Final answer:
Intact RNA seen on an agarose gel electrophoresis will display distinct, sharp bands without smearing, indicating no degradation. Denaturing polyacrylamide gel also shows sharp bands for intact RNA, with urea helping to unfold RNA for separation by molecular weight.
Step-by-step explanation:
When you observe an agarose gel electrophoresis that tests for RNA integrity, intact RNA will appear as distinct, sharp bands. If the RNA is intact, you might see a clear rRNA banding pattern, such as the 28S and 18S ribosomal RNA bands in eukaryotic samples, which should display a ratio of approximately 2:1. The presence of these defined bands with no smearing indicates that the RNA has not degraded. On a denaturing polyacrylamide gel, which is used for the separation of smaller RNA molecules, intact RNA will also appear as sharp, distinct bands, and not as a smear, which would imply degradation.
During the electrophoresis process, urea is used as a chaotrope to unfold the RNA by hydrogen-bonding with the nucleobases, which helps in separating the RNA molecules based on molecular weight. If contamination occurs, such as the presence of RNase A, you will notice a degradation of RNA which results in a loss of this clear banding pattern on an agarose gel-based assay. Compounds are sometimes used to inhibit this degradation, and effective inhibitors will preserve the integrity of the RNA, maintaining distinct bands on the gel.
In summary, visible indicators of intact RNA on a gel include clear, discrete bands at expected sizes without smearing.