So I ran into an interesting problem. I'm getting a linear DNA band that is twice as long (4x bases, but as denatured probably only 2x) as an RNA band running at the same size in a formaldehyde gel.
Both sequences have been isolated an 100% confirmed. The gel was run in MOPS buffer. My experience, and all the publications I've found, show that if anything RNA should run faster. Can anyone think of a reason why the DNA band and RNA band would be running the distance despite the DNA being twice as long?
I've read a lot of fun papers on drag factors in gel matrices now, but none of it leads to this confusing and repeated result.
Edit: Gel and Conditions
Gel was 1M formaldehyde, 1% agarose. Run at 100V for 1.5h. RNA was mixed in a RNA loading dye which contained 15.3% v/v formaldehyde, 41.3% v/v di formamide, 4.6mM EDTA, MOPS, and bromophenol blue. We believe our RNA loading dye to be denaturing, and it ran at expected size with RNA ladder.
Lane 1 is a DNA template plasmid, cut 1 location.
Lane 2 is the Template + DNase from in vitro transcription reaction w/o polymerase.
Lane 3 is the RNA + DNase from in vitro transcription reaction.
There are no other bands in the DNA lane, and it looks like if anything, the DNA is migrating much faster than expected, despite being sequence confirmed (both before the process, and gel purified out and confirmed again).