I am performing HDV ribozyme cleavage of my RNA due to which I have to dephosphorylate the 3' end. After gel elution of my band of interest and RNA precipitation, I have 350 ug of RNA which is very pure (confirmed by urea-PAGE). I dephosphorylate my RNA using 100 mM Imidazole, 10 mM Mgcl2, 0.1 mM ATP, 20ug/ml BSA, 1 mM DTT and 67 U of T4 pnk. I run a gel to confirm dephosophorylation. After this when I perform phenol chloroform extraction (PCA mix 4.5 ph) and precipitate with sodium acetate and 3x volume 100% etoh. I see a pellet but when I resuspend I get only 40 ug with very 260/280 at 3 and 260/230 at 1.5.

I use the same phenol chloroform extraction method after IVT with no issues. why isn't my extraction working?