Formation of RNA-protein complexes

The binding buffer should contain Mg2+ and sufficient monovalent ions to ensure specific binding. Divalent ions, in particular Mg2+, play a critical role in proper tertiary folding of RNA. In general, complex RNA such as rRNA requires 10 mM [Mg2+] whereas less complex molecules such as most mRNAs require a lower Mg2+ concentration to fold properly. The monovalent ion concentration should be about 100-300 mM. KC1 or KOAc is generally used as the main source of monovalent ions to simulate the intracellular conditions. 

The optimal conditions should be determined for each RNA-protein complex. 

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