid biomarkers, microRNA (miRNA) and circulating tumor DNA (ctDNA) were detected and quantified from human serum using an amplification-free fluorescence hybridization assay. Specifically, miRNAs hsa-miR-223-3p and hsa-miR-486-5p with relevance for rheumatoid arthritis and cancer related mutations BRAF and KRAS of ctDNA were directly measured. The required oligonucleotide probes for the assay were rationally designed and synthesized through a novel "clickable" approach which is time and cost-effective. With no need for isolating nucleic acid components from serum, the fluoresence-based assay took only 1 hour. Detection and absolute quantification of targets was successfully achieved despite their notoriously low abundance, with a precision down to individual nucleotides. Obtained miRNA and ctDNA amounts showed overall a good correlation with current techniques. With appropriate probes, our novel assay and signal boosting approach could become a useful tool for point-of-care measuring other low abundance nucleic acid biomarkers.

DNA Nanomachines for Identifying Cancer Biomarkers in Body Fluids and Cells

Identifying molecular biomarkers promises to significantly improve the accuracy in cancer diagnosis at its early stage. DNA nanomachines, which are designable and switchable nanostructures made of DNA, show broad potential to detect tumor biomarkers with noninvasive, inexpensive, highly sensitive, and highly specific advantages. This Feature summarizes the recent DNA nanomachine-based platforms for the early detection of cancer biomarkers, both from body fluids and in cells.

5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches

Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.

Serological comparison of systemic lupus erythematosus with neuropsychiatric lupus using synthetic nucleic acid antigens

Neuropsychiatric systemic lupus erythematosus is an autoimmune disorder characterized by an irregular exchange between the central nervous system and the immune system, leading to the outbreak of neurological conditions with possible disabling effects. Although neuropsychiatric systemic lupus erythematosus is the most common expression of lupus condition, it is still poorly understood. In this study, we focus on the development of an advantageous method based on the application of synthetic nucleic acids and protein-based antigen arrays in order to characterize autoreactive antibodies in neuropsychiatric systemic lupus erythematosus. We confirmed the benefits of using synthetic oligonucleotides such as assay reproducibility, elevated affinity and specificity to autoreactive antibodies. We also demonstrated presence of autoantibodies towards three particular synthetic double stranded antigens and verify similarity of antinuclear antibody patterns in ordinary lupus and neuropsychiatric systemic lupus erythematosus.

Antibodies to synthetic citrullinated peptide epitope correlate with disease activity and flares in rheumatoid arthritis

Rheumatoid arthritis (RA), caused by the abnormal recognition of human joint cells by autoimmune antibodies, remains the world’s most prevalent autoimmune disease, with over five million people affected and as much as 4% of the population at risk of RA. To prevent rapid disease development, hormonal and anti-inflammatory therapies require fast and reliable RA diagnosis. However, difficulty in detecting early specific biomarkers for RA means that it is unclear when treatment needs to begin. Here, we combined synthesis of citrullinated peptide epitopes with molecular diagnostics to verify a new specific biomarker for early RA diagnosis and flare prediction. A fibrinogen-derived 21-amino-acid-long citrullinated peptide showed high reactivity toward autoantibodies in RA samples. Additionally, the level of antibodies to this epitope was elevated prior to flares. In contrast, other citrullinated protein variants had lower reactivity and poorer sensitivity to disease activity. In conclusion, fibrinogen-derived epitope E2 subjected to citrullination facilitated a reliable RA diagnosis with a strong correlation to disease activity. This is of a high value for the diagnosis and management of RA patients who respond poorly to treatment.

Zinc(ii), copper(ii) and cadmium(ii) complexes as fluorescent chemosensors for cations

The fluorescence chemosensing behavior of Zn(ii), Cu(ii), and Cd(ii) based complexes toward cations has been described. Cation detection via conventional mechanisms, metal-metal exchange and chemodosimetric approaches along with the importance of metal ions and the scope, significance, and challenges with regard to the detection of cations by metal complex based probes will be discussed in detail. The fundamentals of photophysical behavior and mechanisms involved in the fluorescence detection of analytes will also be described. This article provides a detailed overview of Zn(ii), Cu(ii), and Cd(ii) based complexes as fluorescent probes for cations, together with essential discussions pertaining to detection mechanisms.

Discrimination of the V600E Mutation in BRAF by Rolling Circle Amplification and Förster Resonance Energy Transfer

The quantification of very low concentrations of circulating tumor DNA (ctDNA) biomarkers from liquid biopsies has become an important requirement for clinical diagnostics and personalized medicine. In particular, the simultaneous detection of wild-type (WT) dsDNA and their cancer-related counterparts presenting single-point mutations with simple, sensitive, specific, and reproducible technologies is paramount for ctDNA assays in clinical practice. Here, we present the development and evaluation of an amplified dsDNA assay based on a combination of isothermal rolling circle amplification (RCA) and time-gated Förster resonance energy transfer (TG-FRET) between a Tb donor and two dye (Cy3.5 and Cy5.5) acceptors. The RCA-FRET assay is free of washing and separation steps and can quantify both WT and mutated (MT) (V600E) dsDNA in the BRAF gene from a single sample in the 75 fM to 4.5 pM (4.5 × 10⁵ to 2.7 × 10⁷ copies) concentration range. This assay includes all steps from denaturation of the dsDNA targets to the final duplexed quantification of WT and MT targets. High assay performance at different dsDNA sequence lengths and high target specificity even in the presence of a large excess of nonspecific cell-free DNA from human plasma samples demonstrated the applicability to clinical samples. The RCA-FRET single-point mutation sensor has the potential to become an important complementary technique for analyzing liquid biopsies in advanced cancer diagnostics.

The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations

Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.

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.

Divide and Control: Comparison of Split and Switch Hybridization Sensors

Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.