Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was investigated by NMR and fluorescence antisotropy as an example of the indirect sequence recognition. The 1H-15N HSQC spectra of the IRF-4/DNA complex containing the CCGAAA sequence indicated that the 1:1 complex was formed. The dissociation constants (Kd) for two DNA oligomers containing CCGAAA and GGGAAA were determined by fluorescence antistropy, but their difference was very small.