Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips

Electrical potential-assisted DNA-RNA hybridization for rapid microRNA extraction

Analysis of microRNAs (miRNAs) is important in cancer diagnostics and therapy. Conventional methods used to extract miRNA for analysis are generally time-consuming. A novel approach for rapid and sensitive extraction of miRNAs is urgently need for clinical applications. Herein, a novel strategy based on electrical potential-assisted DNA-RNA hybridization was designed for miRNA extraction. The entire extraction process was accomplished in approximately 3 min, which is much shorter than the commercial adsorption column method, at more than 60 min, or the TRIzol method, at more than 90 min. Additionally, the method offered the advantages of simplicity and specificity during the extraction process by electrical potential-assisted hybridization of single-stranded DNA and RNA. Taking let-7a as an example, satisfactory results were achieved for miRNA extraction in serum, demonstrating the applicability in miRNA nucleic acid amplification.

Electric field-enhanced electrochemical CRISPR biosensor for DNA detection

DNA detection plays an important role in the rapid screening of cancers and early diagnosis of infectious diseases. Here, we developed a simple, versatile, electric field-enhanced (EFE), electrochemical CRISPR biosensor to detect DNA targets in a homogeneous solution phase. To improve the detection sensitivity, we applied a pulsed electric field to enrich nucleic acids on the electrode surface. The EFE electrochemical CRISPR biosensor takes advantage of the diffusivity difference between electrochemical oligonucleotide probes and CRISPR-cleaved probes toward a negatively charged working electrode, enabling simple and sensitive electrochemical detection of DNA without the need for complicated immobilization processing of electrochemical probes. Our developed CRISPR biosensor directly detects unamplified human papillomavirus-16 (HPV-16) DNA with a sensitivity of 1 pM. Further, the EFE electrochemical CRISPR biosensor coupled with recombinase polymerase amplification (RPA) successfully detects HPV-16 DNA in clinical samples. Thus, the EFE electrochemical CRISPR biosensor provides a simple, robust, and sensitive detection method for nucleic acid-based molecular diagnostics.

Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules

The detection and quantification of biomarkers have numerous applications in biological research and medicine. The most widely used methods to detect nucleic acids require amplification via the polymerase chain reaction (PCR). However, errors arising from the imperfect copying fidelity of DNA polymerases, limited specificity of primers, and heat-induced damage reduce the specificity of PCR-based methods, particularly for single-nucleotide variants. Furthermore, not all analytes can be amplified efficiently. While amplification-free methods avoid these pitfalls, the specificity of most such methods is strictly constrained by probe binding thermodynamics, which for example hampers detection of rare somatic mutations. In contrast, single-molecule recognition through equilibrium Poisson sampling (SiMREPS) provides ultraspecific detection with single-molecule and single-nucleotide sensitivity by monitoring the repetitive interactions of a fluorescent probe with surface-immobilized targets. In this review, we discuss SiMREPS in comparison with other analytical approaches, and describe its utility in quantifying a range of nucleic acids and other analytes.

Electrically Guided DNA Immobilization and Multiplexed DNA Detection with Nanoporous Gold Electrodes

Molecular diagnostics have significantly advanced the early detection of diseases, where the electrochemical sensing of biomarkers (e.g., DNA, RNA, proteins) using multiple electrode arrays (MEAs) has shown considerable promise. Nanostructuring the electrode surface results in higher surface coverage of capture probes and more favorable orientation, as well as transport phenomena unique to nanoscale, ultimately leading to enhanced sensor performance. The central goal of this study is to investigate the influence of electrode nanostructure on electrically-guided immobilization of DNA probes for nucleic acid detection in a multiplexed format. To that end, we used nanoporous gold (np-Au) electrodes that reduced the limit of detection (LOD) for DNA targets by two orders of magnitude compared to their planar counterparts, where the LOD was further improved by an additional order of magnitude after reducing the electrode diameter. The reduced electrode diameter also made it possible to create a np-Au MEA encapsulated in a microfluidic channel. The electro-grafting reduced the necessary incubation time to immobilize DNA probes into the porous electrodes down to 10 min (25-fold reduction compared to passive immobilization) and allowed for grafting a different DNA probe sequence onto each electrode in the array. The resulting platform was successfully used for the multiplexed detection of three different biomarker genes relevant to breast cancer diagnosis.

