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RNA thermal and pH stability/degradation

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Migle

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I have a problem with RNA stability in my reactions: pH=7.4 72 degrees Celsium, 1 h. I see my tRNA degradation after this incubation, when no degradation is observed after 20 min at room temp in the same buffer.
I know that RNA is susceptable to temperature and alkali, but I can not find any concrete information, graphs of RNA stability versus temperature and pH for instance, that could help to adjust my conditions.
I will appreceate any comments, suggestions, your personal experience and links. Thank you.

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 Posted Jul 16, 2008, 13:30 PM
parvoman

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cDNA synthesis reactions are usually about 55-60 degrees and there's no problem with stability there. They do often contain an RNase Inhibitor though - could you include this?

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Posted Jul 17, 2008, 0:09 AM
Migle

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The RNase inhibitor (from Fermentas) is said to be active up to 55 degrees, so I doubt if it's helpful at 70-72.

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Posted Jul 17, 2008, 2:29 AM
parvoman

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I don't know what reaction you're doing at 72 degrees but if it involves a polymerase, it will probably work well at 60 too.

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Posted Jul 19, 2008, 20:41 PM
Migle

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It's an RNA methylation reaction with enzymes from hypertermophilic archaea. The methylation activity drops at lower temperatures.

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Posted Jul 21, 2008, 3:09 AM
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