Biology Reference
In-Depth Information
215
according to the conventional explanation. The two complementary DNA
circles are inter-twined so that they cannot separate from each other unless
one of them is cut covalently. It is well known that many biological active
DNA molecules need to retain their intact circular structure for replication.
Therefore, in view of our present discussion, can this supercoil structure
actually provide some evolutionary advantage?
We shall start with the four-stranded structure (Wu, 1969) as suggested by
the X-ray diffraction picture of sodium salt of DNA fiber at 92% relative
humidity, and consider it as two mutually intercalating stretched out double
helices. We can connect their ends in such a way to give two base-paired
circles of complementary strands. This rod structure (Wu and Wu, 1996;
Stasiak, 1996) would be nearly indistinguishable from the conventional
supercoil under the electron microscope. Nevertheless, in this case, the two
complementary DNA single-stranded circles are not inter-twined and
separable without any covalent bond breakage. Hopefully, with better
resolutions of various types of electron microscopy techniques, the sugar-
phosphate backbones of DNA supercoils may eventually be visible.
FUTURE EXPERIMENTS
As explained throughout this topic, the interplay of experimentation by
molecular biologists and analysis using mathematical and physical methods
should suggest some future experiments. Since the current analysis of DNA
secondary structure is highly unconventional and controversial, few or no
experiments have been suggested and studied. Some will be suggested here.
Agarose Gel Electrophoresis
It is well known that intact plasmid supercoils moves faster than their
linearized molecules on agarose gel electrophoresis. The usual explanation
is that supercoils are more compact and thus move faster. However, one
may ask the simple question of how much faster. Using linearized DNA
molecular weight markers, one can easily measure the corresponding
molecular weight of the intact supercoils. In most cases, they fall within
about 15% of half of the molecular weight of the linearized molecules. This
experiment should be verified with plasmids of different sizes. A possible
