• Sugar Pucker
  • Ribose rings undergoes sugar pucker and become slightly nonplanar.
  • Most structures show that 4 of the five ring atoms are coplanar, 5th atom is out of the plane in a half-chair conformation.
  • Endo- conformation → if out of plane atom is the same side of the ring as the C5'
  • Exo- conformation → if out of plane atom is on the opposite side of the ring as the C5'
  • Most nucleoside and nucleotide structures (not in double helices) out of plane atom is either C2' or C3'.
  • C2'-endo most common; C3'-endo and C3'-exo are also common.

Figure 4.8a: The Sugar ring pucker-A planar ribose ring, viewed down the C3'—C4' bond, are all eclipsed.

Figure 4.8b:   The Sugar ring pucker-The steric strain resulting in planar sugar ring (in Figure 4.8a) is partially relieved by ring puckering in a half-chair conformation in which C3' is the out-of-plane atom (same as C5' so C3'-endo).

• Endo conformation →if out of plane atom is the same side of the ring as the C5'
• Exo- conformation → if out of plane atom is on the opposite side of the ring as the C5'
• Most nucleoside and nucleotide structures (not in double helices) out of plane atom is either C2' or C3'.
• C2'-endo most common; C3'-endo and C3'-exo are also common.
• This ribose pucker determines the relative orientation of the phosphates to the sugar.
• To have a regularly repeating model-need C2'-endo (B-DNA) or C3'-endo (A-DNA, RNA-11)
• Z-DNA purines are all C3'-endo, pyrimidines C2'-endo (dinucleotide repeating unit).
• B-DNA has some flexibility (can be observed as C4'-exo, O4'-endo, C1'-exo and C3'-exo).