Ethynyl Side Chain Hydration during Synthesis and Workup of “Clickable” Oligonucleotides: Bypassing Acetyl Group Formation by Triisopropylsilyl Protection
Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines (ethdC and ethdU) or the 7-position of 7-deazaguanine (ethc7Gd) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass...
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| Published in | Journal of organic chemistry Vol. 78; no. 22; pp. 11271 - 11282 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
WASHINGTON
American Chemical Society
15.11.2013
Amer Chemical Soc |
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| Abstract | Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines (ethdC and ethdU) or the 7-position of 7-deazaguanine (ethc7Gd) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases. |
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| AbstractList | Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases. Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines (ethdC and ethdU) or the 7-position of 7-deazaguanine (ethc7Gd) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases. Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl -> acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases. |
| Author | Leonard, Peter Seela, Frank Ingale, Sachin A Mei, Hui |
| AuthorAffiliation | Center for Nanotechnology Universität Osnabrück Laboratory of Bioorganic Chemistry and Chemical Biology Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien |
| AuthorAffiliation_xml | – name: Center for Nanotechnology – name: Universität Osnabrück – name: Laboratory of Bioorganic Chemistry and Chemical Biology – name: Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien |
| Author_xml | – sequence: 1 givenname: Sachin A surname: Ingale fullname: Ingale, Sachin A – sequence: 2 givenname: Hui surname: Mei fullname: Mei, Hui – sequence: 3 givenname: Peter surname: Leonard fullname: Leonard, Peter – sequence: 4 givenname: Frank surname: Seela fullname: Seela, Frank email: Frank.Seela@uni-osnabrueck.de |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24138578$$D View this record in MEDLINE/PubMed |
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| Keywords | MAJOR GROOVE FUNCTIONALIZATION CYCLOADDITION DUPLEX STABILITY NUCLEOSIDES IN-VIVO TERMINAL ALKYNES DNA-SYNTHESIS AZIDE NUCLEIC-ACIDS |
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| Snippet | Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines (ethdC and ethdU) or the 7-position of 7-deazaguanine (ethc7Gd) are hydrated... Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are... |
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| SubjectTerms | Chemistry Chemistry, Organic Cross-Linking Reagents - chemical synthesis Cross-Linking Reagents - chemistry Guanine - analogs & derivatives Guanine - chemistry Hydrolysis Molecular Conformation Oligonucleotides - chemical synthesis Oligonucleotides - chemistry Physical Sciences Pyrimidines - chemistry Science & Technology Silanes - chemistry Water - chemistry |
| Title | Ethynyl Side Chain Hydration during Synthesis and Workup of “Clickable” Oligonucleotides: Bypassing Acetyl Group Formation by Triisopropylsilyl Protection |
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