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Figure 8 | BMC Molecular Biology

Figure 8

From: The CTCF insulator protein forms an unusual DNA structure

Figure 8

A speculative model of the CTCF-probe topologies in the DNA permutation experiments. A schematic model of the CTCF looping process. CTCF is shown in blue with its eleven zinc fingers as protrusions. The protein uses a set of core zinc fingers to bind to the CTCF binding site (indicated by an arrow), leaving the remaining zinc fingers available for DNA loop formation. In 1, CTCF binds to the CTCF binding site near the end of the probe causing a bend in the DNA (shown in pink). As the length of the probe downstream of the FII insulator element increases, the length of the available DNA for DNA loop formation increases and therefore the size of the DNA loop also increases, as shown in 2 and 3. This results in a decreased electrophoretic mobility (bottom, lanes 1 through 3). As the length of the probe upstream of the FII insulator element decreases to its minimum length and the size of the loop is at its greatest (as shown in 4), the mobility of the CTCF-probe complex increases slightly in the native acrylamide gel (bottom, lane 4). This is due to the reduction in "drag" caused by the DNA upstream of the FII site as the CTCF-probe complex migrates through the acrylamide gel. No attempt is made to portray the sign (+ or -) of the crossing nodes.

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