Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.
Selective alkylation of RNA nucleotides is an important field of RNA biochemistry, e.g. in applications of fluorescent labeling or in structural probing experiments, yet detailed structure-function studies of labeling agents are rare. Here, bromomethylcoumarins as reactive compounds for fluorescent...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23844135/pdf/?tool=EBI |
| _version_ | 1828897362212290560 |
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| author | Stefanie Kellner Laura Bettina Kollar Antonia Ochel Manjunath Ghate Mark Helm |
| author_facet | Stefanie Kellner Laura Bettina Kollar Antonia Ochel Manjunath Ghate Mark Helm |
| author_sort | Stefanie Kellner |
| collection | DOAJ |
| description | Selective alkylation of RNA nucleotides is an important field of RNA biochemistry, e.g. in applications of fluorescent labeling or in structural probing experiments, yet detailed structure-function studies of labeling agents are rare. Here, bromomethylcoumarins as reactive compounds for fluorescent labeling of RNA are developed as an attractive scaffold on which electronic properties can be modulated by varying the substituents. Six different 4-bromomethyl-coumarins of various substitution patterns were tested for nucleotide specificity of RNA alkylation using tRNA from Escherichia coli as substrate. Using semi-quantitative LC-MS/MS analysis, reactions at mildly acidic and slightly alkaline pH were compared. For all tested compounds, coumarin conjugates with 4-thiouridine, pseudouridine, guanosine, and uridine were identified, with the latter largely dominating. This data set shows that selectivity of ribonucleotide alkylation depends on the substitution pattern of the reactive dye, and even more strongly on the modulation of the reaction conditions. The latter should be therefore carefully optimized when striving to achieve selectivity. Interestingly, the highest selectivity for labeling of a modified nucleoside, namely of 4-thiouridine, was achieved with a compound whose selectivity was somewhat less dependent on reaction conditions than the other compounds. In summary, bromomethylcoumarin derivatives are a highly interesting class of compounds, since their selectivity for 4-thiouridine can be efficiently tuned by variation of substitution pattern and reaction conditions. |
| first_indexed | 2024-12-13T14:56:24Z |
| format | Article |
| id | doaj.art-821dda3b8b0a49af96dfb2e4d717bd8d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T14:56:24Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-821dda3b8b0a49af96dfb2e4d717bd8d2022-12-21T23:41:14ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6794510.1371/journal.pone.0067945Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.Stefanie KellnerLaura Bettina KollarAntonia OchelManjunath GhateMark HelmSelective alkylation of RNA nucleotides is an important field of RNA biochemistry, e.g. in applications of fluorescent labeling or in structural probing experiments, yet detailed structure-function studies of labeling agents are rare. Here, bromomethylcoumarins as reactive compounds for fluorescent labeling of RNA are developed as an attractive scaffold on which electronic properties can be modulated by varying the substituents. Six different 4-bromomethyl-coumarins of various substitution patterns were tested for nucleotide specificity of RNA alkylation using tRNA from Escherichia coli as substrate. Using semi-quantitative LC-MS/MS analysis, reactions at mildly acidic and slightly alkaline pH were compared. For all tested compounds, coumarin conjugates with 4-thiouridine, pseudouridine, guanosine, and uridine were identified, with the latter largely dominating. This data set shows that selectivity of ribonucleotide alkylation depends on the substitution pattern of the reactive dye, and even more strongly on the modulation of the reaction conditions. The latter should be therefore carefully optimized when striving to achieve selectivity. Interestingly, the highest selectivity for labeling of a modified nucleoside, namely of 4-thiouridine, was achieved with a compound whose selectivity was somewhat less dependent on reaction conditions than the other compounds. In summary, bromomethylcoumarin derivatives are a highly interesting class of compounds, since their selectivity for 4-thiouridine can be efficiently tuned by variation of substitution pattern and reaction conditions.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23844135/pdf/?tool=EBI |
| spellingShingle | Stefanie Kellner Laura Bettina Kollar Antonia Ochel Manjunath Ghate Mark Helm Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. PLoS ONE |
| title | Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. |
| title_full | Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. |
| title_fullStr | Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. |
| title_full_unstemmed | Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. |
| title_short | Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. |
| title_sort | structure function relationship of substituted bromomethylcoumarins in nucleoside specificity of rna alkylation |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23844135/pdf/?tool=EBI |
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