We present preliminary results of our theoretical studies on the HincII restriction endonuclease that is responsible for binding to specific nucleotide sequence and cleaving DNA at that specific sequence. The aim of our studies was to investigate ability of HincII to indirect readout of its cognate DNA. In our research we applied molecular dynamics technique to study conformational changes occurring in the HincII-DNA complex. Based on the experimental research of Horton et al. we studied complexes of DNA with a native HincII and a mutated HincII enzyme in which glutamine in 138 position was replaced by phenylalanine. Kinetic data obtained by Horton et al. revealed that the aforementioned mutation results in a change in sequence specificity at the center two base pairs of the cognate recognition center. In our approach we took X-ray structures of DNA complexes with native and mutated HincII and by performing MD simulations of these complexes in aqueous solution we studied conformational changes in, both, DNA and enzyme that might lead to indirect recognition of specific nucleotide sequence. We also examined a role of calcium ions Ca2+ that were present in the active center of the enzyme.