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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 acrylyl group is not stable to storage. Acrydite-modified oligonucleotides 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, 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.

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.^[1] 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.^[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 aptamer-functionalized molecularly imprinted polymers

Acrydite-modified aptamers (and also aptamers containing internal acrylamide modifications) have been used to make AptaMIPs, molecularly imprinted polymers that use polymerizable aptamers as monomers for the imprinting. AptaMIPs show enhanced target-binding properties relative to traditional MIPs.^[6]

Acrydite and DNA Computing

Experiments by Braich et al. solving the Satisfiability Problem have demonstrated that Acrydite can be used in DNA computing to implement the extraction operation.^[7]^[8] Previously, a biotin–avidin magnetic bead system was used for this purpose.

References

^ BioTechniques. 1998 Sep;25(3):516-21. Mutation typing using electrophoresis and gel-immobilized Acrydite probes. Kenney M, Ray S, Boles TC.
^ Proc Natl Acad Sci U S A 2006 May 9; 103(19): 7240–7245. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing
^ Flagship Ventures Archived October 17, 2006, at the Wayback Machine
^ 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.
^ BioTechniques. 2002 Apr;32(4):808-10, 812, 814-5. Acrylamide capture of DNA-bound complexes: electrophoretic purification of transcription factors.
^ Poma, Alessandro; Brahmbhatt, Heli; Pendergraff, Hannah M.; Watts, Jonathan K.; Turner, Nicholas W. (2015). "Generation of Novel Hybrid Aptamer-Molecularly Imprinted Polymeric Nanoparticles". Advanced Materials. 27 (4): 750–758. doi:10.1002/adma.201404235. hdl:2086/16991. PMID 25413444. S2CID 27785428.
^ Ravinderjit S. Braich; et al. (2001). "Solution of a satisfiability problem on a gel-based DNA computer" (PDF). DNA Computing. Lecture Notes in Computer Science. Vol. 2054. pp. 27–42. doi:10.1007/3-540-44992-2_3. ISBN 978-3-540-42076-7. Archived from the original (PDF) on 2006-12-05. Retrieved 2006-03-28.
^ Ravinderjit S. Braich; et al. (2002). "Solution of a 20-Variable 3-SAT Problem on a DNA Computer". Science. 296 (5567): 499–502. Bibcode:2002Sci...296..499B. CiteSeerX 10.1.1.69.7051. doi:10.1126/science.1069528. PMID 11896237. S2CID 94262.

[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] Flagship Ventures Archived October 17, 2006, at the Wayback Machine

[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.

[6] Poma, Alessandro; Brahmbhatt, Heli; Pendergraff, Hannah M.; Watts, Jonathan K.; Turner, Nicholas W. (2015). "Generation of Novel Hybrid Aptamer-Molecularly Imprinted Polymeric Nanoparticles". Advanced Materials. 27 (4): 750–758. doi:10.1002/adma.201404235. hdl:2086/16991. PMID 25413444. S2CID 27785428.

[7] Ravinderjit S. Braich; et al. (2001). "Solution of a satisfiability problem on a gel-based DNA computer" (PDF). DNA Computing. Lecture Notes in Computer Science. Vol. 2054. pp. 27–42. doi:10.1007/3-540-44992-2_3. ISBN 978-3-540-42076-7. Archived from the original (PDF) on 2006-12-05. Retrieved 2006-03-28.

[8] Ravinderjit S. Braich; et al. (2002). "Solution of a 20-Variable 3-SAT Problem on a DNA Computer". Science. 296 (5567): 499–502. Bibcode:2002Sci...296..499B. CiteSeerX 10.1.1.69.7051. doi:10.1126/science.1069528. PMID 11896237. S2CID 94262.

