We report a simple electrochemical method referred to as "eMethylsorb" for the detection of DNA methylation. The method relies on the base dependent affinity interaction of DNA with gold. The methylation status of DNA is quantified by monitoring the electrochemical current as a function of the relative adsorption level of bisulphite treated DNA samples onto a bare gold electrode. This method can successfully distinguish methylated and unmethylated epigenotypes at single CpG resolution.

A new strategy to produce stable barcodes using biological self‐assembly of streptavidin‐ and biotin‐functionalized quantum dots is reported. Such systems are of potential use in multiplexed immunoassay and nucleic acid hybridization assays.

BACKGROUND: DNA methylation is a potential source of disease biomarkers. Typically, methylation levels are measured at individual cytosine/guanine (CpG) sites or over a short region of interest. However, regions of interest often show heterogeneous methylation comprising multiple patterns of methylation (epialleles) on individual DNA strands. Heterogeneous methylation is largely ignored because digital methods are required to deconvolute these usually complex patterns of epialleles. Currently, only singlemolecule approaches, such as next generation sequencing (NGS), can provide detailed epiallele information. Because NGS is not yet feasible for routine practice, we developed a single-molecule-like approach, named for epiallele quantification (EpiQ).

DNA methylation has the potential to be a clinically important biomarker in cancer. This communication reports a real-time and label-free biosensing strategy for DNA methylation detection in cancer cell line. This has been achieved by using surface plasmon resonance biosensing combined with the highly specific molecular inversion probe based amplification method, which requires only 50 ng of bisufite treated genomic DNA.DNA methylation is the process in which a methyl group is added to the carbon-5 position of cytosine in a CpG dinucleotide 1 . Differences in DNA methylation levels between normal and cancer cells have been proposed as biomarkers to retrieve clinically relevant information regarding the stage of disease or cancer subtype, which in turn might help to underpin prognosis and appropriate mode of treatment.2 Much attention has been focused on the detection of DNA methylation using different sensors schemes, 3-9 however the most widely used techniques for DNA methylation are bisulfite sequencing 10 and affinityenrichement. 5 Bisulfite-sequencing is a very sensitive technique capable of retrieving single cytosine methylation information, but the methodology itself is complex and prone to DNA amplification errors. Detecting a series of several CpG sites in a region (e.g., the promoter region) has the potential to extract the desired methylation information without requiring single CpG site resolution. In this context, affinity based methods using methyl binding domain proteins that specifically recognize methylated-CpG rich regions offer a better alternative. While all these methods have excellent analytical performances in detecting regional DNA methylation, they are poorly suited for routine diagnostics due to the high running cost, long assay time, complicated chemistries and detection procedures. Surface Plasmon resonance (SPR) is one of the most powerful alternative analytical methods for circumventing these type of problems, while providing label-free, real-time, reproducible and sensitive biomolecular detection.11 In SPR biosensing, the binding of the target analyte to its surface-bound receptor counterpart produces a local change in refractive index over time at the sensing surface, which is quantitative with the relative mass increase associated with target capture, thus enabling the real-time and label-free readout of these targets 12. This method has previously been used to detect regional DNA methylation using proteins with affinity to CpG rich regions. 6,9 However, the reproducibility of affinity based methods depends on antibody specificity and CG-density. 13 Herein, we report a novel strategy which synergistically couples the label-free, real-time nature of the SPR biosensor with the sensitive, specific and multiplexing capability of the molecular inversion probes (MIPs) for accurate detection of regional DNA methylation. The principle involves utilizing a MIP, which is a single stranded oligonucleotide (ss-oligo) capable of hybridizing to a genomic DNA target by two inverted recognition e...

We show that well-defined three-dimensional nanostructures of functional enzymes can be controllably fabricated by layer-by-layer assembly of avidin and biotinylated horseradish peroxidase on micro-contact printing patterned surface templates.

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The analysis of DNA methylation is becoming increasingly important both in the clinic and also as a research tool to unravel key epigenetic molecular mechanisms in biology. Current methodologies for the quantification of regional DNA methylation (i.e., the average methylation over a region of DNA in the genome) are largely affected by comprehensive DNA sequencing methodologies which tend to be expensive, tedious, and time-consuming for many applications. Herein, we report an alternative DNA methylation detection method referred to as "Methylsorb", which is based on the inherent affinity of DNA bases to the gold surface (i.e., the trend of the affinity interactions is adenine > cytosine ≥ guanine > thymine).1 Since the degree of gold-DNA affinity interaction is highly sequence dependent, it provides a new capability to detect DNA methylation by simply monitoring the relative adsorption of bisulfite treated DNA sequences onto a gold chip. Because the selective physical adsorption of DNA fragments to gold enable a direct read-out of regional DNA methylation, the current requirement for DNA sequencing is obviated. To demonstrate the utility of this method, we present data on the regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231 cells. The methylation status of these regions was obtained from the change in relative mass on gold surface with respect to relative adsorption of an unmethylated DNA source and this was detected using surface plasmon resonance (SPR) in a label-free and real-time manner. We anticipate that the simplicity of this method, combined with the high level of accuracy for identifying the methylation status of cytosines in DNA, could find broad application in biology and diagnostics.

We report a tunable alternating current electro-hydrodynamic (ac-EHD) force which drives lateral fluid motion within a few nanometers of an electrode surface. Because the magnitude of this fluid shear force can be tuned externally (e.g., via the application of an ac electric field), it provides a new capability to physically displace weakly (nonspecifically) bound cellular analytes. To demonstrate the utility of the tunable nanoshearing phenomenon, we present data on purpose-built microfluidic devices that employ ac-EHD force to remove nonspecific adsorption of molecular and cellular species. Here, we show that an ac-EHD device containing asymmetric planar and microtip electrode pairs resulted in a 4-fold reduction in nonspecific adsorption of blood cells and also captured breast cancer cells in blood, with high efficiency (approximately 87%) and specificity. We therefore feel that this new capability of externally tuning and manipulating fluid flow could have wide applications as an innovative approach to enhance the specific capture of rare cells such as cancer cells in blood.