We report a mathematical modeling of the DNA-mediated selective aggregation of CdS quantum dots. Addition of hybridized double-stranded DNAs into the suspensions of CdS quantum dots at the optimal salt concentration causes a selective aggregation and a fluorescence-quenching phenomenon depending on the target DNA sequence. We monitor the aggregation process with quasi-elastic light scattering (QELS), zeta potential, and conductivity measurements at different salt concentrations. To model the aggregation process, we use the constant-number Monte Carlo method with the aggregation kernel that accounts for the interparticle interaction from the classical DLVO model. We find that the calculated results are in good agreement with the experiments, and that the fractal dimension of the quantum dot aggregates is 2.3. Modeling also allows us to estimate that the total number of initial quantum dots in aggregates at the beginning of the fluorescence-quenching phenomenon is approximately 200. The insights gained in this study should be useful in the design of biosensors based on the fluorescence-quenching phenomenon caused by the quantum dot aggregation. (C) 2010 Elsevier Inc. All rights reserved.