Question

In addition to negative charge repulsion, give another thermodynamic reason why phosphates would be on the outside of the double helix and the bases on the inside? (10 pts)

Answer 1

DNA has a double helix structure. The outer edges are formed by alternating deoxyribose sugar molecules and phosphate groups, which make up the sugar-phosphate backbone. The two strands run in opposite directions, one going in a 3' to 5' direction and the other going in a 5' to 3' direction. The nitrogenous bases are positioned inside the helix structure like "rungs on a ladder," due to the hydrophobic effect, and stabilized by hydrogen bonding.

The two strands run in opposite directions to form the double helix. The strands are held together by hydrogen bonds and hydrophobic interactions. The H-bonds are formed between the base pairs of the anti-parallel strands. The base in the first strand forms a H-bond only with a specific base in the second strand. Those two bases form a base-pair (H-bond interaction that keeps strands together and form double helical structure). The base–pairs in DNA are adenine-thymine(A-T) and cytosine-guanine (C-G). Such interactions provide us an understanding that nitrogen-containing bases are located inside of the DNA double helical structure, while sugars and phosphates are located outside of the double helical structure.

The component consisting of the base and the sugar is known as the nucleoside. DNA contains deoxyadenosine (deoxyribose sugar bonded to adenine), deoxyguanosine (deoxyribose sugar bonded to guanine), deoxycytidine (deoxyribose sugar bonded to cytosine), and deoxythymidine (deoxyribose sugar bonded to thymine). The linkage of the bonds between the base to the sugar is known as the beta-N-Glycosidic linkage. In purines, this occurs between the N-9 and C-1' and in pyrimidines this occurs between the N-1 and C-1'. A nucleoside and a phosphate group make up a nucleotide. The bond between the deoxyribose sugar of the nucleoside and the phosphate group is a 3'-5' phosphodiester linkage.

The bases, located inside the double helix, are stacked. Stacking bases interact with each other through the Van der Waals forces. Although the energy associated with a Van der Waals interaction is relatively small, in a helical structure, a large number of atoms are intertwined in such interactions and the net sum of the energy is quite substantial. The distance between two neighboring bases that are perpendicular to the main axis is 3.4 Å. The DNA structure is repetitive. There are ten bases per turn, that is the structure repeats after 34 Å, so every base has a 36° angle of rotation. The radius of the double helix is approximately 10 Å.