Electrostatic Cycling of Hybridization Using Nonionic DNA Mimics

This study demonstrates efficient electrostatic control of surface hybridization through use of morpholinos, a charge-neutral DNA mimic, as the immobilized "probes". In addition to being compatible with low ionic strengths, use of uncharged probes renders the field interaction specific to the nucleic acid analyte. In contrast to DNA probes, morpholino probes enable facile cycling between hybridized and dehybridized states within minutes. Impact of ionic strength and temperature on the effectiveness of electrostatics to direct progress of hybridization is evaluated. Optimal electrostatic control is found when stability of probe-analyte duplexes is set so that electrostatics can efficiently switch between the forward (hybridization) and reverse (dehybridization) directions.

Saliva Liquid Biopsy for Point-of-Care Applications

Saliva is a non-invasive biofluid, which is easy to collect, transport, and store. Because of its accessibility and connection to systemic diseases, saliva is one of the best candidates for the advancement of point-of-care medicine, where individuals are able to easily monitor their health status by using portable convenient tools such as smartphones. There are a variety of scenarios with which saliva can be used: studies have been conducted on using saliva to measure stress hormones, enzyme levels, developmental disease biomarkers, and even cancer mutations. If validated biomarkers were combined with high-quality detection tools, saliva would open up a new frontier in high-quality healthcare, allowing physicians and patients to work together for real-time health monitoring and high-impact personalized preventative medicine. One of the most exciting emerging frontiers of saliva is liquid biopsy, which is a non-invasive means to assess the presence and characteristics of cancer in a patient. This article will review current basic knowledge of biomarkers, review their relation to different diseases and conditions, and explore liquid biopsy for point-of-care applications.

Direct electrical control of IgG conformation and functional activity at surfaces

We have devised a supramolecular edifice involving His-tagged protein A and antibodies to yield surface immobilized, uniformly oriented, IgG-type, antibody layers with Fab fragments exposed off an electrode surface. We demonstrate here that we can affect the conformation of IgGs, likely pushing/pulling electrostatically Fab fragments towards/from the electrode surface. A potential difference between electrode and solution acts on IgGs' charged aminoacids modulating the accessibility of the specific recognition regions of Fab fragments by antigens in solution. Consequently, antibody-antigen affinity is affected by the sign of the applied potential: a positive potential enables an effective capture of antigens; a negative one pulls the fragments towards the electrode, where steric hindrance caused by neighboring molecules largely hampers the capture of antigens. Different experimental techniques (electrochemical quartz crystal microbalance, electrochemical impedance spectroscopy, fluorescence confocal microscopy and electrochemical atomic force spectroscopy) were used to evaluate binding kinetics, surface coverage, effect of the applied electric field on IgGs, and role of charged residues on the phenomenon described. These findings expand the concept of electrical control of biological reactions and can be used to gate electrically specific recognition reactions with impact in biosensors, bioactuators, smart biodevices, nanomedicine, and fundamental studies related to chemical reaction kinetics.

Liquid biopsy for detection of actionable oncogenic mutations in human cancers and electric field induced release and measurement liquid biopsy (eLB)

Oncogenic activations by mutations in key cancer genes such as EGFR and KRAS are frequently associated with human cancers. Molecular targeting of specific oncogenic mutations in human cancer is a major therapeutic inroad for anti-cancer drug therapy. In addition, progressive developments of oncogene mutations lead to drug resistance. Therefore, the ability to detect and continuously monitor key actionable oncogenic mutations is important to guide the use of targeted molecular therapies to improve long-term clinical outcomes in cancer patients. Current oncogenic mutation detection is based on direct sampling of cancer tissue by surgical resection or biopsy. Oncogenic mutations were recently shown to be detectable in circulating bodily fluids of cancer patients. This field of investigation, termed liquid biopsy, permits a less invasive means of assessing the oncogenic mutation profile of a patient. This paper will review the analytical strategies used to assess oncogenic mutations from biofluid samples. Clinical applications will also be discussed.

Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization

Surface-confined DNA hybridization reactions are sensitive to the number and identity of DNA capture probes and experimental conditions such as the nature and the ionic strength of the electrolyte solution. When the surface probe density is high or the concentration of bulk ions is much lower than the concentration of ions within the DNA layer, hybridization is significantly slowed down or does not proceed at all. However, high-density DNA monolayers are attractive for designing high-sensitivity DNA sensors. Thus, circumventing sluggish DNA hybridization on such interfaces allows a high surface concentration of target DNA and improved signal/noise ratio. We present potential-assisted hybridization as a strategy in which an external voltage is applied to the ssDNA-modified interface during the hybridization process. Results show that a significant enhancement of hybridization can be achieved using this approach.

