Thioflavin can refer to either of two dyes used for histology

Histology

Histology is the study of the microscopic anatomy of cells and tissues of plants and animals. It is performed by examining cells and tissues commonly by sectioning and staining; followed by examination under a light microscope or electron microscope...

 staining and biophysical

Biophysics

Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems. Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems...

 studies of protein aggregation.

Thioflavin T (Basic Yellow 1 or CI 49005) is a benzothiazole

Benzothiazole

Benzothiazole is an aromatic heterocyclic compound with the chemical formula . It is colorless, slightly viscous liquid. Although the parent compound, benzothiazole is not widely used, many of its derivatives are found in commercial products or in nature...

 salt obtained by the methylation of dehydrothiotoluidine with methanol

Methanol

Methanol, also known as methyl alcohol, wood alcohol, wood naphtha or wood spirits, is a chemical with the formula CH3OH . It is the simplest alcohol, and is a light, volatile, colorless, flammable liquid with a distinctive odor very similar to, but slightly sweeter than, ethanol...

 in the presence of hydrochloric acid

Hydrochloric acid

Hydrochloric acid is a solution of hydrogen chloride in water, that is a highly corrosive, strong mineral acid with many industrial uses. It is found naturally in gastric acid....

. The dye is widely used to visualize and quantify the presence of misfolded protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 aggregates called amyloid

Amyloid

Amyloids are insoluble fibrous protein aggregates sharing specific structural traits. Abnormal accumulation of amyloid in organs may lead to amyloidosis, and may play a role in various neurodegenerative diseases.-Definition:...

, both in vitro

In vitro

In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

 and in vivo

In vivo

In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...

 (e.g., plaques

Senile plaques

Senile plaques are extracellular deposits of amyloid in the gray matter of the brain. The deposits are associated with degenerative neural structures and an abundance of microglia and astrocytes...

 composed of amyloid beta

Amyloid beta

Amyloid beta is a peptide of 36–43 amino acids that is processed from the Amyloid precursor protein. While it is most commonly known in association with Alzheimer's disease, it does not exist specifically to cause disease...

 found in the brains of Alzheimer's disease

Alzheimer's disease

Alzheimer's disease also known in medical literature as Alzheimer disease is the most common form of dementia. There is no cure for the disease, which worsens as it progresses, and eventually leads to death...

 patients).

When it binds to beta sheet

Beta sheet

The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...

-rich structures, such as those in amyloid aggregates, the dye displays enhanced fluorescence

Fluorescence

Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...

 and a characteristic red shift

Red shift

-Science:* Redshift, the increase of wavelength of detected electromagnetic radiation with respect to the original wavelength of the emission* Red shift, an informal term for a bathochromic shift...

 of its emission spectrum

Emission spectrum

The emission spectrum of a chemical element or chemical compound is the spectrum of frequencies of electromagnetic radiation emitted by the element's atoms or the compound's molecules when they are returned to a lower energy state....

. This change in fluorescent behavior can be caused by many factors that affect the excited state

Excited state

Excitation is an elevation in energy level above an arbitrary baseline energy state. In physics there is a specific technical definition for energy level which is often associated with an atom being excited to an excited state....

 charge distribution

Electron density

Electron density is the measure of the probability of an electron being present at a specific location.In molecules, regions of electron density are usually found around the atom, and its bonds...

 of Thioflavin T, including binding to a rigid, highly-ordered amyloid structure, or to specific chemical interactions with a protein.

Thioflavin T fluorescence is often used as a diagnostic of amyloid structure, but it is not perfectly specific for amyloid. Depending on the particular protein and experimental conditions, Thioflavin T may or may not undergo a spectroscopic change upon binding to precursor monomers, small oligomers, unaggregated material with a high beta sheet

Beta sheet

The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...

 content, or even alpha helix

Alpha helix

A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...

-rich proteins. Conversely, some amyloid fibers do not affect Thioflavin T fluorescence, raising the prospect of false negative results.
An article published online in Nature on 30 March 2011 showed that Thioflavin T exposure on adult C. elegans resulted "in a profoundly extended lifespan and slowed aging" at some levels, but decreased lifespan at higher levels.

Thioflavin S is a homogenous mixture of compounds that results from the methylation of dehydrothiotoluidine with sulfonic acid

Sulfonic acid

Sulfonic acid usually refers to a member of the class of organosulfur compounds with the general formula RS2–OH, where R is an alkyl or aryl. The formal part of acid, HS2–OH, are formally derivatives of the "parent" inorganic compound with the formula HSO2.-Preparation:Sulfonic acid is...

. It is also used to stain amyloid plaques. Like Thioflavin T it binds to amyloid fibrils but not monomers and gives a distinct spectral shift upon binding. However the dye is unable to be used in quantitative measurements of fibril solutions due to its high background fluorescence. Another dye that is used to identify amyloid structure is Congo Red

Congo red

Congo red is the sodium salt of 3,3'-bis. It is a secondary diazo dye...

.