Magnesium ions are needed when you purify some structured RNA and want to keep it structured throughout your purification process. For example, tRNA have several Mg(2+) binding sites which are important for the maintenance of its L-shape. In the absence of Mg(2+) ions, tRNAs tend to loose their characteristic fold and become unable to interact with tRNA-specific proteins.

Also, even if your target RNA does not specifically need Mg(2+) for structure maintenance, Mg(2+) ions may still bind to it as to any other polyanion. Due to divalent nature of Mg(2+), it causes inter- and intramolecular "crosslinking" of RNA chains and thus makes them to adapt compact folds and stick to each other. It affects RNA behavior during size exclusion chromatography or precipitation.



Maybe this article helps you: Article Short Structured RNAs with Low GC Content Are Selectively Lo...

Regards,

Pedro

Magnesium ions are needed when you purify some structured RNA and want to keep it structured throughout your purification process. For example, tRNA have several Mg(2+) binding sites which are important for the maintenance of its L-shape. In the absence of Mg(2+) ions, tRNAs tend to loose their characteristic fold and become unable to interact with tRNA-specific proteins.

Also, even if your target RNA does not specifically need Mg(2+) for structure maintenance, Mg(2+) ions may still bind to it as to any other polyanion. Due to divalent nature of Mg(2+), it causes inter- and intramolecular "crosslinking" of RNA chains and thus makes them to adapt compact folds and stick to each other. It affects RNA behavior during size exclusion chromatography or precipitation.



I agree with Victor G Stepanov answer

Dear Victor,

Thank you for the helpful comment.

Sharif

Hi Sharif,

I see that the question is a bit old, but since nobody really answered it, I'd like to try and contribute.

No doubt that Mg2+ has fundamental roles in stabilizing RNA tertiary structure as well as as RNA-protein interactions, so it is absolutely required when preparing polyribosomes or performing an RNA-IP or in any other application involving native RNA and RNPs.

But I guess the tip of using 2-5 mM Mg2+ was given to you for simple protocols to extract cytoplasmic RNA from cells or tissues (that is, if you don't apply Trizol directly to a cell pellet or a tissue). In this case, Mg2+ has a totally different role, it is believed to stabilize the nuclear envelope in order to avoid spill-out of genomic DNA from pores that form even when using mild detergents to only solubilize the cytoplasmic membrane. This approach is thought to improve the purity of your RNA reducing the contamination from DNA. In fact in my experience it is only partially efficient, since the role of Mg2+ on the nuclear envelope is stronger when increasing the temperature to 37-42 °C, which is not standard procedure when extracting RNA: typically this is done on ice! So you will always need a DNAse treatment at the end of your extraction protocol, whichever it is. But possibly it is indeed reducing the amount of DNA so that a DNAse treatment will be sufficient to clean up quite thoroughly the RNA from gDNA.

Cheers.

Sorry, last point that just came to my mind: it has been shown that Mg2+ has a specific role in favouring recovery of select miRNAs (the ones with low GC content) during alcoholic precipitation after Trizol extraction only if carrier RNA from the cells (rRNA, lncRNA and mRNA) is not enough, i.e. you have little starting material for the RNA extraction. This is probably due to the reason that Victor was mentioning. But in standard RNA extraction there is no evidence that Mg2+ has any role to improve precipitation.

Cheers.