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Scintillation proximity assay for measurement of RNA methylation.

Baker MR, Zarubica T, Wright HT, Rife JP - Nucleic Acids Res. (2009)

Bottom Line: Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA-protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time.In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC' most efficiently methylates protein-depleted or protein-free 23S rRNA.We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0133, USA.

ABSTRACT
Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA-protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time. This has traditionally required the separation of radiolabeled product from radiolabeled methyl donor through a filter binding assay. We have adapted and optimized a scintillation proximity assay (SPA) to replace the more costly, wasteful and cumbersome filter binding assay and demonstrate its utility in studies of three distinct methyltransferases, RmtA, KsgA and ErmC'. In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC' most efficiently methylates protein-depleted or protein-free 23S rRNA. This assay does not utilize engineered affinity tags that are often required in SPA, and is capable of detecting either radiolabeled RNA or RNA-protein complex. We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors. This assay can be carried out with techniques routinely used in a typical biochemistry laboratory or could be easily adapted for a high throughput screening format.

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Related in: MedlinePlus

Extent of methylation. Time courses measured by SPA in this figure are expressed in number of methyl groups incorporated into RNA. Formulas derived from Figure 3 were used to convert SPA measurements into ‘filter binding equivalent’ values for quantitation of methyl group incorporation. RmtA + wild-type 30S (maroon); KsgA + ksgR 30S (orange).
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Figure 4: Extent of methylation. Time courses measured by SPA in this figure are expressed in number of methyl groups incorporated into RNA. Formulas derived from Figure 3 were used to convert SPA measurements into ‘filter binding equivalent’ values for quantitation of methyl group incorporation. RmtA + wild-type 30S (maroon); KsgA + ksgR 30S (orange).

Mentions: Excel was used to obtain a linear fit of data in Figures 3, 6 and background data in Figure 2, and a logarithmic fit of signal data in Figures 2 and 4.Figure 3.


Scintillation proximity assay for measurement of RNA methylation.

Baker MR, Zarubica T, Wright HT, Rife JP - Nucleic Acids Res. (2009)

Extent of methylation. Time courses measured by SPA in this figure are expressed in number of methyl groups incorporated into RNA. Formulas derived from Figure 3 were used to convert SPA measurements into ‘filter binding equivalent’ values for quantitation of methyl group incorporation. RmtA + wild-type 30S (maroon); KsgA + ksgR 30S (orange).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651799&req=5

Figure 4: Extent of methylation. Time courses measured by SPA in this figure are expressed in number of methyl groups incorporated into RNA. Formulas derived from Figure 3 were used to convert SPA measurements into ‘filter binding equivalent’ values for quantitation of methyl group incorporation. RmtA + wild-type 30S (maroon); KsgA + ksgR 30S (orange).
Mentions: Excel was used to obtain a linear fit of data in Figures 3, 6 and background data in Figure 2, and a logarithmic fit of signal data in Figures 2 and 4.Figure 3.

Bottom Line: Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA-protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time.In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC' most efficiently methylates protein-depleted or protein-free 23S rRNA.We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0133, USA.

ABSTRACT
Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA-protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time. This has traditionally required the separation of radiolabeled product from radiolabeled methyl donor through a filter binding assay. We have adapted and optimized a scintillation proximity assay (SPA) to replace the more costly, wasteful and cumbersome filter binding assay and demonstrate its utility in studies of three distinct methyltransferases, RmtA, KsgA and ErmC'. In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC' most efficiently methylates protein-depleted or protein-free 23S rRNA. This assay does not utilize engineered affinity tags that are often required in SPA, and is capable of detecting either radiolabeled RNA or RNA-protein complex. We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors. This assay can be carried out with techniques routinely used in a typical biochemistry laboratory or could be easily adapted for a high throughput screening format.

Show MeSH
Related in: MedlinePlus