Multi-strand binding of nuclear factors to a repressor of mouse mammary tumor virus transcription can be distinguished kinetically.

NRE1 is a DNA sequence element in the long terminal repeat of mouse mammary tumor virus that represses viral transcription in mature T cells. In addition to double-stranded binding activity, factors in Jurkat T cell nuclear extracts bind specifically to each of the two single-strands of NRE1. Here we show that binding to the three forms of NRE1 can be distinguished kinetically. The on rates for double, upper and lower-strand NRE1 binding were 1.5, 3, and 11 min, respectively. Binding was extremely stable with off-rates varying from 30 and 60 min for double and upper-strand binding to 12 h for lower-strand binding. In addition, a truncated form of NRE1 that is only bound as a double-strand was observed to have an on rate of binding of 4 min and an off rate of 4 h.