A single-molecule view of conformational switching of DNA tethered to a gold electrode

Surfaces that can actively regulate binding affinities or catalytic properties in response to external stimuli are a powerful means to probe and control the dynamic interactions between the cell and its microenvironment. Active surfaces also enable novel functionalities in biosensors and biomolecular separation technologies. Although electrical stimuli are often appealing due to their speed and localization, the operation of these electrically activated surfaces has mostly been characterized with techniques averaging over many molecules. Without a molecular-scale understanding of how biomolecules respond to electric fields, achieving the ultimate detection sensitivity or localized biological perturbation with the ultimate resolution would be difficult. Using electrochemical atomic force microscopy, we are able to follow the conformational changes of individual, short DNA molecules tethered to a gold electrode in response to an applied potential. Our study reveals conformations and dynamics that are difficult to infer from ensemble measurements: defects in the self-assembled monolayer (SAM) significantly perturb conformations and adsorption/desorption kinetics of surface-tethered DNA; on the other hand, the SAM may be actively molded by the DNA at different potentials. These results underscore the importance of characterizing the systems at the relevant length scale in the development of electrically switchable biofunctional surfaces.

Nucleic acid-based diagnostics for infectious diseases in public health affairs

Infectious diseases, mostly caused by bacteria and viruses but also a result of fungal and parasitic infection, have been one of the most important public health concerns throughout human history. The first step in combating these pathogens is to get a timely and accurate diagnosis at an affordable cost. Many kinds of diagnostics have been developed, such as pathogen culture, biochemical tests and serological tests, to help detect and fight against the causative agents of diseases. However, these diagnostic tests are generally unsatisfactory because they are not particularly sensitive and specific and are unable to deliver speedy results. Nucleic acid-based diagnostics, detecting pathogens through the identification of their genomic sequences, have shown promise to overcome the above limitations and become more widely adopted in clinical tests. Here we review some of the most popular nucleic acid-based diagnostics and focus on their adaptability and applicability to routine clinical usage. We also compare and contrast the characteristics of different types of nucleic acid-based diagnostics.

Electrokinetic effects on detection time of nanowire biosensor

We develop a multiphysics model to study the contribution of electrokinetics on the biomolecular detection process and provide a physical explanation of the two to three orders of magnitude difference in detection time between experimental results and theoretical predications at ultralow concentration. The electrokinetic effects, including electrophoretic force and electroosmotic flow, have been systematically studied under various sensor design and test conditions. In a typical single nanowire-based sensor, it is found that electrokinetic effects could result in a reduction of detection time over 90 times, compared with that induced by pure biomolecular diffusion. The detection time difference is further enhanced by increasing the applied gate voltage or the number of nanowires. It is proposed that accelerated biomolecular detection at ultralow concentration could be achieved by appropriate combinations of electrokinetic effects and nanowire sensor design.

Enhancing DNA hybridization kinetics through constriction-based dielectrophoresis

The enhancement of signal sensitivity through the scaling-down of sensors presents mass transport limitations that can arrest the sensitivity gains obtained as a result of miniaturization. To alleviate these limitations, we study the application of constriction-based dielectrophoresis methods to enhance transport through pre-concentration of target DNA in the vicinity of the diffusion layer of the sensor, on which capture probe DNA molecules were immobilized. We demonstrate that constriction-based DEP pre-concentration was not impeded by scaling-down of the sensor, as long as the sensor electrode was composed of nanostructured edges and was coupled to an equally scaled down insulating constriction within a microfluidic channel to enhance the focusing effects of the constrictions and edges. Furthermore, as a result of the high focusing fields, pre-concentration of single-stranded target DNA occurred in the vicinity of the sensor pad within the relatively high ionic strength buffers required for DNA hybridization, with minimal degradation of capture probe molecules. Finally, constriction-based DEP resulted in an almost immediate pre-concentration of target DNA in the vicinity of the sensor electrode diffusion layer, resulting in a ten-fold enhancement of the DNA hybridization kinetics at target concentration values down to the sensitivity limit of 10 pM for the sensor platform.

