Sometimes I notice that there are two lines, which imply that some of the solution formed into another Shape.
I know the line which doesn’t fit our needs is purified out.
A) Just wondering, are we able to measure how much of the solution, converted to the ideal shape or the unwanted shape? Which I assume would be the real-life equivalent of MFE Structure Frequency.
B) If we could possibly have a solution where the ideal shape is purified out, and the SHAPE data is gathered for the Shape we didnt expect?
The bands in the gel are the results of DNA sequence assembly. The smaller bands aren’t different shapes, they’re different strands of DNA.
When we create DNA, we have to make it out of several smaller pieces of DNA. Usually, they assemble in the correct order to make the desired DNA. However, sometimes they’ll assemble incorrectly and may be missing one of the pieces necessary to make the complete strand of DNA. This shows up as a small band. We then purify the DNA to get only the strands that assembled correctly.
The DNA is then transcribed into RNA, which folds into the shapes you see in EteRNA. During analysis of the RNA, we also test the sequence to ensure that the RNA we’re analyzing is just how you designed it.