Molecular knot

In chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot. Naturally-forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules. The mechanism by which knots naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous. The study of molecular knots involves the formation and applications of both naturally occurring and chemically synthesized molecular knots. Applying chemical topology and knot theory to molecular knots allows biologists to better understand the structures and synthesis of knotted organic molecules. The term knotane was coined by Vögtle et al. in 2000 to describe molecular knots by analogy with rotaxanes and catenanes, which are other mechanically interlocked molecular architectures. The term has not been broadly adopted by chemists and has not been adopted by IUPAC.

Naturally occurring molecular knots Organic molecules containing knots may fall into the categories of slipknots or pseudo-knots. They are not considered mathematical knots because they are not a closed curve, but rather a knot that exists within an otherwise linear chain, with termini at each end. Knotted proteins are thought to form molecular knots during their tertiary structure folding process, and knotted nucleic acids generally form molecular knots during genomic replication and transcription, though details of knotting mechanism continue to be disputed and ambiguous. Molecular simulations are fundamental to the research on molecular knotting mechanisms. Knotted DNA was found first in single-stranded, circular, bacterial DNA, though double-stranded circular DNA has been found to also form knots. Naturally knotted RNA has not yet been reported. A number of proteins containing naturally occurring molecular knots have been identified. The knot types found to be naturally occurring in proteins are the + 3 1 , − 3 1 , 4 1 , − 5 2 , {\displaystyle +3_{1},-3_{1},4_{1},-5_{2},} and + 6 1 {\displaystyle +6_{1}} knots, as identified in the KnotProt database of known knotted proteins.

Chemically synthesized molecular knots

Several synthetic molecular knots have been reported. Knot types that have been successfully synthesized in molecules are 3 1 , 4 1 , 5 1 {\displaystyle 3_{1},4_{1},5_{1}} and 819 knots. Though the − 5 2 {\displaystyle -5_{2}} and + 6 1 {\displaystyle +6_{1}} knots have been found to naturally occur in knotted molecules, they have not been successfully synthesized. Small-molecule composite knots have also not yet been synthesized. Artificial DNA, RNA, and protein knots have been successfully synthesized. DNA is a particularly useful model of synthetic knot synthesis, as the structure naturally forms interlocked structures and can be easily manipulated into forming knots control precisely the raveling necessary to form knots. Molecular knots are often synthesized with the help of crucial metal ion ligands.

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