Electrophoretic Mobility Of RNA Research Articles

Analysis of natural populations and possible natural reassortment of Cucumber mosaic virus

Plants naturally infected with Cucumber mosaic virus (CMV) were collected and analyzed by electrophoresis of the replicative form of dsRNA and by Northern blot hybridization using CMV RNA-specific probes. Some of the CMV-infected plants, especially winter crops, contained two kinds of RNA 1 segments or RNA 2 segments (or both), suggesting that mixed infections of CMV occurred naturally. Single-aphid-transmitted isolates (SATIs) from the field isolate containing two RNA 1 segments were grouped into three types by the electrophoretic mobility of RNA 1 (i.e., those containing one slow segment, those containing one fast segment, and those containing both). Furthermore, SATIs and single-lesion isolates, generated from the plants inoculated with a mixture of two CMV isolates that could be differentiated by their electrophoretic dsRNA profiles, were analyzed by dsRNA, indicating that nonparental progenies were observed. These results suggested that genetic reassortment of CMV RNA may occur in nature and that this is an important mechanism in CMV evolution.

Detection of β-Amyloid Peptide Aggregation Using DNA Electrophoresis

DNA could readily associate with the aggregated forms of the β-amyloid peptides β(1–40) and β(25–35), giving rise to a shift in the electrophoretic mobility of DNA. As a result, DNA was retained at the top of a 1% agarose gel. In contrast, the electrophoretic mobility of DNA was little influenced by the monomeric forms of β(1–40) and β(25–30). DNA from different sources such as λ phage, Escherichia coli plasmid, and human gene showed similar results. However, the electrophoretic mobility of RNA was shifted by the monomeric β(1–40) and β(25–35) as well as by the aggregated β(1–40) and β(25–35). The association of DNA with the aggregated β-amyloid peptides could occur at pH 4–9. The inhibitory action of hemin on β-amyloid aggregation could be confirmed using the DNA mobility shift assay. These results indicate that the DNA mobility shift assay is useful for kinetic study of β-amyloid aggregation as well as for testing of agents that might modulate β-amyloid aggregation.

The effect of temperature and ionic strength of the electrophoretic mobility of yeast mitochondrial RNA.

The electrophoretic mobilities of mitochondrial and cell‐sap ribosomal RNAs from Saccharomyces carlsbergensis have been measured relative to the mobility of Escherichia coli rRNA in 2.4% polyacrylamide gels at various temperatures and ionic strengths. At 5° C and in 20 mM sodium acetate, 40 mM Tris‐acetate, 2 mM EDTA (pH 7.8), mitochondrial and cell‐sap rRNAs co‐migrated and were only partially resolved from E. coli rRNA. When the temperature of electrophoresis was increased the mobility of the mitochondrial rRNAs (and to a lesser extent of the cell‐sap rRNAs) decreased relative to the mobility of the E. coli rRNA species, reaching a minimum between 9 and 16° C. As a consequence the mitochondrial and cell‐sap rRNAs were completely resolved in this buffer at temperatures above 9° C. Similar effects of temperature on relative electrophoretic mobility were observed in 90 mM Tris‐borate buffer at pH 8.3 and the effect was even more pronounced at low ionic strength (10 mM NaCl, 5 mM Tris‐HCl, 2 mM EDTA, pH 7.5).At low ionic strength the decrease in the relative electrophoretic mobility of mitochondrial rRNA with an increase in temperature was accompanied by a decrease in sedimentation coefficient from 21–22 S (large component) and 14 S (small component) at 5° C to 16 and 11.5 S at 20° C (calculated in relation to assumed S‐values of 23 and 16 S for the rRNA species of E. coli).We conclude that the electrophoretic mobility of RNA in polyacrylamide gels is more dependent on secondary structure than previous work had suggested and that caution is needed to interpret the relative mobility of mitochondrial RNA on gels in terms of molecular weight. In addition, our results show that judicious variation of temperature and ionic strength may allow the separation on gels of RNA mixtures that cannot be resolved under standard conditions.