Capture of genomic DNA on glass microscope slides

Abstract

It is well known that DNA strands bind to silica surfaces in the presence of high concentrations of chaotropic salts. We developed simple methods to evaluate binding and recovery of DNA on flat glass microscope slides and compared their properties to commercially available silica "spin columns". Surprisingly, genomic DNA was recovered efficiently from untreated glass slides. Binding and elution times from glass slides were optimized in experiments with DNA samples of various sizes and defined buffers. Average DNA recovery from 500 ng of input genomic DNA varied from 25-53 % for the glass slide protocol. Yields were comparable to spin columns. Human serum albumin and plasma components decreased DNA binding to glass several-fold in a concentration dependent manner. These results support the concept of using flat glass slides as DNA purification surfaces in microfluidics devices for PCR sample preparation. Keywords DNA extraction; silica surfaces; PCR; microfluidicsThe use of powdered glass or other high surface area silica materials has been widely adopted as a basic technique for purifying DNA from biological samples [1]. DNA strands bind efficiently to silica particles in the presence of high concentrations of chaotropic salts such as guanidinium thiocyanate or sodium perchlorate. After washing away contaminating substances with high salt buffers, the bound DNA is released from the silica surface in the presence of water or low salt buffer. The recovered DNA is suitable for use in PCR or other amplification methods. These methods are used extensively in medical diagnostics and forensics, in recombinant technology and for molecular genetics.Silica-based DNA purification is compatible with microfluidic diagnostic devices. Such "lab on a chip" devices may help bring the benefits of PCR-based molecular diagnosis to users and point-of-care settings that lack the capacity for standard laboratory-based DNA purification [2] [3]. In such applications there are significant pressures to keep costs low. Therefore, DNA purification devices must be designed to use the least expensive materials possible, and without unnecessary engineering. Early researchers showed that the curved inner surfaces of glass test tubes could be used to purify DNA from agarose gels, but their binding capacity was deemed too small for most preparative experiments [4]. Currently, it is standard practice to maximize DNA binding surface area, for example by using silica glass bead matrices. However, such engineering measures may not be necessary to achieve satisfactory DNA purification yields.

DNA Binding to the Silica Surface

“…DNA binding to silica in the presence of chaotropic salts, such as guanidinium thiocyanate and sodium perchlorate, is a standard purification method. [12][13][14][15][16][17][18] There are also many reports of DNA binding to silica in the absence of chaotropic slates, and at pH values where the silica surface is negatively charged. In the absence of chaotropic salts, Fujiwara et al found weak binding of double-stranded DNA to silica under neutral or basic pH values.…”

Extraction of MS2 Phage RNA from Upper Respiratory Tract Specimens by Use of Flat Glass Devices

“…Although open flat glass slides were demonstrated to capture genomic DNA (12), this is the first report of using flat glass surfaces to capture trace amounts of viral RNA. Capture of the MS2 RNA inside the thin, glasswalled S channel was efficient, and impurities were effectively washed off using the described wash buffers.…”

“…We have previously demonstrated that glass microscope slides could be used to purify genomic DNA from various sample types in an open system (12), but the method was slow and technically challenging. Subsequently, we developed a disposable device consisting of a thin (0.7-mm) 1.5-ml-volume serpentine channel formed between two larger glass microscope slides (Fig.…”

The Glass Slide Extraction System Snap Card Improves Non-Invasive Prenatal Genotyping in Pregnancies with Antibodies

“…DNA extraction fromcell-free plasma by binding to the surface of a glass slide introduces an innovative approach for this purpose [25]. The SNAP card consists of an S-shaped plastic channel sandwiched by two glass slides.…”