Transcriptional regulation is an important component in genetics, with transcriptional factors (TFs) and regulatory DNA regions involved in. In this paper, we observe cooperativity between two significant TFs Oct-l and Sox-2 at their enhancer DNA binding sites in collective motions. Normal mode analysis (NMA) is carried out to simulate the motions of two POU/HMG/DNA complexes, with molecular dynamics (MD) results used as a comparison. We have discovered several types of cooperative interactions between the two TFs in these obtained motions.