Development of new substrates for high-sensitive genotyping of minority mutated alleles

An unsurpassed level of sensitivity was reached in the detection of minority mutated alleles. A low-density microarray was printed on a substrate specifically designed to provide an interference effect which amplifies the collection of the light emitted on the support and reinforces the intensity of excitation light. Optimal performance of the array was obtained by maximizing the probe density and the binding efficiency to the target through a polymeric coating made by the adsorption of a copolymer of N,N-dimethylacrylamide (97% of moles), N,N-acryloyloxysuccinimide (2%) and 3-(trimethoxysilyl)propyl methacrylate (1%) synthesized by free radical copolymerization. The new substrate was used in the identification of fetal mutations in the maternal plasma DNA. Amino-modified amplicons from genomic DNA corresponding to the locus of eight beta-thalassemia mutations were immobilized and interrogated with dual-color oligonucleotide targets. Compared with the conventional glass substrates, the new substrate showed a great enhancement of fluorescence signals thanks to the combination of the optics with the highly efficient polymeric coating, allowing specific detection of all mutations. The high sensitivity and selectivity obtained made it possible to develop assays for the identification of paternally inherited mutations on fetal DNA in the maternal plasma in couples at risk for beta-thalassemia.

Cationic copolymer-mediated DNA immobilization: interfacial structure and composition as determined by ellipsometry, dual polarization interferometry, and neutron reflection

DNA immobilization onto support surfaces is required in biotechnological applications such as microarrays and gene delivery. This important interfacial molecular process can be mediated from a preadsobred cationic polymer. There is, however, a lack of understanding over the control of the interfacial composition and structural distribution of the DNA immobilized. We have used a combined approach of spectroscopic ellipsometry (SE), dual polarization interferometry (DPI) and neutron reflection (NR) to determine the interfacial polymer adsorption and the subsequent DNA binding. Cationic diblock copolymers incorporating 30 phosphorylcholine (PC) groups and different diethylaminoethyl groups, referred to as MPC30-DEAn, were chosen because of their well-defined molecular architecture. While our studies revealed different effects of surface charge and hydrophobicity, the amount of copolymers adsorbed on both model surfaces showed a broad trend of increase with solution pH, indicating a strong effect arising from pH-dependent charge density on the copolymers. In contrast, the copolymer structure and solution concentration showed a weak effect under the conditions studied. The subsequent DNA binding at pH 7 showed that on both surfaces the amount of DNA immobilized followed an approximate 1:1 charge interaction for all different DNA samples studied, irrespective of single or double strand, or different DNA size, indicating the dominant effect of electrostatic interaction between the two species. Both DPI and NR revealed consistent thickness increase upon DNA binding. Furthermore, with increasing DNA size, the interfacial layer became much thicker, and charge interaction drove more extensive interfacial mixing between the two species. Our results show that the amount of DNA immobilized is controlled by the amount of cationic copolymer preadsorbed that is in turn controlled by the solution pH and surface chemistry but that is barely affected by the type and concentration of DNA or cationic copolymer.

Dynamic control of biomolecular activity using electrical interfaces

The development of novel interfaces between electronic devices and biological systems is a rapidly evolving research area that may lead to new insights into biological behavior, clinical diagnostics and therapeutic treatments. Full electrical integration into biological networks will require bioactuators which can translate an electrical pulse into a specific biochemical signal the system can understand. One approach has been the use of electrostatic fields near the surface of an electrode to locally alter the ionic and electrostatic environment within an ionic double layer. In this scheme, normally active biological macromolecules are suspended in a 'low-salt buffer' that is depleted of necessary ions, such as Mg2+, rendering them inactive. Upon application of an electrical potential these ions are concentrated at the electrode surface, locally activating biomolecular function. An initial demonstration of this method is presented for the dynamic polymerization of actin filaments from electrode surfaces. In principle, electrodes functionalized with different proteins could be individually activated to translate an electrical potential into a specific biochemical signal or behavior.

Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization reactions are considered to occur in isolation; and multiplex hybridization, where desired and competitive cross-hybrid reactions between all possible pairs of strands are considered. In addition, sensitivities of the hybridization process of the perfect match duplex, to temperature, target concentration, and existence of sequence homology with other strands, are examined. This general approach also considers explicit sequence-dependent interactions between targets and probes involved in the reactions. Sequence-dependent stabilities of all perfect match and mismatch duplex complexes are explicitly considered and effects of relative stability of cross-hybrid complexes are also explored. Results reveal several interdependent factors that strongly influence DNA multiplex hybridization behavior. These include: relative concentrations of all probes and targets; relative thermodynamic stability of all perfect match and mismatch complexes; sensitivity to temperature, particularly for mismatches; and amount of sequence homology shared by the probe and target strands in the multiplex mix.