Nucleic Acids Research, 1992, Vol. 20, No. 18 4727-4731
© 1992
MOLECULAR BIOLOGY |
A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex
MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK
Received July 17, 1992. Revised August 17, 1992. Accepted August 17, 1992.
We have re-examined DNase I footprinting data for the binding of transcription factor IIIA (TFIIIA) to the 5S RNA gene, taking into account the protein-DNA contacts observed in the crystal structure of the DNase I complex (1, 2). This structure was not available when many of the original footprlnting experiments on the TFIIIA/DNA complex were performed. In this way the pattern of DNase I cleavage can be Interpreted to map out with greater precision the regions on the 5S DNA occupied by TFIIIA. Then, assuming the binding site for a zinc-finger may be the same as that found in the structure of the zinc-finger protein Zif268/DNA complex (3), and taking into account footprinting data for truncated forms of TFIIIA, the TFIIIA zinc-fingers were fitted within the permitted regions. On the basis of this, an alignment of the zinc-fingers of TFIIIA with its DNA binding site is proposed, which combines features of earlier models (4).
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