A Synthetic DNA Molecule in Three Knotted Topologies

The construction of knotted topologies is a key goal of stereochemistry. In order to measure the chiral properties of knotted molecules, it is necessary to produce both enantiomers of a knot from the same molecule. A molecule containing the same backbone structure that is an amphichiral knot can provide a useful control molecule for such measurements. In the case of molecules with chiral backbones, configurational chirality, exclusive of the chirality due to knotting, must be measured from the circle of the same sequence. Trefoil knots of both chiralities, an amphichiral knot, and an unknotted circular molecule have all been constructed by enzymatic closure of the same linear DNA molecule. The molecule contains two double helical domains that can be induced to assume the right-handed B conformation or the left-handed Z conformation under selected solution conditions. The molecules expected to contain left-handed DNA have been shown to bind an anti-Z-DNA antibody in gel-retention assays.