I suggest you do the Trizol extraction, and then treat with DNase. Heat inactivation would be fine for most RNA, but if you really are worried the repeated Trizol cleanup will be fine. You can also consider using Phasemaker tubes (Thermo) to maximize aqueous phase recovery without worrying about disturbing the interface.

Added file.

By heat inactivation and treating with proteinase K followed by phenol:chloroform extraction

Dear Katy,

Your ideas and your approaches are spot on. I modestly feel that the third option of yours would be better for your approach. However, I would suggest you to perform a trial-and-error experiment using the mentioned approaches; Alternatively, if you feel you don't have the time and enough samples for your extraction, I would suggest you to use the products from the same brand where there maybe high chances for maximal recovery of your intended product. I resort to doing this for complicated extractions.

There are four main steps to extract nucleic acids

The lysis of cells

Protein denaturation and nucleoprotein complexes

The inactivation of nucleases

The purification of nucleic acids (DNA or RNA)

Thank you all for your answers ! :)

I tried different methods and realised that based on the growth medium I used, I had very various amounts of impurities so I will have to work with trial-and-error experiments.