mfold - Salt concentration on RNA folding

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traldi
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Joined: 02/21/2013

When using mfold to fold RNA, is it possible to change the salt concentration, just like we can do for DNA folding?
Thanks!

zukerm
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Joined: 11/12/2010
It is not possible to change

It is not possible to change the salt concentration for RNA because we do not have experimental data for RNA. We do not know what sort of correction to apply. We guess that it would be similar to the correction for DNA, but we don't know the "numbers". In a recent collaboration with an experimentalist, I was asked to apply the DNA correction to RNA. The computed results agreed fairly well with his observations. However, this is just a single example.

Right now, the software will not allow the user to modify salt concentrations for RNA. To get around this without modifying the code, I copied the RNA energy parameters into the current directory. I renamed them to look like DNA energy files. Then I ran an appropriate UNAFold program and told it that I was folding/hybridizing DNA. It allowed me to change salt concentrations. However, the software always looks first in the current working directory for energy files, so it used the RNA energy files renamed to look like DNA energy files. When and if we obtain reliable information on changing salt concentrations for RNA, the software will be modified to allow this without resorting to tricks. :-)

zukerm
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Joined: 11/12/2010
No, salt concentration cannot

No, salt concentration cannot be changed for RNA

zukerm
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Joined: 11/12/2010
I just posted a more detailed

I just posted a more detailed reply than my first one to Dr. Traldi. Please take a look. I also want to add that the experiments for determining RNA free energy parameters are performed in 1 M [Na+] and with no Mg++. These experimental conditions turn out to be roughly equivalent to human physiological conditions: 100-150 mM [Na+] and 10-15 mM [Mg++]. This is not true for DNA. Thus, the RNA parameters are already appropriate for high salt concentrations. One caveat is that if Mg++ is also present, which is almost certainly true, then the net effect is unknown. Although Na+ and Mg++ act together in lower concentrations, they act against one another at higher concentrations. I really can't help you. I suggest that you contact Professor Doug Turner (Chemistry, U. of Rochester, NY) or other researchers who work with microbes that live in extreme environments.