Which factor decreases the stability of a DNA double helix during denaturation?

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11ecba2d_0e72_776a_a3bf_8dbc2a18919e_MD0008_00 The DNA double helix is arranged such that the sugar-phosphate backbone (linked by phosphodiester bonds) lies on the outside and the nitrogen-containing bases (paired by hydrogen bonds) lie on the inside. During double helix formation, complementary strands of DNA anneal through the creation of hydrogen bonds between the nitrogenous bases. Once the double helix is formed, energy is required to denature the duplex into two separate strands. Increasing the temperature during the melting step provides the heat energy necessary to break the hydrogen bonds between bases and separate the double helix. (Choice A) The base pairs in the double helix are "stacked" almost on top of each other; however, base stacking is interrupted, not enhanced, when the DNA helix denatures during melting. Stacking interactions, which are due to hydrophobic effects and nonpolar van der Waals forces between the bases, are primarily responsible for the stability of the double helix structure. (Choice B) Hydrophobic effects decrease during the melting step because hydrophobic bases are exposed to water. In aqueous solution, hydrophobic effects force hydrophobic bases toward the double helix interior and away from the polar solvent (water). In contrast, the hydrophilic, negatively charged phosphates in the backbone can hydrogen bond with water molecules. (Choice D) Covalent phosphodiester bonds of the sugar-phosphate backbone maintain the structure of single-stranded DNA. These linkages are not affected when the double helix is separated during denaturation. Educational objective: During DNA double helix formation, hydrogen bonds form between the bases and release energy. Heat energy provided in a DNA melting reaction is used to disrupt interactions that contribute to DNA double helix structure: hydrogen bonding, base stacking, and hydrophobic effects.

Which Factor Decreases the Stability of a DNA Double Helix