Sugar Puckering in Nucleic Acids

Sugar puckering refers to the conformation of the five-membered furanose ring (either deoxyribose in DNA or ribose in RNA). The ring is not planar, and different atoms can be displaced from the plane formed by the other atoms. The two most common puckering modes relevant to double-stranded nucleic acids are C-2' endo and C-3' endo.

• C-2' endo: In this conformation, the 2' carbon atom is displaced on the same side as the C5'-O5' bond (which is typically above the ring plane). This puckering is characteristic of B-form DNA.
• C-3' endo: In this conformation, the 3' carbon atom is displaced on the same side as the C5'-O5' bond. This puckering is characteristic of A-form DNA and A-form RNA.

Nucleic Acid Double Helix Forms and Puckering

Double-stranded nucleic acids can exist in different helical forms, primarily A-form and B-form, which are associated with specific sugar puckering:

Analyzing the Options

Let's evaluate the sugar puckering in the structures mentioned in the options:

• C-2' endo in double stranded DNA: Double-stranded DNA typically exists in the B-form under physiological conditions, which has C-2' endo puckering. However, dsDNA can transition to A-form under dehydrating conditions, exhibiting C-3' endo puckering. Therefore, C-2' endo is common but not exclusive for dsDNA.
• C-3' endo in double stranded DNA: As mentioned, dsDNA can adopt the A-form under certain conditions, which involves C-3' endo puckering. This is not the typical form, so C-3' endo is not exclusive to dsDNA.
• C-2 endo in double stranded RNA: Double-stranded RNA universally adopts the A-form helix, primarily due to steric hindrance by the 2'-hydroxyl group of ribose sugars. The A-form is characterized by C-3' endo puckering, not C-2' endo. Therefore, C-2' endo is not typically found in dsRNA.
• C-3' endo in hybrid duplex with one strand as DNA and the other as RNA: A DNA-RNA hybrid duplex, like dsRNA, strongly favors the A-form helix. This is driven by the RNA strand, which imposes the A-form geometry. The A-form helix is associated with C-3' endo sugar puckering. Among the given options, the A-form structure adopted by the hybrid duplex makes C-3' endo the characteristic and dominant puckering. While the term "exclusively" is strong, relative to the variability of dsDNA and the absence of C-2' endo in typical dsRNA, the C-3' endo puckering is the most consistently observed pattern in hybrid duplexes due to their A-form nature.

Considering the common and stable forms of these nucleic acids, the C-3' endo puckering is characteristic of the A-form structure adopted by DNA-RNA hybrid duplexes.