Currently I am trying different concentrations of HIV RNA, 1um, 4um, 6um, and 10um. I'm wondering if anyone has tried this perhaps in another RNA virus model and had success; by changing pH or Magnesium concentration?
Are you talking about fragments of HIV-1 RNA synthesized by in vitro transcription? If this is the case, you have to adjust the gel type depending on the RNA length. Otherwise, the key parameters are temperature of the gel (0°C or room temperature) and salt concentration, especially Mg2+ both in the incubation buffer and the electrophoresis buffer.
Make sure that you don't non-denaturing loading dye as it will a native PAGE (without Urea).
In normal conditions you have usually formamide in the loading buffer which is also a denaturing agent...in non-denaturing loading buffers (you have glycerol instead (the one which is used for agarose gel...check 6X loading dye from ThermoScientific). Both contains same gel tracking dyes (Bromophenol blue and Cyanol).
So if you use non-denaturing buffer (commonly called as loading dye in many labs) you are sure that native conformation of RNA is not tampered by loading buffer..
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