Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases
An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphord...
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| Veröffentlicht in: | Organic & biomolecular chemistry 2006-01, Vol.4 (6), p.1115-1123 |
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| creator | Dahl, Britta M Henriksen, Ulla Dahl, Otto |
| description | An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphordiester dimers were stable. Phosphordiester dimers were obtained by replacing cyanoethyl phosphoramidites 2 with phosphoramidites 3, which gave phosphordiesters directly upon oxidation. The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C). |
| doi_str_mv | 10.1039/b517504f |
| format | Article |
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The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C).</description><identifier>ISSN: 1477-0520</identifier><identifier>EISSN: 1477-0539</identifier><identifier>DOI: 10.1039/b517504f</identifier><identifier>PMID: 16525556</identifier><language>eng</language><publisher>England</publisher><subject>Amides ; Base Sequence ; Chromatography, High Pressure Liquid ; Indicators and Reagents ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosides - chemistry ; Oligonucleotides - chemical synthesis ; Oligonucleotides - isolation & purification ; Organophosphates - chemistry ; Organophosphonates - chemistry ; Phosphoramides ; Phosphoric Acids ; Spectrometry, Mass, Fast Atom Bombardment</subject><ispartof>Organic & biomolecular chemistry, 2006-01, Vol.4 (6), p.1115-1123</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c301t-7572fe28e4c9979ac34db8778329aaf2167c6a110fb7defac62e8fed079abed93</citedby><cites>FETCH-LOGICAL-c301t-7572fe28e4c9979ac34db8778329aaf2167c6a110fb7defac62e8fed079abed93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,2831,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16525556$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dahl, Britta M</creatorcontrib><creatorcontrib>Henriksen, Ulla</creatorcontrib><creatorcontrib>Dahl, Otto</creatorcontrib><title>Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases</title><title>Organic & biomolecular chemistry</title><addtitle>Org Biomol Chem</addtitle><description>An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphordiester dimers were stable. Phosphordiester dimers were obtained by replacing cyanoethyl phosphoramidites 2 with phosphoramidites 3, which gave phosphordiesters directly upon oxidation. The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C).</description><subject>Amides</subject><subject>Base Sequence</subject><subject>Chromatography, High Pressure Liquid</subject><subject>Indicators and Reagents</subject><subject>Magnetic Resonance Spectroscopy</subject><subject>Models, Molecular</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleosides - chemistry</subject><subject>Oligonucleotides - chemical synthesis</subject><subject>Oligonucleotides - isolation & purification</subject><subject>Organophosphates - chemistry</subject><subject>Organophosphonates - chemistry</subject><subject>Phosphoramides</subject><subject>Phosphoric Acids</subject><subject>Spectrometry, Mass, Fast Atom Bombardment</subject><issn>1477-0520</issn><issn>1477-0539</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkdFKHDEYhUOpuNYKfYKSq7IFsyaTmcmkd0WqLki9sVciQybzZyeaSdbJbHVezydrZNcKXp1z8fFx4CD0hdEFo1yeNAUTBc3NB3TAciEILbj8-L9ndIY-xXhHKZOizPfRjJVFVhRFeYCel_16CH-hxXHyYwfRRhwMDs6ugt9oB2G0LUT8aMcOK4-Vc5OzGjdK3zfBwwJfvUd18KOy3voVVnrSiT5OpbODcnjLxcQlmXJhtYH4A_8mDIchhSQ3nHRTO4SniWRkvqs9jN3kvqeha8II-MndbkWNihA_oz2jXISjXR6iP2e_rk8vyOXV-fL05yXRnLKRiEJkBrIKci2lkErzvG0qISqeSaVMxkqhS8UYNY1owShdZlAZaGliG2glP0Tftt604yHtHuveRg3OKQ9hE-tSCE5lRRM434J6CDEOYOr1YHs1TDWj9ctf9etfCf26c26aHto3cHcQ_wc03JVp</recordid><startdate>20060101</startdate><enddate>20060101</enddate><creator>Dahl, Britta M</creator><creator>Henriksen, Ulla</creator><creator>Dahl, Otto</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20060101</creationdate><title>Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases</title><author>Dahl, Britta M ; Henriksen, Ulla ; Dahl, Otto</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c301t-7572fe28e4c9979ac34db8778329aaf2167c6a110fb7defac62e8fed079abed93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Amides</topic><topic>Base Sequence</topic><topic>Chromatography, High Pressure Liquid</topic><topic>Indicators and Reagents</topic><topic>Magnetic Resonance Spectroscopy</topic><topic>Models, Molecular</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleosides - chemistry</topic><topic>Oligonucleotides - chemical synthesis</topic><topic>Oligonucleotides - isolation & purification</topic><topic>Organophosphates - chemistry</topic><topic>Organophosphonates - chemistry</topic><topic>Phosphoramides</topic><topic>Phosphoric Acids</topic><topic>Spectrometry, Mass, Fast Atom Bombardment</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dahl, Britta M</creatorcontrib><creatorcontrib>Henriksen, Ulla</creatorcontrib><creatorcontrib>Dahl, Otto</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Organic & biomolecular chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dahl, Britta M</au><au>Henriksen, Ulla</au><au>Dahl, Otto</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases</atitle><jtitle>Organic & biomolecular chemistry</jtitle><addtitle>Org Biomol Chem</addtitle><date>2006-01-01</date><risdate>2006</risdate><volume>4</volume><issue>6</issue><spage>1115</spage><epage>1123</epage><pages>1115-1123</pages><issn>1477-0520</issn><eissn>1477-0539</eissn><abstract>An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphordiester dimers were stable. Phosphordiester dimers were obtained by replacing cyanoethyl phosphoramidites 2 with phosphoramidites 3, which gave phosphordiesters directly upon oxidation. The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C).</abstract><cop>England</cop><pmid>16525556</pmid><doi>10.1039/b517504f</doi><tpages>9</tpages></addata></record> |
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| ispartof | Organic & biomolecular chemistry, 2006-01, Vol.4 (6), p.1115-1123 |
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| source | MEDLINE; Royal Society of Chemistry Journals Archive (1841-2007); Royal Society Of Chemistry Journals 2008-; Alma/SFX Local Collection |
| subjects | Amides Base Sequence Chromatography, High Pressure Liquid Indicators and Reagents Magnetic Resonance Spectroscopy Models, Molecular Nucleic Acid Conformation Nucleosides - chemistry Oligonucleotides - chemical synthesis Oligonucleotides - isolation & purification Organophosphates - chemistry Organophosphonates - chemistry Phosphoramides Phosphoric Acids Spectrometry, Mass, Fast Atom Bombardment |
| title | Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases |
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