Acrydite

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 nucleophiles such as thiols (Michael addition chemistry), this forms the basis of the ez-rays chemistry which was used for microarrays. More importantly, Acrydite modified oligonucleotides can be incorporated, stochiometrically, 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.

Additional recommended knowledge

Daily Sensitivity Test

Weighing the right way

How to quickly check pipettes?

Chemical Structure

The chemical structures shown in the box are somewhat misleading as they show a molecule that does not actually exist. It is recommended that literature be consulted for more details.

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 Electron Corp. Acrydite is commercially available from Biosearch Technologys, Novato, CA. Acrydite-modified oligonucleotides can be obtained from vendors such as IDT.

Hybridgel

The first use of Acrydite was in a technology called hybridgel^[1]. 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^[2]. Acrydite technology can also be used to purify DNA, as in the Pre-gen colon cancer test^[3] developed by Exact Sciences.

Polonys

Mitra and Church at Harvard Medical School^[4] 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 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^[5]

Acrydite and DNA Computing

Recent experiments by Braich et al. solving the Satisfiability Problem have demonstrated that Acrydite can be used in DNA computing to implement the extraction operation. Previously, a biotin-avidin magnetic bead system was used for this purpose.

Exact Scientific Colon Cancer Test

Acrydite technology has been evaluated by Exact Scientific for use in its colon cancer test.

Citations

1. ^ Biotechniques. 1998 Sep;25(3):516-21. Mutation typing using electrophoresis and gel-immobilized Acrydite probes. Kenney M, Ray S, Boles TC.
2. ^ Proc Natl Acad Sci U S A. 2006 May 9; 103(19): 7240–7245. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing
3. ^ http://www.flagshipventures.com/news/12132002p.html
4. ^ Nucleic Acids Res. 1999 Dec 15;27(24):e34. In situ localized amplification and contact replication of many individual DNA molecules. Mitra RD, Church GM.
5. ^ Biotechniques. 2002 Apr;32(4):808-10, 812, 814-5. Acrylamide capture of DNA-bound complexes: electrophoretic purification of transcription factors.

References

• Mary Kenney, Satyajit Ray and T. Christian Boles (1998). "Mutation Typing Using Electrophoresis and Gel-Immobilized Acrydite(TM) Probes". Biotechniques (25): 516–521. — A paper about Acrydite and its applications.
• Ravinderjit S. Braich et al. (2000). "Solution of a Satisfiability Problem on a Gel-Based DNA Computer". Lecture Notes In Computer Science 2054: 27–42. — A paper describing an experiment solving a 6-variable 3-SAT problem.
• Ravinderjit S. Braich et al. (2002). "Solution of a 20-Variable 3-SAT Problem on a DNA Computer". Science (journal) 296: 499–502. — A paper describing an experiment solving a 20-variable 3-SAT problem.