Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

Autoren

Stefanie Kellner
Laura Bettina Kollar
Antonia Ochel
Manjunath Ghate
Mark Helm

Autoren-URL

https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000321733000118&DestLinkType=FullRecord&DestApp=WOS_CPL

DOI

10.1371/journal.pone.0067945

Externe Identifier

Clarivate Analytics Document Solution ID: 182HT
PubMed Identifier: 23844135

ISSN

1932-6203

Ausgabe der Veröffentlichung

7

Zeitschrift

PLOS ONE

Artikelnummer

ARTN e67945

Datum der Veröffentlichung

2013

Status

Published

Titel

Structure-Function Relationship of Substituted Bromomethylcoumarins in Nucleoside Specificity of RNA Alkylation

Sub types

Article

Ausgabe der Zeitschrift

8

Datenquelle: Web of Science (Lite)

Autoren

Stefanie Kellner
Laura Bettina Kollar
Antonia Ochel
Manjunath Ghate
Mark Helm

DOI

10.1371/journal.pone.0067945

Editoren

Michael M Meijler

eISSN

1932-6203

Ausgabe der Veröffentlichung

7

Zeitschrift

PLoS ONE

Sprache

en

Online publication date

2013

Paginierung

e67945 - e67945

Status

Published online

Herausgeber

Public Library of Science (PLoS)

Herausgeber URL

http://dx.doi.org/10.1371/journal.pone.0067945

Datum der Datenerfassung

2018

Titel

Structure-Function Relationship of Substituted Bromomethylcoumarins in Nucleoside Specificity of RNA Alkylation

Ausgabe der Zeitschrift

8

Datenquelle: Crossref

Abstract

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.

Addresses

Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany.

Autoren

Stefanie Kellner
Laura Bettina Kollar
Antonia Ochel
Manjunath Ghate
Mark Helm

DOI

10.1371/journal.pone.0067945

eISSN

1932-6203

Externe Identifier

PubMed Identifier: 23844135
PubMed Central ID: PMC3700928

Open access

true

ISSN

1932-6203

Ausgabe der Veröffentlichung

7

Zeitschrift

PloS one

Schlüsselwörter

Escherichia coli
Coumarins
Nucleosides
RNA, Bacterial
RNA, Transfer
Fluorescent Dyes
Staining and Labeling
Structure-Activity Relationship
Alkylation

Sprache

eng

Medium

Electronic-Print

Online publication date

2013

Open access status

Open Access

Paginierung

e67945

Datum der Veröffentlichung

2013

Status

Published

Publisher licence

CC BY

Datum der Datenerfassung

2013

Titel

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.

Sub types

Research Support, Non-U.S. Gov't
research-article
Journal Article

Ausgabe der Zeitschrift

8

Files

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0067945&type=printable https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23844135/pdf/?tool=EBI https://europepmc.org/articles/PMC3700928?pdf=render

Datenquelle: Europe PubMed Central

Abstract

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.

Date of acceptance

2013

Autoren

Stefanie Kellner
Laura Bettina Kollar
Antonia Ochel
Manjunath Ghate
Mark Helm

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/23844135

DOI

10.1371/journal.pone.0067945

eISSN

1932-6203

Externe Identifier

PubMed Central ID: PMC3700928

Ausgabe der Veröffentlichung

7

Zeitschrift

PLoS One

Schlüsselwörter

Alkylation
Coumarins
Escherichia coli
Fluorescent Dyes
Nucleosides
RNA, Bacterial
RNA, Transfer
Staining and Labeling
Structure-Activity Relationship

Sprache

eng

Country

United States

Paginierung

e67945

PII

PONE-D-13-09930

Datum der Veröffentlichung

2013

Status

Published online

Datum, an dem der Datensatz öffentlich gemacht wurde

2014

Titel

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

8

Datenquelle: PubMed

Author's licence

CC-BY

Autoren

Stefanie Kellner
Laura Bettina Kollar
Antonia Ochel
Manjunath Ghate
Mark Helm

Hosting institution

Universitätsbibliothek Mainz

Sammlungen

DFG-OA-Publizieren (2012 - 2017)

Resource version

Published version

DOI

10.1371/journal.pone.0067945

Funding acknowledgements

DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin

File(s) embargoed

false

Open access

true

ISSN

1932-6203

Ausgabe der Veröffentlichung

7

Zeitschrift

PLoS one

Schlüsselwörter

500 Naturwissenschaften
500 Natural sciences and mathematics

Sprache

eng

Open access status

Open Access

Paginierung

e67945

Datum der Veröffentlichung

2013

Public URL

https://openscience.ub.uni-mainz.de/handle/20.500.12030/7847

Herausgeber

PLoS

Herausgeber URL

http://dx.doi.org/10.1371/journal.pone.0067945

Datum der Datenerfassung

2022

Datum, an dem der Datensatz öffentlich gemacht wurde

2022

Zugang

Public

Titel

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

Ausgabe der Zeitschrift

8

Files

structurefunction_relationshi-20220914003538694.pdf

Datenquelle: OPENSCIENCE.UB

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

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