Designing anthraquinone–pyrrole redox intercalating probes for electrochemical gene detection

Allele-specific PCR with a novel data processing method based on difference value for single nucleotide polymorphism genotyping of ALDH2 gene

Single nucleotide polymorphism (SNP) analysis based on allele-specific polymerase chain reaction (AS-PCR) is a relatively effective and economical method compared with other genotyping technologies such as DNA sequencing, DNA hybridization and isothermal amplification strategies. But AS-PCR is limited by its labor-intensive optimization of reaction parameters and time-consuming result assessment. In this study, we put forward a novel idea of data processing to address this problem. SNP analysis was accomplished by AS-PCR with endpoint electrochemical detection. For each sample, two separate reactions were run simultaneously with two sets of allele-specific primers (wild-type primers for W system and mutant primers for M system). We measured their redox current signals on screen-printed electrodes once AS-PCR finished and calculated the difference value of current signals between two systems to determine the genotyping result. Based on the difference value of fluorescent signals, real-time fluorescent PCR was used to study reaction parameters in AS-PCR. With screened parameters, we obtained the genotyping results within 50 min. 36 hair-root samples from volunteers were analyzed by our method and their genotypes of ALDH2 gene (encoding aldehyde dehydrogenase 2) were totally identical with data from commercialized sequencing. Our work first employed difference value between two reaction systems to differentiate allele and provided a novel idea of data processing in AS-PCR method. It is able to promote the quick analysis of SNP in the fields of health monitor, disease precaution, and personalized diagnosis and treatment.

Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes

A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.

Bisintercalating DNA redox reporters for real-time electrochemical qLAMP

The electrochemical detection methods have emerged as a potential alternative to the bench-top optical systems in monitoring nucleic acid amplification. DNA intercalating redox reporters play a crucial role in such monitoring schemes. Here, a series of bisintercalating redox probes have been tailor-made to meet specific requirements of electrochemical quantitative loop-mediated isothermal amplification (qLAMP). The probes composed of two naphthoquinone-imidazole (NQIM) derivatives as signal motifs that are covalently bridged by different linkers (R). They are bis-NQIM-R; R = Alkane (Ak), ethylene glycol (EG) and phenyl (Ph). The linkers allow the probes to be fine-tuned for securing ideal redox reporter. DNA binding studies via electrochemical and fluorescence techniques demonstrate that the bis-NQIM-R probes possess better ds-DNA bisintercalating ability compared to their mono-analogs. The bis-NQIM-Ph was implemented in a real-time electrochemical qLAMP, for which a prototype custom-made device that can perform fully automated multiplexed analyses is devised. A single copy of Salmonella DNA was quantified in just 10 min and the performance is comparable to the benchtop fluorescence method. Thus, the bisintercalating redox reporters incorporated electrochemical detection schemes hold great promise in qLAMP.

PCR Technologies for Point of Care Testing: Progress and Perspectives

Since the Human Genome Project completed in 2000, the sequencing of the first genome, massive progress has been made by medical science in the early diagnosis and personalized therapies based on nucleic acids (NA) analysis. To allow the extensive use of these molecular methods in medical practice, scientific research is nowadays strongly focusing on the development of new miniaturized and easy-to-use technologies and devices allowing fast and low cost NA analysis in decentralized environments. It is now the era of so-called genetic "Point-of-Care" (PoC). These systems must integrate and automate all steps necessary for molecular analysis such as sample preparation (extraction and purification of NA) and detection based on PCR (Polymerase Chain Reaction) technology in order to perform, by unskilled personnel, in vitro genetic analysis near the patient (in hospital, in the physician office, clinic, or home), with rapid answers and low cost. In this review, the recent advances in genetic PoC technologies are discussed, including the extraction and PCR amplification chemistry suitable for PoC use and the new frontiers of research in this field.