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TnpA product encoded by the transposable element En‐1 of Zea mays is a DNA binding protein.

TnpA protein, the function encoded by the most abundant transcript of En‐1 was expressed in Escherichia coli. DNA binding experiments with partially purified tnpA protein revealed that it binds to the subterminal repetitive region of En‐1. TnpA protein recognizes a 12‐bp‐long sequence motif which is reiterated several times at the termini of En‐1. Binding is reduced if the cytosine residues of CG dinucleotides and CNG trinucleotides within the motif are methylated. These data suggest a model in which the product of tnpA serves as a regulator of element activity.