Intercalation (chemistry)

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Intercalation (chemistry)

In chemistry

Chemistry

Chemistry is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions....
, intercalation is the reversible inclusion of a molecule

Molecule

In chemistry, a molecule is defined as a sufficiently stable, electric charge neutral group of at least two atoms in a definite arrangement held together by very strong chemical bonds....
(or group) between two other molecules (or groups). Examples include DNA intercalation and in graphite intercalation compound

Graphite intercalation compound

Graphite intercalation compounds are complex materials having formula XCy where element or molecule X is inserted between the graphite layers.....
s.

e are several ways molecules - in this case, also known as "ligands

Ligand (biochemistry)

In biochemistry, a ligand is a Chemical substance that is able to bind to and form a Complex with a biomolecule to serve a biological purpose....
" - can interact with DNA.

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In chemistry

Chemistry

Molecule

Graphite intercalation compound

Graphite intercalation compounds are complex materials having formula XCy where element or molecule X is inserted between the graphite layers.....
s.

DNA intercalation

There are several ways molecules - in this case, also known as "ligands

Ligand (biochemistry)

In biochemistry, a ligand is a Chemical substance that is able to bind to and form a Complex with a biomolecule to serve a biological purpose....
" - can interact with DNA. Ligands may interact with DNA by covalently binding, electrostatically binding, or intercalating. Intercalation occurs when ligands of an appropriate size and chemical nature fit themselves in between base pairs of DNA. These ligands are mostly polycyclic, aromatic, and planar, and therefore often make good nucleic acid stains

Staining (biology)

Staining is an auxiliary technique used in microscopy to enhance contrast in the microscopic image.In biochemistry it involves adding a class-specific dye to a substrate to qualify or quantify the presence of a specific compound....
. Intensively studied DNA intercalators include ethidium bromide

Ethidium bromide

Ethidium bromide is an intercalation agent commonly used as a fluorescent tag in molecular biology laboratories for techniques such as agarose gel electrophoresis....
, proflavine

Proflavine

Proflavine , also called proflavin and diaminoacridine, is an acriflavine derivative, a disinfectant bacteriostatic against many gram-positive bacteria....
, daunomycin, doxorubicin

Doxorubicin

Doxorubicin is a pharmaceutical used in cancer chemotherapy. It is an anthracycline antibiotic, closely related to the natural product daunorubicin, and like all anthracyclines it intercalation DNA....
, and thalidomide

Thalidomide

Thalidomide is a sedative-hypnotic, and multiple myeloma medication. The drug is a potent Teratology in rabbits and primates including humans: this means that severe birth defects may result if the drug is taken during pregnancy....
. DNA intercalators are used in chemotherapeutic

Chemotherapy

Chemotherapy, in its most general sense, refers to treatment of disease by chemicals that kill cells, specifically those of micro-organisms or cancer....
treatment to inhibit DNA replication in rapidly growing cancer cells. Examples include, doxorubicin (adriamycin) and daunorubicin (both of which are used in treatment of Hodgkin's lymphoma), and dactinomycin (used in Wilm's tumour, Ewing's Sarcoma, rhabdomyosarcoma).

In order for an intercalator to fit between base pairs, the DNA must dynamically open a space between its base pairs by unwinding. The degree of unwinding varies depending on the intercalator, for example, ethidium cation (the ionic form of ethidium bromide

Ethidium bromide

Ethidium bromide is an intercalation agent commonly used as a fluorescent tag in molecular biology laboratories for techniques such as agarose gel electrophoresis....
found in aqueous solution) unwinds DNA by about 26° while proflavine unwinds it by about 17°. This unwinding causes the base pairs to separate, or "rise", creating an opening of about 0.34 nm (3.4 Å). This unwinding induces local structural changes to the DNA strand, such as lengthening of the DNA strand, or twisting of the base pairs. These structural modifications can lead to functional changes, often to the inhibition of transcription

Transcription (genetics)

Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process of transcribing DNA nucleotide sequence information into RNA sequence information....
and replication

DNA replication

DNA replication, the basis for heredity, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative replication" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand....
and DNA repair processes, which makes intercalators potent mutagen

Mutagen

In biology, a mutagen is a physical or chemical agent that changes the genetic information of an organism and thus increases the frequency of mutations above the natural background level....
s. For this reason, DNA intercalators are often carcinogenic

Carcinogen

The term carcinogen refers to any substance, radionuclide or radiation that is an agent directly involved in the promotion of cancer or in the increase of its propagation....
, such as the exo

Endo-exo isomerism

Endo-exo isomerism is a special type of isomerism found in organic compounds with a substituent on a bridged ring system. The prefix endo is reserved for the isomer with the substituent located closest, or "syn," to the longest bridge....
(but not the endo) 8,9 epoxide

Epoxide

An epoxide is a cyclic ether with only three ring atoms. This ring approximately is an equilateral triangle which makes it highly ring strain....
of aflatoxin

Aflatoxin

Aflatoxins are naturally occurring mycotoxins that are produced by many species of Aspergillus, a fungus, most notably Aspergillus flavus and Aspergillus parasiticus....
B₁, acridine

Acridine

Acridine, C13H9N, is an organic compound and a heterocyclic compound. Acridine is also used to describe compounds containing the C13N tricycle....
s such as proflavine

Proflavine

Proflavine , also called proflavin and diaminoacridine, is an acriflavine derivative, a disinfectant bacteriostatic against many gram-positive bacteria....
or quinacrine

Quinacrine

Quinacrine is a medication with a number of different medicine applications....
, or ethidium bromide.

Intercalation as a mechanism of interaction between cationic, planar, polycyclic aromatic systems of the correct size (on the order of a base pair) was first proposed by Leonard Lerman

Leonard Lerman

Leonard Lerman is an American scientist most noted for his work on DNA.As a graduate student with Linus Pauling at the California Institute of Technology, Lerman discovered that antibodies have two binding sites....
in 1961. One proposed mechanism of intercalation is as follows: in aqueous isotonic solution, the cationic intercalator is attracted electrostatically to the polyanionic DNA. The ligand displaces a sodium and/or magnesium cation that always surround DNA (to balance its charge) and forms a weak electrostatic bond with the outer surface of DNA. From this position, the ligand may then slide into the hydrophobic environment found between the base pairs and away from the hydrophilic outer environment surrounding the DNA. The base pairs transiently form such openings due to energy absorbed during collisions with solvent molecules.

Intercalation (chemistry)

DNA intercalation

See also