We simulated the interaction of the small nucleotide chain (NC) with gold nanoparticles (NPs) inside carbon nanotube (CNT) of an open ended boundary. Such system represents a great interest in many aspects of today biochemical and nanotechnological research (diagnostic applications, drug delivery in cell, nanorobotic design and related manipulations). The entire system (the NC chain, gold NPs and CNT) were allowed to interact with each other by the Van der Waals (VdW) forces only. The CNT was described through a quantum-chemistry potential, though the trajectory calculation for the whole NC-NP-CNT model was performed via the classical molecular dynamics (MD) approach. The Lennard-Jones short-ranged interaction is assumed between the NC, NP and CNT. We have carried out a series of MD simulations on different NC-NP-CNT configurations to investigate the pequliarities of NC-NP bonding and structural formation along with dynamical behavior inside a CNT matrix under rather a weak VdW interaction.