Integrated microfluidic devices for the purification, amplification, and detection of nucleic acids are a prevalent area of research due to their potential for miniaturization, assay integration, and increased efficiency over benchtop assays. These devices frequently contain micrometer-sized magnetic beads with a large surface area for the capture and manipulation of biological molecules such as DNA and RNA. Although magnetic beads are a standard tool for many biological assays, beads functionalized with biological molecules can adhere to microchannel walls and prevent further manipulation of the beads within the channel. Here, we analyze the effects of solution composition, microchannel hydrophobicity, and bead surface hydrophobicity on DNA-functionalized bead adhesion in a borosilicate glass microfluidic device. Bead adhesion is primarily a result of adsorption of the bead-linked DNA molecule to the microchannel wall; >81% of beads are consistently removed when not functionalized with DNA. Hydrophobicities of both the microchannel walls and the microbead surface are the primary determinants of bead adhesion, rather than electrostatic interactions and ion bridging. Surprisingly, DNA-functionalized bead adhesion in a standard RNA amplification solution was virtually eliminated by using hydrophobic microbeads with hydrophobic microchannel walls; under such conditions, 96.6 ± 1.6% of the beads were removed in one 43 nl/s, 10-min wash. The efficiency of a downstream RNA amplification reaction using DNA-functionalized beads did not appear to be affected by the hydrophobicity of the microbead surface. These findings can be applied to assays that require the efficient use of magnetic beads in DNA-based microfluidic assays.
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