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. 2012 Jun;18(6):1267–1278. doi: 10.1261/rna.031229.111

FIGURE 4.

FIGURE 4.

VapCPAE0151 and VapCPAE2754 target GGUG and GGGG sequences. (A) MALDI-TOF MS of 932 RNA oligonucleotide five negative controls (RNA 0 and 60 min and EDTA) show no degradation of the RNA oligonucleotide due to ribonuclease contamination. Time course assays of VapCPAE0151 (right panel) and VapCPAE2754 (left panel) show very little activity after 1 min at 37°C with VapC. After 5 min, a cut site at GGUG (red fragments in B) is observed with other less optimal cut sites appearing later in the time course (15–60 min; black fragments in B). (B) 932 RNA oligonucleotide five with corresponding cut sites and m/z values; dotted lines represent fragments that were below the MS detection limit. (C) Analysis of VapC cleavage sites across 932 RNA oligonucleotides as calculated by WebLogo (Crooks et al. 2004). The VapC cleavage position is indicated by an arrow. The height of the letter is proportional to the frequency of that base at that particular position.