Visual DNA - Identification of DNA sequence variations by bead trapping

Abstract

In this paper we describe a method that uses the nearly covalent strength biotin-streptavidin interaction to attach a paramagnetic bead of micrometer size to a DNA molecule of nanometer size, scaling up the spatial size of a query DNA strand by a factor of 1000, making it visible to the human eye. The use of magnetic principles enables rapid binding and washing of detector beads, facilitating a readout of amplified DNA sequences in a few minutes. Here we exemplify the method on mitochondrial DNA variations using an array platform. Visual identification and documentation can be performed with an ordinary mobile phone equipped with a built-in camera.

Visual DNA as a diagnostic tool

“…The described proof of principle employs the Visual DNA concept [6] that is based on a magnetic bead detection platform. In short, it is constituted of an integrated system with a DNA microarray, an on-chip multiplex proteasemediated allele-specific primer extension [17,18], and a visual detection of the mutations by trapping of micrometersized superparamagnetic beads allowing final investigation and genotype characterization by the naked eye.…”

“…The concept of Visual DNA [6] provides efficient and accurate genotype visualization of genetic markers due to the highly improved readout. Printing and immobilization of allele-specific primers in an array format onto a glass slide provides the means for running an in situ allele-discriminating assay with biotinylated nucleotides.…”

An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis

“…Lee et al developed a recirculating microfluidic device that repeatedly flowed samples to a probe array using a peristaltic pump to reduce the hybridization time from 6 to 2 h. 20 Recently, Karsenty et al employed an isotachophoretic method to focus targets to arrays in a straight channel, demonstrating two orders of magnitude improvement in limit of detection. 21 In parallel with the development of the microfluidic-based microarray, a variety of non-fluorescence-based detection methods, including electrochemical measurement, 22,23 chemiluminescence, 24 gold, 25 and magnetic particles, 26 have been demonstrated on microchips to further reduce the cost of the systems. For example, Pettersson et al utilized a magnetic field to deliver magnetic bead (MB)-labeled target nucleic acids to complementary probes immobilized on a glass surface in less than 15 s. 19 The detection of the hybridization results was achieved instantly since the beads became visible on the surface.…”

A lateral flow protein microarray for rapid determination of contagious bovine pleuropneumonia status in bovine serum

“…However, protein microarray assays are still largely limited to laboratory conditions, and efforts have been made in development of solutions that can make microarray technology more accessible to low-resource and on-site settings (Carter and Cary, 2007;Stahl et al, 2007;Leblanc et al, 2009;Gantelius et al, 2009).…”