Abstract
The Ner protein encoded by the transposable coliphage D108, an 8.6 kDa λ Cro-like repressor, binds to an operator spanning 50 bp of DNA. The distinguishing features of this operator are two perfect 11-bp inverted repeats (5′-CCGTGAGCTAC-3′) that are separated by an 8-bp AT-rich spacer. Hyperreactivity of the ner operator to potassium permanganate and the hydroxyl radical indicate that the AT-rich spacer assumes a variant conformation consistent with a bend. Using an electrophoretic mobility shift assay, we demonstrated that Ner does not display significant affinity for a single 11-bp site. Furthermore, DNase I protection analysis and circular-permutation binding assays reveal that alterations in the length and sequence of the AT-rich spacer that separates the 11-bp inverted repeats significantly alter Ner-operator interactions, and demonstrate that the intrinsically bent ner operator is conformationally altered upon protein binding.
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Received: 29 September 1999 / Accepted: 21 December 1999
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Kukolj, G., DuBow, M. The bacteriophage D108 Ner repressor binds a conformationally distinct operator. Mol Gen Genet 263, 592–600 (2000). https://doi.org/10.1007/s004380051206
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DOI: https://doi.org/10.1007/s004380051206