Abstract: The aim of this study was to simulate an in vitro protocol that selects maximally mismatched DNA sequences (words). This simulation helps in estimating the protocol results and helps in expecting the difference in the results when running the protocol for very long times. It also assists in characterizing Non Cross-Hybridizing (NCH) DNA words. In addition, the simulation might be used to produce large libraries of Non Cross Hybridizing (NCH) DNA words in silico. Selection of words with good properties is important for reliable DNA based applications because words should hybridize as designed in order to provide correct results. These words can be used in solving large problems and in nano technology applications. Furthermore, several applications were proposed to show the applicability of the selection protocol in different disciplines. Analysis of the simulation of the protocol showed that the concentrations of the NCH words did increase in the population which shows an evidence of the ability of the protocol to produce NCH words. Most of the changes in concentrations occurred during the first few rounds of the protocol and not much change occurred after that. In addition, the results showed that only a small portion of the population will not crosshybridize. The results of the simulation model were verified experimentally with the lab results.