Transcription simulation – gel analysis

This interactive page simulates a transcription reaction, analyzed by gel electrophoresis. You can specify the length of the RNA and the (uniform) probability of random dissociation throughout the length. You can also optionally specify a (single) termination site.

The point of this exercise is to illustrate that for long RNAs, even a small chance of position-independent termination/release can significantly reduce the yield of the full length, encoded product with little indication in the gel. Moreover, since most detection methods (staining or incorporation of alpha-labeled NTPs) intensities depend on mass, not molarity, the problem is far worse than expected. You can toggle below between “count” (detected by 5′ 32P or fluorescent labeling) and “stain.”

Finally, you can “zoom” sensitivity by lowering the y-axis maximum (which will clip your full length product intensity).

Runoff RNA length        % fall off at each length         Termination: position    % termination

y-axis maximum