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Often, it is desirable to obtain high MW RNA, free of degradation fragments of small RNAs (i.e. tRNAs), for either rRNA sequence analysis or Northern analysis of mRNAs. The method can also be used in reverse - small RNAs can be isolated free of high MW rRNA components. This can be accomplished by taking advantage of the differences in soluability of RNAs of different size in high concentrations of NaCl. High MW RNAs are insoluable, at 0C, in 2M NaCl, whereas low MW RNAs are soluable.
Remember to use RNase-free technique!


  1. Dissolve RNA to about 5mg/ml in ddH2O or TE, then add an equal volume of 4M NaCl.
  2. Incubate overnight at 0C (i.e. in an ice bath at 4C).
  3. Centrifuge for 10min. in an eppendorf microfuge at 4C, discard the pellet, and dissolve the high MW RNA in the original volume of TE. If you want the low MW RNA, dilute the supernatant in 9 volumes of 300mM NaOAC, then add 3X the new volume of EtOH. Incubate at -70 for 2hr, and centrifuge 15KRPM, 4C, 20min. (SS34 rotor), drain & dry the pellet and dissolve in a small volume of TE.
  4. Measure A260 to determine the exact concentration of RNA (it should be ~80% in high MW RNA and ~20% in low MW RNA).


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