Footprinting analysis of BWYV pseudoknot-ribosome complexes
نویسندگان
چکیده
منابع مشابه
Quantitative analysis of ribosome–mRNA complexes at different translation stages
Inhibition of primer extension by ribosome-mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved te...
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Conditions are described for using a primer extension inhibition (toeprinting) assay to study the initiation step of protein synthesis in rabbit reticulocyte lysates. These studies revealed that chloramphenicol acetyltransferase mRNA, which is widely used as a reporter, forms unusually labile initiation complexes. This and other unexpected problems were solved by adjustments in pH and temperatu...
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Development of high-throughput approaches to map the RNA interaction sites of individual RNA binding proteins (RBPs) transcriptome-wide is rapidly transforming our understanding of post-transcriptional gene regulatory mechanisms. Here we describe a ribonucleoprotein (RNP) footprinting approach we recently developed for identifying occupancy sites of both individual RBPs and multi-subunit RNP co...
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Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome fo...
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Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a ...
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ژورنال
عنوان ژورنال: RNA
سال: 2009
ISSN: 1355-8382
DOI: 10.1261/rna.1385409