Topology in Molecular Biology

2 Topology in Biology: From DNA Mechanics to Enzymology 13

kb-laddersupercolled plasmidknotted plasmidlinear plasmidknotted plasmidsupercolled plasmidkb-ladder

unknotted

'

nicked plasmid

3-noded knot

5-noded knot

7-noded knot

9-noded knot

sc plasmid

unresolved

knots

linear plasmid

4-kb linear

3-kb linear

Well

Fig. 2.7.Knotted products generated by phageλintegrative site-specific recombi-
nation. A 4,600-bp plasmid bearingλ-att recombination sites was incubated with
λintegrase in the presence of IHF protein, nicked with DNase I to remove residual
supercoiling, and subjected to electrophoresis on a 1% agarose gel in TBE buffer.
Products were made visible by staining with ethidium bromide and the gel image
captured using a Peltier-cooled CCD camera. Knotted products appear as bands
that are separated by intervals of two nodes; this is consistent with the exclusive
formation of knots that belong to the torus family

2.1.5 Flexibility and Topology of DNA, and Their Relation
to Genome Organization

In the genomes of prokaryotic and eukaryotic organisms DNA is present in
condensed nucleoprotein complexes rather than naked, extended molecules.
Moreover, in the nucleii of eukaryotic cells genomes are partitioned among
multiple, distinct chromosomes. These aspects of genome organization facili-
tate the 10^6 -fold compaction required to store an enormous amount of genetic