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Differential Adhesion of Microspheres Mediated by DNA Hybridization I: Experiment

Ying Zhang ^* , Valeria T. Milam ^* , David J. Graves ^*  and Daniel A. Hammer ^*  

Departments of ^* Chemical and Biomolecular Engineering and Bioengineering, and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104

Correspondence: Address reprint requests to Daniel A. Hammer, Dept. of Bioengineering, University of Pennsylvania, 120 Hayden Hall, 3320 Smith Walk, Philadelphia, PA 19104. Tel.: 215-573-6761; Fax: 215-573-2071; Email: hammer{at}seas.upenn.edu.

We have developed a novel method to study collective behavior of multiple hybridized DNA chains by measuring the adhesion of DNA-coated micron-scale beads under hydrodynamic flow. Beads coated with single-stranded DNA probes are linked to surfaces coated with single target strands through DNA hybridization, and hydrodynamic shear forces are used to discriminate between strongly and weakly bound beads. The adhesiveness of microspheres depends on the strength of interaction between DNA chains on the bead and substrate surfaces, which is a function of the degree of DNA chain overlap, the fidelity of the match between hybridizing pairs, and other factors that affect the hybridization energy, such as the salt concentration in the hybridization buffer. The force for bead detachment is linearly proportional to the degree of chain overlap. There is a detectable drop in adhesion strength when there is a single base mismatch in one of the hybridizing chains. The effect of single nucleotide mismatch was tested with two different strand chemistries, with mutations placed at several different locations. All mutations were detectable, but there was no comprehensive rule relating the drop in adhesive strength to the location of the defect. Since adhesiveness can be coupled to the strength of overlap, the method holds promise to be a novel methodology for oligonucleotide detection.