Roya Tavallaie

Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation

Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation.

Toward biosensors for the detection of circulating microRNA as a cancer biomarker: an overview of the challenges and successes

Considerable attention has been dedicated to developing feasible point-of-care tests for cancer diagnosis and prognosis. An ideal biomarker for clinical use should be easily assayed with minimally invasive medical procedures but possess high sensitivity and specificity. The role of microRNAs (miRNAs) in the regulation of different cellular processes, the unique altered patterns in cancer patients and presence in body fluids in the stable form, points to their clinical utility as blood-based biomarkers for diagnosis, prognosis, and treatment of cancer. Although a variety of selective and sensitive laboratory-based methods are already exist for the detection of circulating miRNA, having a simple, low-cost and rapid assay, which could be routinely used in clinical practice, is still required. Among different approaches that have developed for circulating miRNA detection, biosensors, due to the high sensitivity, ease of use, short assay time, non-toxic experimental steps, and adaptability to point-of-care testing, exhibit very attractive properties for developing portable devices. With this view, we present an overview of some of the challenges that still need to be met to be able to use circulating miRNAs in clinical practice, including their clinical significance, sample preparation, and detection. In particular, we highlight the recent advances in the rapidly developing area of biosensors for circulating miRNA detection, along with future prospects and challenges.

Quantitative determination of target gene with electrical sensor

Integrating loop-mediated isothermal amplification (LAMP) with capacitively coupled contactless conductivity detection (C4D), we have developed an electrical sensor for the simultaneous amplification and detection of specific sequence DNA. Using the O26-wzy gene as a model, the amount of initial target gene could be determined via the threshold time obtained by monitoring the progression of the LAMP reaction in real time. Using the optimal conditions, a detection limit of 12.5 copy/μL can be obtained within 30 min. Monitoring the LAMP reaction by C4D has not only all the advantages that existing electrochemical methods have, but also additional attractive features including being completely free of carryover contamination risk, high simplicity and extremely low cost. These benefits all arise from the fact that the electrodes are separated from the reaction solution, that is C4D is a contactless method. Hence in proof of principle, the new strategy promises a robust, simple, cost-effective and sensitive method for quantitative determination of a target gene, that is applicable either to specialized labs or at point-of-care.

Nucleic-acid recognition interfaces: how the greater ability of RNA duplexes to bend towards the surface influences electrochemical sensor performance

The influence of RNA versus DNA on the performance of electrochemical biosensors where redox-labelled nucleic acid duplexes bend towards the electrode surface has been assessed. Faster electron transfer was observed for duplexes containing RNA, suggesting duplexes with RNA are more flexible. These data are of particular importance for microRNA biosensors.

Dual Signaling DNA Electrochemistry: An Approach To Understand DNA Interfaces

Electrochemical DNA biosensors composed of a redox marker modified nucleic acid probe tethered to a solid electrode is a common experimental construct for detecting DNA and RNA targets, proteins, inorganic ions, and even small molecules. This class of biosensors generally relies on the binding-induced conformational changes in the distance of the redox marker relative to the electrode surface such that the charge transfer is altered. The conventional design is to attach the redox species to the distal end of a surface-bound nucleic acid strand. Here we show the impact of the position of the redox marker, whether on the distal or proximal end of the DNA monolayer, on the DNA interface electrochemistry. Somewhat unexpectedly, greater currents were obtained when the redox molecules were located on the distal end of the surface-bound DNA monolayer, notionally furthest away from the electrode, compared with currents when the redox species were located on the proximal end, close to the electrode. Our results suggest that a limitation in ion accessibility is the reason why smaller currents were obtained for the redox markers located at the bottom of the DNA monolayer. This understanding shows that to allow the quantification of the amount of redox labeled target DNA strand that hybridizes to probe DNA immobilized on the electrode surface, the redox species must be on the distal end of the surface-bound duplex.

Nucleic acid hybridization on an electrically reconfigurable network of gold-coated magnetic nanoparticles enables microRNA detection in blood

There is intense interest in quantifying the levels of microRNA because of its importance as a blood-borne biomarker. The challenge has been to develop methods that can monitor microRNA expression both over broad concentration ranges and in ultralow amounts directly in a patient’s blood. Here, we show that, through electric-field-induced reconfiguration of a network of gold-coated magnetic nanoparticles modified by probe DNA (DNA–Au@MNPs), it is possible to create a highly sensitive sensor for direct analysis of nucleic acids in samples as complex as whole blood. The sensor is the first to be able to detect concentrations of microRNA from 10 aM to 1 nM in unprocessed blood samples. It can distinguish small variations in microRNA concentrations in blood samples of mice with growing tumours. The ultrasensitive and direct detection of microRNA using an electrically reconfigurable DNA–Au@MNPs network makes the reported device a promising tool for cancer diagnostics.An ultrasensitive miRNA sensor based on gold-coated magnetic nanoparticles modified with redox-labelled probe DNA is capable of detecting miRNA at a concentration of 10 aM to 1 nM in unprocessed blood, and following tumour-induced variation in miRNA levels.

DNA-hybridisation detection on Si(100) surfaces using light-activated electrochemistry: a comparative study between bovine serum albumin and hexaethylene glycol as antifouling layers.

Light can be used to spatially resolve electrochemical measurements on a semiconductor electrode. This phenomenon has been explored to detect DNA hybridization with light-addressable potentiometric sensors and, more recently, with light-addressable amperometric sensors based on organic-monolayer-protected Si(100). Here, a contribution to the field is presented by comparing sensing performances when bovine serum albumin (BSA) and hexaethylene glycol (OEG6) are employed as antifouling layers that resist nonspecific adsorption to the DNA-modified interface on Si(100) devices. What is observed is that both sensors based on BSA or OEG6 initially allow electrochemical distinction among complementary, noncomplementary, and mismatched DNA targets. However, only surfaces based on OEG6 can sustain electroactivity over time. Our results suggest that this relates to accelerated SiO x formation occasioned by BSA proteins adsorbing on monolayer-protected Si(100) surfaces. Therefore, DNA biosensors were analytically explored on low-doped Si(100) electrodes modified on the molecular level with OEG6 as an antifouling layer. First, light-activated electrochemical responses were recorded over a range of complementary DNA target concentrations. A linear semilog relation was obtained from 1.0 × 10-11 to 1.0 × 10-6 mol L-1 with a correlation coefficient of 0.942. Then, measurements with three independent surfaces indicated a relative standard deviation of 4.5%. Finally, selectivity tests were successfully performed in complex samples consisting of a cocktail mixture of four different DNA sequences. Together, these results indicate that reliable and stable light-activated amperometric DNA sensors can be achieved on Si(100) by employing OEG6 as an antifouling layer.