THE BIOPHYSICS OF DNA HYBRIDIZATION WITH IMMOBILIZED OLIGONUCLEOTIDE PROBES

A mathematical model based on receptor-ligand interactions at a cell s urface has been modified and further developed to represent heterogene ous DNA-DNA hybridization on a solid surface, The immobilized DNA mole cules with known sequences are called probes, and the DNA molecules in solution with unknown sequences are called targets in this model. Cap ture of the perfectly complementary target is modeled as a combined re action-diffusion limited irreversible reaction. In the model, there ar e two different mechanisms by which targets can hybridize with the com plementary probes: direct hybridization from the solution and hybridiz ation by molecules that adsorb nonspecifically and then surface diffus e to the probe. The results indicate that nonspecific adsorption of si ngle-stranded DNA on the surface and subsequent two-dimensional diffus ion can significantly enhance the overall reaction rate. Heterogeneous hybridization depends strongly on the rate constants for DNA adsorpti on/desorption in the non-probe-covered regions of the surface, the two -dimensional (2D) diffusion coefficient, and the size of probes and ta rgets, The model shows that the overall kinetics of DNA hybridization to DNA on a solid support may be an extremely efficient process for ph ysically realistic 2D diffusion coefficients, target concentrations, a nd surface probe densities. The implication for design and operation o f a DNA hybridization surface is that there is an optimal surface prob e density when 2D diffusion occurs; values above that optimum do nor i ncrease the capture rate. Our model predicts capture rates in agreemen t with those from recent experimental literature. The results of our a nalysis predict that several things can be done to improve heterogeneo us hybridization: 1) the solution phase target molecules should be abo ut 100 bases or less in size to speed solution-phase and surface diffu sion; 2) conditions should be created such that reversible adsorption and two-dimensional diffusion occur in the surface regions between DNA probe molecules; 3) provided that 2) is satisfied, one can achieve re sults with a sparse probe coverage that are equal to or better than th ose obtained with a surface totally covered with DNA probes.