Focusing and stabilization of bis-intercalating dye-DNA complexes for high-sensitive CE-LIF DNA analysis

Multiple labeling of nucleic acids by intercalative dyes is a promising method for ultrasensitive nucleic acid assays. The properties of the fast dissociation and instability of dye-DNA complexes may prevent from their wide applications in CE-LIF nucleic acid analysis. Here, we describe an optimum CE focusing method by using appropriately paired sample and separation buffers, Tris-glycine buffer and Tris-glycine-acetic acid buffer. The developed method was applied in both uncoated and polyacrylamide coated fused-silica capillary-based CE-LIF analysis while the sample and separation buffers were conversely used. The complexes of intercalative dye benzoxazolium-4-pyridinium dimer and dsDNA were greatly focused (separation efficiency: 1.8 million theoretical plates per meter) by transient isotachophoresis mechanism in uncoated capillary, and moderately focused by transient isotachophoresis in combination of field amplified sample stacking and further stabilized by the paired buffer in polyacrylamide coated capillary. Based on the developed focusing strategy, an ultrasensitive DNA assay was developed for quantitation of calf thymus dsDNA (from 0.02 to 2.14 pM). By the use of an excitation laser power as low as 1 mW, the detection limits of calf thymus dsDNA (3.5 kb) are 7.9 fM in concentration and 2.4x10(-22) mol (150 molecules) in mass. We further demonstrate that the non-gel sieving CE-LIF analysis of DNA fragments can be enhanced by the same strategy. Since the presented strategy can be applied to uncoated and coated capillaries and does not require special device, it is also reasonable to extend to the applications in chip-based CE DNA analysis.