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@@ Line 1: / Line 1: @@
+[[File:Acrydite.svg|thumb|right|Acrydite]]
-{{Chembox new
+'''Acrydite''' is a [[phosphoramidite]] that allows the synthesis of [[oligonucleotides]] with a [[Methacrylic acid|methacryl group]] at the 5' end (less commonly 3' or internal). Acryl oligonucleotides have been tested, but the [[acrylyl group]] is not stable to storage. Acrydite-modified oligonucleotides 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]].
-|   Name = Acrydite
-|   ImageFile = Acrydite Line-Structure.png
-<!-- | ImageSize = 200px -->
-|   ImageName = Line Structure
-|   ImageFile1 = Acrydite 3D-Ball-Stick.png
-<!-- | ImageSize1 = 200px  -->
-|   ImageName1 = 3D Ball and Stick
-|   ImageFile2 = Acrydite Space-Filling.png
-<!-- | ImageSize = 200px -->
-|   ImageName2 = Animation
-|   IUPACName = 6-methacrylamidohexyl phosphate
-| Section1 = {{Chembox Identifiers
-|   CASNo =
-|   SMILES = O=P(O)(O)OCCCCCCNC(C(C)=C)=O
-  }}
-| Section2 = {{Chembox Properties
-|   Formula = C<sub>10</sub>H<sub>20</sub>NO<sub>4</sub>P
-|   MolarMass = 249.246 g/mol
-|   Density =
-|   MeltingPt =
-|   BoilingPt =
-  }}
-}}
-'''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.
-==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.
+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).
-==Hybridgel==
+==Hybrigel==
-The first use of Acrydite was in a technology called hybridgel<ref> Biotechniques. 1998 Sep;25(3):516-21. Mutation typing using electrophoresis and gel-immobilized Acrydite probes. Kenney M, Ray S, Boles TC.</ref>.  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<ref> Proc Natl Acad Sci U S A. 2006 May 9; 103(19): 7240–7245. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing</ref>.  Acrydite technology can also be used to purify DNA, as in the Pre-gen colon cancer test<ref> http://www.flagshipventures.com/news/12132002p.html</ref> developed by Exact Sciences.
+The first use of Acrydite was in a technology called Hybrigel.<ref>BioTechniques. 1998 Sep;25(3):516-21. Mutation typing using electrophoresis and gel-immobilized Acrydite probes. Kenney M, Ray S, Boles TC.</ref>  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.<ref>Proc Natl Acad Sci U S A 2006 May 9; 103(19): 7240–7245. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing</ref>  Acrydite technology can also be used to purify DNA, as in the Pre-gen colon cancer test<ref>[http://www.flagshipventures.com/news/12132002p.html Flagship Ventures<!-- Bot generated title -->] {{webarchive |url=https://web.archive.org/web/20061017212344/http://www.flagshipventures.com/news/12132002p.html |date=October 17, 2006 }}</ref> developed by Exact Sciences.
 ==Polonys==
-Mitra and Church at Harvard Medical School<ref>  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.</ref> developed a novel DNA sequencing technology based on Acrydite modified probes; this technology is used by Agencourt.
+Mitra and Church at Harvard Medical School<ref>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.</ref> 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.
+Surprisingly, the Acrydite group survives [[Polymerase chain reaction|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<ref> Biotechniques. 2002 Apr;32(4):808-10, 812, 814-5. Acrylamide capture of DNA-bound complexes: electrophoretic purification of transcription factors.</ref>
+Acrydite-modified oligonucleotides have been used to study protein DNA interactions<ref>BioTechniques. 2002 Apr;32(4):808-10, 812, 814-5. Acrylamide capture of DNA-bound complexes: electrophoretic purification of transcription factors.</ref>
+==Acrydite and aptamer-functionalized molecularly imprinted polymers==
+Acrydite-modified [[aptamer]]s (and also aptamers containing internal acrylamide modifications) have been used to make AptaMIPs, [[molecularly imprinted polymer]]s that use polymerizable aptamers as monomers for the imprinting. AptaMIPs show enhanced target-binding properties relative to traditional MIPs.<ref>{{Cite journal|last1=Poma|first1=Alessandro|last2=Brahmbhatt|first2=Heli|last3=Pendergraff|first3=Hannah M.|last4=Watts|first4=Jonathan K.|last5=Turner|first5=Nicholas W.|title=Generation of Novel Hybrid Aptamer-Molecularly Imprinted Polymeric Nanoparticles|journal=Advanced Materials|volume=27|issue=4|pages=750–758|doi=10.1002/adma.201404235|pmid=25413444|year=2015|hdl=2086/16991|s2cid=27785428 |hdl-access=free}}</ref>
 ==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.
+Experiments by Braich ''et al.'' solving the [[Satisfiability Problem]] have demonstrated that Acrydite can be used in [[DNA computing]] to implement the extraction operation.<ref>
+{{cite book
+ |author          = Ravinderjit S. Braich
-==Exact Scientific Colon Cancer Test==
+ |chapter = Solution of a satisfiability problem on a gel-based DNA computer
-Acrydite technology has been evaluated by Exact Scientific for use in its colon cancer test.
+ |series = Lecture Notes in Computer Science
+ |date = 2001
-==Citations==
+ |title = DNA Computing
-<references/>
+ |volume          = 2054
+ |pages           = 27–42
-==References==
+ |chapter-url             = http://www.usc.edu/dept/molecular-science/papers/fp-gel-baseddna600.pdf
+ |doi             = 10.1007/3-540-44992-2_3
-*{{cite journal
+ |display-authors = etal
- |  author = Mary Kenney, Satyajit Ray and T. Christian Boles
- |    date = [[1998]]
+ |isbn            = 978-3-540-42076-7
+ |access-date     = 2006-03-28
- |   title = Mutation Typing Using Electrophoresis and Gel-Immobilized Acrydite(TM) Probes
+ |archive-url     = https://web.archive.org/web/20061205034454/http://www.usc.edu/dept/molecular-science/papers/fp-gel-baseddna600.pdf
- | journal = [[Biotechniques]]
- |   issue = 25
+ |archive-date    = 2006-12-05
+ |url-status        = dead
- |   pages = 516–521
+}}
- |     url = http://www.biotechniques.com/
+</ref><ref>{{cite journal
- }} — A paper about Acrydite and its applications.
+ |  author = Ravinderjit S. Braich
-*{{cite journal
+ |    year = 2002
- |  author = Ravinderjit S. Braich ''et al.''
- |    date = [[2000]]
- |   title = Solution of a Satisfiability Problem on a Gel-Based DNA Computer
- | journal = Lecture Notes In Computer Science
- |  volume = 2054
- |   pages = 27–42
- |     url = http://www.usc.edu/dept/molecular-science/papers/fp-gel-baseddna600.pdf
- }} — A paper describing an experiment solving a 6-variable 3-SAT problem.
-*{{cite journal
- |  author = Ravinderjit S. Braich ''et al.''
- |    date = [[2002]]
  |   title = Solution of a 20-Variable 3-SAT Problem on a DNA Computer
- | journal = [[Science (journal)]]
+ | journal = [[Science (journal)|Science]]
  |  volume = 296
  |   pages = 499–502
  |     url = http://www.science.org/
+ |  doi = 10.1126/science.1069528
- }} — A paper describing an experiment solving a 20-variable 3-SAT problem.
+ |  pmid = 11896237
+ |  issue = 5567
+ | bibcode = 2002Sci...296..499B
+ |display-authors=etal|    citeseerx = 10.1.1.69.7051
+ | s2cid = 94262
+ }}</ref> Previously, a biotin–avidin magnetic bead system was used for this purpose.
+==References==
+{{reflist}}
-[[Category:Amides]]
+[[Category:Carboxamides]]
 [[Category:Organophosphates]]