Does cation concentration change hybridization ranking ?

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Axel
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Joined: 03/24/2013

Hello Everybody,

I plan to calculate the free energies of many different DNA hybridizations and I'm interested in the ranking (which hybridization gives the largest free energy) and not so much in the absolute values.

Changing cation concentrations results in different delta G values, but what happens to the ranking? Is it also changed or can I assume that the ranking remains the same?

Many thanks,
Axel

Axel
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Joined: 03/24/2013
okay, I now tested it myself

okay, I now tested it myself the primitive way.
I performed 5000 hybridizations under 1M and 0.1M sodium concentration and ranked them according to the free energy. Many of the entries changed their index position, but only minimally (e.g. from position 10 to 15). For me that's good enough and perhaps this information is also useful for others.

Axel