Hybridization Reaction Kinetics of DNA Probes on Beads Arrayed in a Capillary Enhanced by Turbulent Flow

• Published in: Analytical chemistry (Washington) Vol. 75; no. 13; pp. 3079 - 3085
• Main Author: Kohara, Yoshinobu
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 01.07.2003
• Subjects: Analytical chemistry; Arrays; Base Sequence; Blood vessels; Chemistry; Deoxyribonucleic acid; DNA; DNA Probes - chemistry; DNA Probes - genetics; Exact sciences and technology; Kinetics; Microscopy, Fluorescence; Microspheres; Miscellaneous; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Rheology; DNA
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac0341214

The hybridization reaction kinetics of DNA probes on beads arrayed in a capillary was investigated experimentally and theoretically by using fluid mechanical methods. A device was prepared to contain DNA probes conjugated on 103-μm-diameter beads that were queued in a 150-μm-diameter capillary. The hybridization experiments were performed by introducing sample into the capillary and moving it with a one-way or a reciprocal flow. From the relation between Reynolds number and the resistance coefficient of the system, we found that the flow in the system was turbulent and not laminar as has been said of other microfluidic devices. The reaction efficiency was estimated using a mass-transfer coefficient derived from Chilton−Colburn's analogy. The estimate agreed well with the experimental data. A diffusion equation under laminar assumption was also solved, but this estimated value was 4.0−10.4 times smaller than the experimental data. Using the device achieved a hybridization efficiency as high as ∼90% in 10 min. It was concluded that the high hybridization performance of the device resulted from turbulent flow and that the flow compensated the slow molecular diffusion. Using this bead-included structure resulted in a rapid and effective reaction at the solid−liquid interface, and the device seems very promising for many future applications.