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I was reading a paper and came across this table showing $ \Delta \Delta G$ numbers of different nucleotide sequences in DNA/RNA. I know that $\Delta G$ is free energy and $ \Delta \Delta G$ is relative free energy with respect to L. variegatus 5 S RNA gene. What does this numbers signify actually?

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    $\begingroup$ Can you please link the paper. It is important to have the context of the measurement. $\endgroup$ – Chris Mar 20 '15 at 20:31
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    $\begingroup$ These are likely binding energies relative to a known interaction. Without seeing the paper, it's impossible to say for sure. $\endgroup$ – jerepierre Mar 20 '15 at 23:16
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Very basically, what they've done in the paper was incubate different DNA sequences with histone octamers which were then separated on a gel. From this they could measure the ratio between nucleosomal and free DNA, which represents an equilibrium constant. This can then be expressed as a change in free energy ($\Delta G=-RTln(K)$), which is what the table shows. A lower (more negative) free energy change corresponds to a higher equilibrium constant which represents a greater proportion of DNA bound to histones. In other words, the free energy change quantifies the propensity of these different DNA sequences to form nucleosomes.

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