Can I reconstitute ds siRNA in DW, - instead of 100 mM KOAC-20 mM HEPES? (Sep/05/2008 )
Someone asked me if it is OK to use DW, not supplied 100 mM KOAC-20 mM HEPES to dissolve the dried siRNA pair he received from IDT, cook these to 98C and cool it down to make it ds siRNA. I think it probably will be OK, what do you think?
If you have to anneal two ssRNAs to made a dsRNA, you have to use the buffer they provided. For dsRNA already annealed (such as dsRNA provided by Invitrogen), you just need to resuspend it in RNase free water.
I just found out from IDT that these siRNAs came as annealed products. Thanks, pcrman!
In deionized water, the anion-anion repulsion of the phosphate backbones will drive the strands apart. The ions of the buffer help to stabilize the close approach of the phosphates needed to form stable Watson-Crick pairs. You can blow apart the secondary structure of mRNA by putting it into pure water. I don't know whether pre-annealed siRNA strands will separate if put into pure water; it seems likely considering the behavior of mRNA under similar conditions. PCRman, will the duplex be stable if dissolved in pure water, or are you relying on reannealing when introduced into a cell?