Chemistry Reference
In-Depth Information
Not only does DNA form itself into catenated and knotted structures, it also
rotaxanates itself with macrocyclic enzymes.
-Exonuclease [
30
,
37
] is an enzyme
that participates in DNA replication and repair by fully encircling DNA as it
sequentially hydrolyzes nucleotides - a biomolecular rotaxane! The structure of
the enzyme is shown in Fig.
3d
. T4 DNA polymerase holoenzyme [
38
]isan
analogous example; its protein subunits “clamp” around a DNA strand to form a
toroid in what chemists of the mechanical bond would call a “clipping” process. It
should be noted that chemists have been able to mimic this concept of a topologi-
cally linked catalyst on a polymer [
39
] using traditional organic catalytic reactions.
DNA is not the only entity that can serve as component of biological MIMs.
A recent discovery was the extraordinary interlocked structure of the bacteriophage
HK97 capsid. The icosohedral shell of the phage is composed of topologically
linked protein macrocycles (Fig.
3e
)[
31
]. This “molecular chainmail” is no less
beautiful than it is far beyond the reaches of our current artificial mimicry at the
molecular and supramolecular level. It is also known that mitochondria recruit
various proteins to encircle them in the form of a nanotube (Fig.
3f
) that participates
in mitochondrial fission by applying a contractile force [
32
,
40
], as shown by
microscopy in Fig.
3g, h
. The phenomenon of a ring contracting as it encircles a
rod in order to sever it is not unlike certain digestive processes or a common method
of bovine castration;
l
it is intriguing that
this mechanical “pinching” process
happens at the intracellular level as well.
It is apparent that our efforts in the chemistry of the mechanical bond have been
surpassed by Nature as usual. Nature executes this chemistry with a level of
elegance, complexity, and beauty that we can only strive for, yet will surely use
as a source of inspiration for centuries to come.
2.2
In Art
Nowhere is the beauty of the mechanical bond more validated than in the world of
art. If anything can speak to the beauty of the mechanical bond, it is the art that
portrays it, and it so happens that artists have been drawing, painting, carving, and
sculpting mechanical bonds for thousands of years!
Borromean Rings are a mechanically interlocked species that deserve special
attention, for despite being largely absent in the natural world, they are among the
most prevalent topologies found in art, spanning many cultures and thousands of
years. Their name originates from the Borromeo family of northern Italy, on whose
crest (Fig.
4b
) and estates the rings frequently appear. The rings have been
associated with the Borromeo family from at least the fifteenth century, though
recorded use of the symbols date back to the thirteenth century in Christian
iconography (Fig.
4c
), the twelfth century in Japanese emblems, and the ninth
century in Viking symbols (Fig.
4d
), making them a remarkably universal icon
(for many images of ancient and modern artwork of Borromean Rings, see [
41
]).
Topologically speaking, the three rings are interlocked in such a way that breaking
