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FORCES THAT AFFECT THE STABILITY OF THE DNA DOUBLE HELIX


Three types of forces that contribute to maintaining the stability of the DNA double helix are: (1) hydrophobic interactions, (2) stacking interactions and (3) hydrogen bonding.
The base pairs in the interior of the DNA molecules create a hydrophobic environment, with the negatively charged phosphates along the backbone being exposed to the solvent. Thus, in an aqueous environment, the double stranded structure is stabilized by the hydrophobic interior. Reagents that solubilize the DNA bases (eg. Methanol) destabilize the double helix. Stacking interactions and hydrogen bonding interactions are relatively Weak but additive.

Reagents that disrupt hydrogen bonding (eg. Formamide urea, and solutions with very low PH (PH<2, 3) or very high PH (Pl-bio) destabilize the double helix:

Electrostatic repulsion by negatively charged phosphates along the DNA backbone destabilizes the double helix. For example, if the phosphates are left unshielded, as when DNA is dissolved in distilled water, the DNA strands will separate at room temperature. 

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