This work is devoted to the interaction of nucleotides. The goal of this study is to learn or try to learn how the interaction between nucleotides with exposure to a liquid takes place. Will the interacting forces of the nucleotides be sufficient to approach the incision? A numerical imitation of the interaction is conducted using the discrete element method and a Gears predictor–corrector as part of the integrated scheme. In this work, the results reflect the dynamics of nucleotides: velocity, displacement, and force graphs are presented with and without the effect of the liquid. During changes caused by the influence of a liquid, the nucleotide interaction transforms and passes three stages: a full stop, one similar to viscous damping, and one similar to non-dissipative behaviors. The main contribution of this work is a better understanding of the behavior of infinitely small objects that would be difficult to observe in vivo. The changing influence of a liquid can transform into certain effects. As a result, a model is provided, which can be based on the results of well-known physical experiments (DNA unzipping) for modeling nucleotide interactions.