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Giant Spacer Entropic Effect In Binding to Surface Attached Probes: DNA Microarrays

Arnold Vainrub, College of Veterinary Medicine, Auburn University, 109 Greene Hall, Auburn, AL 36849-5518, Xiaolian Gao, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, and B. Montgomery Pettitt, Department of Chemistry, University of Houston, Houston, TX 77204-5003.

In DNA microarray a free in solution assayed genomic DNA hybridizes with an oligonucleotide probe attached to the surface and forms a DNA duplex. Restriction of translational and rotational motion of the duplex because of the surface attachment gives rise to the entropy decrease. The rotational entropy penalty is shown to be substantial and account for a giant linker effect in the hybridization on the surface. The translational motion entropy effect is shown to vanish. A simple gas model is used to elucidate the physics and calculate the reduction of equilibrium binding constant for surface attached biomolecular probes. The rotational entropy barrier decreases when the probe is attached to the surface through a spacer molecule (oligomer) and disappears when the spacer allows free rotation of the duplex. Experiments were done for various lengths of (dT)n oligomer spacer and different surface densities of oligonucleotide probes. The theory is shown to be in complete accord with the experiments.


Web Page: www.vetmed.auburn.edu/index.pl/vainrub