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Ribotyping is a molecular technique for bacterial identification and characterization that uses information from rRNA-based phylogenetic analyses. [1] It is a rapid and specific method widely used in clinical diagnostics and analysis of microbial communities in food, water, and beverages.
In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs). Therefore it can be deduced that in both bacteria and archaea there is one rRNA gene that codes for all three rRNA types :16S, 23S and 5S. [27] Bacterial 16S ribosomal RNA, 23S ...
Gel electrophoresis of large DNA or RNA is usually done by agarose gel electrophoresis. See the " chain termination method " page for an example of a polyacrylamide DNA sequencing gel. Characterization through ligand interaction of nucleic acids or fragments may be performed by mobility shift affinity electrophoresis .
Following the restriction reaction, the mixture of fragments is separated using either capillary or polyacrylamide electrophoresis in a DNA sequencer and the sizes of the different terminal fragments are determined by the fluorescence detector. Because the excised mixture of amplicons is analyzed in a sequencer, only the terminal fragments (i.e ...
The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements.. The integrity of RNA is a major concern for gene expression studies and traditionally has been evaluated using the 28S to 18S rRNA ratio, a method that has been shown to be inconsistent. [1]
A mobility shift assay is electrophoretic separation of a protein–DNA or protein–RNA mixture on a polyacrylamide or agarose gel for a short period (about 1.5-2 hr for a 15- to 20-cm gel). [4] The speed at which different molecules (and combinations thereof) move through the gel is determined by their size and charge, and to a lesser extent ...
The RNA degradosome is a huge multi-enzyme association that is involved in RNA metabolism and post-transcriptional control of gene expression in numerous bacteria such as Escherichia coli and Pseudoalteromonas haloplanktis. The multi-protein complex also serves as a machine for processing structured RNA precursors in the course of their maturation.
The 40S subunit contains a 18S ribosomal RNA (abbreviated 18S rRNA), which is homologous to the prokaryotic 16S rRNA. The 60S subunit contains a 28S rRNA that is homologous to the prokaryotic 23S ribosomal RNA. In addition, it contains a 5.8S rRNA that corresponds to the 5' end of the 23S rRNA, and a short 5S rRNA.
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