2′-endo-deoxyribose. Toggle spacefill.

The sugar conformation is critical for the nucleic acid structure because it defines how the nucleotides are linked to each other in space. The term sugar pucker refers to the conformation of the ribose or deoxyribose. The sugar pucker is defined by the positions of C2′ and C3′ atoms relative to a plane formed by the C1′, O4′, and C4′ atoms. A sugar with the C2′ is above the plane in the 2′-endo conformation; in the 3′-endo conformation, the C3′ is above the plane.

Switch between 2′-endo-deoxyribose and 3′-endo-ribose.

In the 3′-endo conformation, the 2′–OH points away from the base.

A major difference between A- and B-DNA double helices is caused by different sugar puckers. In A-DNA, the deoxyribose is in the C3′-endo conformation, with the carbon 3′ above the plane of the sugar ring. In B-DNA, the ring has the C2′-endo conformation, with the C2′ atom above the sugar plane.

Switch between close-ups of the A-DNA backbone versus the B-DNA backbone.

The N-glycosidic Torsion Angle

Two-nucleotide fragment (pCpGp) from Z-DNA. Toggle spacefill.

Rotation of the base around the N-glycosidic bond is sterically restricted. The two possibilities are syn- and anti-. In the anti-conformation the base is rotated out, away from the ribose plane. In the syn-conformation, the purine base is rotated in, over the ribose plane. Only the anti-conformation is allowed for pyrimidines because of steric interference between ribose and the C2 substituent of the pyrimidine (see Fig. 1). The anti-conformation is typical for B-DNA and RNA. However, in Z-DNA the purine bases are syn.

Note how the oxygen atom at the C2 position of cytidine locks the pyrimidine base in the anti-conformation.

Mystery DNA

Write a description of the structural features of the following DNA molecule.