The novel Mrf-2 DNA-binding domain recognizes a five-base core sequence through major and minor-groove contacts.
Recent NMR studies of the purified Mrf-2 DNA-binding domain peptide have shown that its structure differs significantly from previously characterized classes of DNA-binding domains. Here we report biochemical studies of the DNA-binding properties of this peptide. Binding interference and binding site selection assays indicated that Mrf-2 requires the core sequence AATA(C/T) for high affinity binding. Kinetic analyses of several selected sequences indicated that the core sequence alone is not sufficient for high affinity binding, however. Kinetic analyses were also performed using a series of synthetic oligonucleotides with single base analogues at each position in the core sequence. Base analogues that altered the major groove structure reduced or eliminated Mrf-2 binding when present in the second, third, and fourth base-pairs of the core sequence, but had little or no effect in the first and fifth positions. These results suggest that Mrf-2 contacts both the major and minor grooves of its target sequences.
D001483:Base Sequence; D001665:Binding Sites; D017931:DNA Primers; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D018006:Myogenic Regulatory Factors / Q000737:chemistry / Q000378:metabolism*