Single-Stranded Nucleic Acid Topology in
Ned Seeman's Laboratory.
The DNA polyhedra that we make in our
program are catenanes of cyclic unknotted DNA molecules. That means that they are held together like the links of a chain. However, there exists a
simple relationship between knots and catenanes.
Thus, we are interested in knotted molecules, as well as catenated molecules. We expect that complex foldings of single-stranded DNA molecules will offer a
route to cloning DNA polyhedra.
Furthermore, knotted molecules can provide a means to generate stressed DNA in relatively small molecules. B-DNA provides topologically negative nodes, but left-handed Z-DNA generates positive nodes. We can make
four topological species
from the same strand: A circle, a trefoil knot of each chirality, and a figure-8 knot. We have observed their
interconversion by DNA topoisomerases
. The interconversion of knots and circles by topoisomerases makes this a good system to seek topoisomerase activity; we have used this interconversion to demonstrate that E. coli DNA topoisomerase III is an RNA topoisomerase. We have shown that there is a general way to
design any knot from DNA,
by equating a node in a projection of a knot with a half-turn of DNA. A consequence of this relationship was the discovery of
antijunctions and mesojunctions.
These molecules are closely related to the pseudoknots found in ribozymes. A second result of this relationship is that we have been able to construct Borromean Rings from DNA.
Go to Seeman Lab Single-Stranded Nucleic Acid Topology Bibliography
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