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Guanidium salts like (G-isothiocyanate) disrupt the hydrophobic interactions inside a protein or nucleic acid and denature it. What happens when hydrophobic interactions in DNA are broken? (I don't think it should get ssDNA because guanidium doesn't break hydrogen bonds within molecules)

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Guanidium is a chaotrope i.e it increases the entropy in the solution. It doesn't disrupt hydrophobic interactions. Guanidium and urea act by forming hydrogen bonds. They can bond with both the dissolved macromolecule and water. The water molecules are arranged as a shell around the hydrophobic regions so as to contain it, which leads to the reduction of entropy. This containment causes hydrophobic regions to come together and give rise to a pseudo-interaction (hydrophobic interaction. See the figure below). Guanidium interacts with the water shell and disorders it, thereby reducing the hydrophobic effect. Guanidium can also interact with macromolecules directly, by forming hydrogen bonds. In this process they can disrupt the normal H-bonds in the macromolecule.

enter image description here

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So what would its effect be on dna ? –  biogirl Jun 9 at 17:36
    
Just think about it: a molecule which can disrupt hydrogen bonds and increase water entropy. What can it do? :) –  WYSIWYG Jun 10 at 6:31
    
DNA becomes single stranded ? –  biogirl Jun 14 at 13:07
    
yes it would... –  WYSIWYG Jun 19 at 19:24

It is important to realize that the hydrophobic effect is largely due to the exclusion of water from non-polar surfaces, which increases entropy. This effect is a major contributor to the helical structure of DNA, which effectively brings the bases closer together and excludes water from contacting their hydrophobic rings. Chaotropic agents like guanidine thiocyanate increase water entropy by disrupting its hydrogen bonding network (decreasing it's order) and this makes it more favourable for hydrophobic surfaces to be exposed to water, thus denaturation can occur. Implicit in that process is that GITC is a hydrogen bond competitor, which is also evident when looking at its structure. So, in fact, GITC can disrupt the hydrogen bonds between base pairs and denature dsDNA at high enough concentrations.

That all said, we're ignoring a major component of aqueous solutions that can also form hydrogen bonds with the bases: water itself! So we must ask ourselves that if a compound capable of hydrogen bonding (water) is present, what exactly is it that holds helical DNA together? While base pairing certainly does contribute, the major factors are the hydrophobic and base stacking interactions.

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hydrophobic effect is largely due to the exclusion of water from non-polar surfaces, which increases entropy: It decreases the entropy because of ordering of the water molecules. –  WYSIWYG Jun 9 at 6:58
    
The entropy of the hydrophobic region increases, though. –  WYSIWYG Jun 9 at 8:12

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