Acrydite
Encyclopedia
Acrydite is a phosphoramidite
that allows the synthesis of oligonucleotides with a methacryl group
at the 5' end (less commonly 3' or internal). Acryl oligonucleotides have been tested, but the acryl group
is not stable to storage. Acrydite modified oligonucletides can react with nucleophile
s such as thiol
s (Michael addition chemistry), this forms the basis of the ez-rays chemistry which was used for microarray
s. More importantly, Acrydite modified oligonucleotides can be incorporated, stoichiometrically, into hydrogels such as polyacrylamide
, using standard free radical polymerization
chemistry, where the double bond in the Acrydite group reacts with other activated double bond
containing compounds such as acrylamide
.
was developed by T. Christian Boles, while working at Mosaic Technologies, a now-defunct biotechnology company located in Waltham, MA. The IP was licensed, along with a microarray technology ("ez-rays") to Matrix Technologies, of Hudson, NH, which is now part of Thermo Scientific. Acrydite-modified oligonucleotides can be obtained from vendors such as Integrated DNA Technologies (IDT).
, the coupling of Acrydite-modified PCR products is inefficient, as the ends of the molecules are not accessible.
to implement the extraction operation. Previously, a biotin-avidin magnetic bead system was used for this purpose.
Phosphoramidite
Nucleoside phosphoramidites are derivatives of natural or synthetic nucleosides. They are used to synthesize oligonucleotides, relatively short fragments of nucleic acid and their analogs. Nucleoside phosphoramidites were first introduced in 1981 by Beaucage and Caruthers...
that allows the synthesis of oligonucleotides with a methacryl group
Methacrylic acid
Methacrylic acid, abbreviated MAA, is an organic compound. This colourless, viscous liquid is a carboxylic acid with an acrid unpleasant odor. It is soluble in warm water and miscible with most organic solvents. Methacrylic acid is produced industrially on a large scale as a precursor to its...
at the 5' end (less commonly 3' or internal). Acryl oligonucleotides have been tested, but the acryl group
Acryl group
In organic chemistry, the acryloyl group is the functional group with structure H2C=CH–C–; it is the acyl group derived from acrylic acid. The preferred IUPAC name for the group is prop-2-enoyl, and it is also known as acrylyl or simply acryl...
is not stable to storage. Acrydite modified oligonucletides can react with nucleophile
Nucleophile
A nucleophile is a species that donates an electron-pair to an electrophile to form a chemical bond in a reaction. All molecules or ions with a free pair of electrons can act as nucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases.Nucleophilic describes the...
s such as thiol
Thiol
In organic chemistry, a thiol is an organosulfur compound that contains a carbon-bonded sulfhydryl group...
s (Michael addition chemistry), this forms the basis of the ez-rays chemistry which was used for microarray
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
s. More importantly, Acrydite modified oligonucleotides can be incorporated, stoichiometrically, into hydrogels such as polyacrylamide
Polyacrylamide
Polyacrylamide is a polymer formed from acrylamide subunits. It can be synthesized as a simple linear-chain structure or cross-linked, typically using N,N-methylenebisacrylamide. Polyacrylamide is not toxic...
, using standard free radical polymerization
Radical polymerization
Free radical polymerization is a method of polymerization by which a polymer forms by the successive addition of free radical building blocks. Free radicals can be formed via a number of different mechanisms usually involving separate initiator molecules...
chemistry, where the double bond in the Acrydite group reacts with other activated double bond
Double bond
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that between two carbon atoms, can be found in alkenes. Many types of double bonds between two different elements exist, for example in...
containing compounds such as acrylamide
Acrylamide
Acrylamide is a chemical compound with the chemical formula C3H5NO. Its IUPAC name is prop-2-enamide. It is a white odourless crystalline solid, soluble in water, ethanol, ether, and chloroform. Acrylamide is incompatible with acids, bases, oxidizing agents, iron, and iron salts...
.
History
The idea of acrylamide modified DNADNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
was developed by T. Christian Boles, while working at Mosaic Technologies, a now-defunct biotechnology company located in Waltham, MA. The IP was licensed, along with a microarray technology ("ez-rays") to Matrix Technologies, of Hudson, NH, which is now part of Thermo Scientific. Acrydite-modified oligonucleotides can be obtained from vendors such as Integrated DNA Technologies (IDT).
Hybridgel
The first use of Acrydite was in a technology called hybridgel. In Hybridgel, Acrydite-modified oligos are incorporated into a standard polyacrylamide gel system; as complementary ss nucleic acid moves past the immobilized Acrydite oligos, the complementary DNA is captured. Hybridgel-like technology is widely used as a DNA purification system, as in a DNA sequencing technology developed at Berkeley. Acrydite technology can also be used to purify DNA, as in the Pre-gen colon cancer test developed by Exact Sciences.Polonys
Mitra and Church at Harvard Medical School developed a novel DNA sequencing technology based on Acrydite modified probes; this technology is used by Agencourt.Acrydite and PCR
Surprisingly, the Acrydite group survives PCR, so Acrydite-modified PCR products can be prepared and used as oligos. However, as is common with polymers that are longer than the persistence lengthPersistence length
The persistence length is a basic mechanical property quantifying the stiffness of a polymer or of a string.Informally, for pieces of the polymer that are shorter than the persistence length, the molecule behaves rather like a flexible elastic rod, while for pieces of the polymer that are much...
, the coupling of Acrydite-modified PCR products is inefficient, as the ends of the molecules are not accessible.
Acrydite and Protein
Acrydite-modified oligonucleotides have been used to study protein DNA interactionsAcrydite and DNA Computing
Recent experiments by Braich et al. solving the Satisfiability Problem have demonstrated that Acrydite can be used in DNA computingDNA computing
DNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area...
to implement the extraction operation. Previously, a biotin-avidin magnetic bead system was used for this purpose.