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See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq. Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression. They show number of protein protected ...


6

You have two possibilities: When you only need a quick check if your RNA is ok and you indeed only get one band, you can try a "quick and dirty" method. Heat the sample for 5 minutes at 65°C and then immediately cool it down in an icebath and keep it there until loading. By doing so, you melt up the secondary structure of the RNA and keep it in this state. ...


2

RNA is amenable to folding, which produces secondary structure and alters its mobility (compare to supercoiled DNA). Therefore, if you don't denature your RNA appropriately, even a single species will produce a smear. A common strategy is to incorporate denaturing chemicals such as formaldehyde into the procedure. See this Life Technologies protocol. ...



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