To determine whether the indel in the STRE motif alters transcription factor binding, we performed EMSA using oligonucleotides from B6 (49 bp) and D2 (50 bp). The EMSA detected two DNA-protein complexes that were unique to the D2 promoter sequence and absent in B6 (Figure 3a). Super-shift assay with the PER3 antibody revealed no difference and no evidence of autoregulation (data not shown). The EMSA result supports the hypothesis that the -/T polymorphism in STRE affects binding of transcription factors.
