Hi,
Some elusion buffers contain salts such as NaCl. Presence of NaCl on total RNA sample, can effect on RNA structure? If yes, which RNA coding or non-coding could be affected more? DOes it act as co-factor for RNase enzymes? If not, could we deny the NaCl contaminant influence on RNA for real-time PCR?
I will appreciate your suggestions.
Thanks
Hi Maryam, I think I can answer some of your questions.
First of all, salt concentration will have an effect on the stability of RNA-structure (i.e. free energy of the RNA-secondary structures such as loops etc.). This is modeled by equation 1 defined in this publication:Article Theory for RNA Folding, Stretching, and Melting Including Lo...
Secondly, since (in general) coding RNAs have less stable structures than non-coding RNAs, the former will be affected more (physically). On the other hand, non-coding RNA-structures are thought to be more functionally important, therefore if they are affected, this may have stronger biological implications. However, note that UTRs of mRNAs are thought to have biologically important structures, which may also lead to effects on translation.
Jan
reprecipitate the RNA. Many protocols are available to clean up samples before use in other experiments which has issues with salt.
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