Acrydite is a

phosphoramidite A phosphoramidite (RO)2PNR2 is a monoamide of a phosphite diester. The key feature of phosphoramidites is their markedly high reactivity towards nucleophiles catalyzed by weak acids ''e.c''., triethylammonium chloride or 1''H''-tetrazole. In these ...

that allows the synthesis of

oligonucleotides Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids c ...

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 oligonucleotides can react with

nucleophile In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...

s such as

thiol In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl gro ...

s (

Michael addition In organic chemistry, the Michael reaction or Michael addition is a reaction between a Michael donor (an enolate or other nucleophile) and a Michael acceptor (usually an α,β-unsaturated carbonyl) to produce a Michael adduct by creating a carbon ...

chemistry), this forms the basis of the ez-rays chemistry which was used for

microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon t ...

s. More importantly, Acrydite-modified oligonucleotides can be incorporated, stoichiometrically, into hydrogels such as

polyacrylamide Polyacrylamide (abbreviated as PAM) is a polymer with the formula (-CH2CHCONH2-). It has a linear-chain structure. PAM is highly water-absorbent, forming a soft gel when hydrated. In 2008, an estimated 750,000,000 kg were produced, mainly fo ...

, using standard free

radical polymerization In polymer chemistry, free-radical polymerization (FRP) is a method of polymerization by which a polymer forms by the successive addition of free-radical building blocks (repeat units). Free radicals can be formed by a number of different mechanis ...

chemistry, where the double bond in the Acrydite group reacts with other activated

double bond In chemistry, a double bond is a covalent bond between two atoms involving four bonding electrons as opposed to two in a single bond. Double bonds occur most commonly between two carbon atoms, for example in alkenes. Many double bonds exist betw ...

containing compounds such as

acrylamide Acrylamide (or acrylic amide) is an organic compound with the chemical formula CH2=CHC(O)NH2. It is a white odorless solid, soluble in water and several organic solvents. From the chemistry perspective, acrylamide is a vinyl-substituted primary ...

History

The idea of acrylamide-modified DNA 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).

Hybrigel

The first use of Acrydite was in a technology called Hybrigel. In Hybrigel, 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. Hybrigel-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 length The persistence length is a basic mechanical property quantifying the bending stiffness of a polymer. The molecule behaves like a flexible elastic rod/beam (beam theory). Informally, for pieces of the polymer that are shorter than the persistence l ...

, 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 interactions

Acrydite and aptamer-functionalized molecularly imprinted polymers

Acrydite-modified

aptamer Aptamers are short sequences of artificial DNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range of affinities ( KD in the pM to μM range), with little or no off-target binding ...

s (and also aptamers containing internal acrylamide modifications) have been used to make AptaMIPs,

molecularly imprinted polymer A molecularly imprinted polymer (MIP) is a polymer that has been processed using the molecular imprinting technique which leaves cavities in the polymer matrix with an affinity for a chosen "template" molecule. The process usually involves initiatin ...

s that use polymerizable aptamers as monomers for the imprinting. AptaMIPs show enhanced target-binding properties relative to traditional MIPs.

Acrydite and DNA Computing

Experiments by Braich ''et al.'' solving the

Satisfiability Problem In mathematical logic, a formula is ''satisfiable'' if it is true under some assignment of values to its variables. For example, the formula x+3=y is satisfiable because it is true when x=3 and y=6, while the formula x+1=x is not satisfiable over ...

have demonstrated that Acrydite can be used in

DNA computing DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, a ...

to implement the extraction operation. Previously, a biotin–avidin magnetic bead system was used for this purpose.

References

{{reflist Carboxamides Organophosphates