Home FAQs I need to know what types of gel to use to run RNA ladders?

FAQ: I need to know what types of gel to use to run RNA ladders?

In general, when working with single-stranded RNA molecules, one should use a denaturing gel, a denaturing sample loading buffer/dye containing either formamide or urea, and SYBR Gold for staining. The SYBR Gold stain binds preferentially to single-stranded molecules and therefore it give good visualization of the bands after gel electrophoresis.

In some instances, when ssRNA molecules are large in size such as the ssRNA Ladder (N0362S), one can use a native gel and stain the gel with ethidium bromide. But keep in mind that the ssRNA samples must always be prepared using a denaturing sample loading buffer/dye containing either formamide or urea.

When dealing with double-stranded RNA molecules, one only needs to use a native gel, a non-denaturing sample loading buffer/dye, and stain the gel with either ethidium bromide, SYBR Green or SYBR Safe.