Ethidium bromide (EB) is commonly used as a fluorescent probe of B-DNA. The mechanism is the intercalation of EB into DNA base pairs to form a stable complex. It was found that the intercalation of EB had sequence specificity for B-DNA based on molecular simulation. Statistical analysis shows that EB prefers to intercalate into DNA from the minor groove, rather than from the major one. Comparing the binding energy of EB with different base pairs, it was found that EB had special recognition among base pairs with the maximum binding energy with CA. Through analyzing the driving energy of intercalation and the force of sequence special recognition, it can be concluded that both the intercalation and special recognition are mainly through electrostatical interaction.

Key words: ethidium bromide, specificity recognition, computer simulation, DNA, base pair