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Topoisomers or topological isomers are molecules with the same chemical formula and stereochemical bond connectivities but different topologies. Examples of molecules for which there exist topoisomers include DNA, which can form knots, and catenanes. Each topoisomer of a given DNA molecule possesses a different linking number associated with it. DNA topoisomers can be interchanged by enzymes called topoisomerases . Using a topoisomerase along with an intercalator, topoisomers with different linking number may be separated on an agarose gel via gel electrophoresis.

Three topoisomers of a closed circular DNA molecule. Left: negatively supercoiled; center: relaxed; right: positively supercoiled DNA Topoisomers.png
Three topoisomers of a closed circular DNA molecule. Left: negatively supercoiled; center: relaxed; right: positively supercoiled

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Rotaxane class of chemical compounds

A rotaxane is a mechanically interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a "macrocycle". The name is derived from the Latin for wheel (rota) and axle (axis). The two components of a rotaxane are kinetically trapped since the ends of the dumbbell are larger than the internal diameter of the ring and prevent dissociation (unthreading) of the components since this would require significant distortion of the covalent bonds.

Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double-helical structure. During DNA replication and transcription, DNA becomes overwound ahead of a replication fork. If left unabated, this torsion would eventually stop the ability of DNA or RNA polymerases involved in these processes to continue down the DNA strand.

Supramolecular chemistry is the domain of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. Whereas traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.

Catenane class of chemical compounds

A catenane is a mechanically-interlocked molecular architecture consisting of two or more interlocked macrocycles, i.e. a molecule containing two or more intertwined rings. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. Catenane is derived from the Latin catena meaning "chain". They are conceptually related to other mechanically interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings. Recently the terminology "mechanical bond" has been coined that describes the connection between the macrocycles of a catenane. Catenanes have been synthesised in two different ways: statistical synthesis and template-directed synthesis.

Interlock can refer to the following:

Molecular knot class of chemical compounds

In chemistry, a molecular knot, or knotane, is a mechanically-interlocked molecular architecture that is analogous to a macroscopic knot. Naturally forming knotanes 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 knotanes naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous. The study of knotanes 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.

Nucleic acid double helix The structure formed by double-stranded molecules of nucleic acids such as DNA.

In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure. The term entered popular culture with the publication in 1968 of The Double Helix: A Personal Account of the Discovery of the Structure of DNA by James Watson.

Topoisomerase IV is one of two Type II topoisomerases in bacteria, the other being DNA gyrase. Like gyrase, topoisomerase IV is able to pass one double-strand of DNA through another double-strand of DNA, thereby changing the linking number of DNA by two in each enzymatic step. Both share a hetero-4-mer structure formed by a symmetric homodimer of A/B heterodimers, usually named ParC and ParE.

Jean-Pierre Sauvage French nanotechnologist

Jean-Pierre Sauvage is a French coordination chemist working at Strasbourg University. He graduated from the National School of Chemistry of Strasbourg, in 1967. He has specialized in supramolecular chemistry for which he has been awarded the 2016 Nobel Prize in Chemistry along with Sir J. Fraser Stoddart and Bernard L. Feringa.

Mechanically interlocked molecular architectures (MIMAs) are molecules that are connected as a consequence of their topology. This connection of molecules is analogous to keys on a keychain loop. The keys are not directly connected to the keychain loop but they cannot be separated without breaking the loop. On the molecular level the interlocked molecules cannot be separated without the breaking of the covalent bonds that comprise the conjoined molecules, this is referred to as a mechanical bond. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings. Work in this area was recognized with the 2016 Nobel Prize in Chemistry to Bernard L. Feringa, Jean-Pierre Sauvage, and J. Fraser Stoddart.

DNA supercoil The compressed DNA loop supercoiled by prokaryotes to fit it within a small space.

DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand. Supercoiling is important in a number of biological processes, such as compacting DNA, and by regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism and possibly gene expression. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription. Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA.

DNA topoisomerase or simply Topoisomerase is an enzyme with systematic name DNA topoisomerase. This enzyme catalyzes the following chemical reaction

Type II topoisomerase class of enzymes

Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP, unlike Type I topoisomerase. In this process, these enzymes change the linking number of circular DNA by ±2.

Residual topology is a descriptive stereochemical term to classify a number of intertwined and interlocked molecules, which cannot be disentangled in an experiment without breaking of covalent bonds, while the strict rules of mathematical topology allow such a disentanglement. Examples of such molecules are rotaxanes, catenanes with covalently linked rings, and open knots (pseudoknots) which are abundant in proteins.

David Alan Leigh FRS FRSE FRSC is a British chemist, Royal Society Research Professor and, since 2014, the Sir Samuel Hall Chair of Chemistry in the School of Chemistry at the University of Manchester. He was previously the Forbes Chair of Organic Chemistry at the University of Edinburgh (2001–2012) and Professor of Synthetic Chemistry at the University of Warwick (1998–2001).

A molecular switch is a molecule that can be reversibly shifted between two or more stable states. The molecules may be shifted between the states in response to environmental stimuli, such as changes in pH, light, temperature, an electric current, microenvironment, or in the presence of ions and other ligands. In some cases, a combination of stimuli is required. The oldest forms of synthetic molecular switches are pH indicators, which display distinct colors as a function of pH. Currently synthetic molecular switches are of interest in the field of nanotechnology for application in molecular computers or responsive drug delivery systems. Molecular switches are also important in biology because many biological functions are based on it, for instance allosteric regulation and vision. They are also one of the simplest examples of molecular machines.

In chemistry, isomers are ions or molecules with identical formulas but distinct structures. Isomers do not necessarily share similar properties. Two main forms of isomerism are structural isomerism and stereoisomerism.

Obsolete models of DNA structure

In addition to the variety of verified DNA structures, there have been a range of obsolete models that have either been disproven, or lack evidence.

Cyclobis(paraquat-<i>p</i>-phenylene) chemical compound

Cyclobis(paraquat-p-phenylene) belongs to the class of cyclophanes, and consists of aromatic units connected by methylene bridges. It is able to incorporate small guest molecule and has played an important role in host–guest chemistry and supramolecular chemistry.


A polyrotaxane is a type of mechanically interlocked molecule consisting of strings and rings, in which multiple rings are threaded onto a molecular axle and prevented from dethreading by two bulky end groups. As oligomeric or polymeric species of rotaxanes, polyrotaxanes are also capable of converting energy input to molecular movements because the ring motions can be controlled by external stimulus. Polyrotaxanes have attracted much attention for decades, because they can help build functional molecular machines with complicated molecular structure.