Bowtie Junctions

Bowtie junctions are variants of the conventional Holliday junction in which the crossover strands contain 5', 5' and 3', 3' linkages. The remarkable thing about them is that they form junctions in which the non-crossover strands are closer to parallel than to antiparallel. In the drawing below, (a) shows the angle convention, along with slightly distorted antiparallel and parallel ideal junctions. (b) shows the differences between normal and Bowtie junctions. Note that the Bowtie junction has 5', 5' and 3', 3' linkages in two of its strands. (c) below shows what these molecules would look like if they were ideally antiparallel or parallel. In Mg(+2)- containing solutions, the normal junction looks like the antiparallel junction on the upper left, and the Bowtie junction looks like the parallel junction on the lower right. The key feature is that both prefer a chain-direction-reversing structure for the crossover strands.

How do we know that these molecules are parallel, rather than antiparallel? Preliminary evidence was obtained from gel mobility studies, but the more interesting demonstration was provided by AFM. Neither normal nor Bowtie junctions are ideally parallel or antiparallel. Rather, they differ from these structures by about 60 - 70 degrees. Thus, we we talk about parallel or antiparallel, we are asking the question in the top line of (a) in the diagram below. To establish which is the correct structure, we made the four parallelograms below, labeled I, II, III and IV. If parallel, the parallelograms will look like the blue ones on the second line, and if antiparallel, the parallelograms will look like the red ones on the third line. We can make V-shaped arrays of these parallelograms, using I or II at the vertex, and III and IV as the extenders to form the sides of the 'V'. (b) of the diagram below shows that a V-shaped array made from I, III, and IV will have an acute angle if parallel, and an obtuse angle if antiparallel. Likewise, a V-shaped array made from II, III and IV will have an obtuse angle if parallel and an acute angle if antiparallel.

The answers are shown below. First, the I, III, IV array:

Next, the II, III, IV array:

From this experiment it is clear that Bowtie junctions are parallel, rather than antiparallel.

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