DNA Structure Activity

Problem 5: Is the deoxyribose ring flat or puckered?

Do all the atoms of the sugar ring lie in the same plane? (Note: You can measure this directly by clicking on 4 consecutive ring atoms with the dihedral angle tool at the far right of the tool bar. If the ring is planar, the measured angle will be close to either 0 or 180 degrees).


sugar ring

Only 4 of the 5 atoms of the deoxyribose sugar ring are close to being in the same plane. If we measure the angle between carbon atoms 1-2 and carbon atoms 3-4 with the dihedral angle tool as shown in the illustration, the angle of pucker in the ring is measured to be -25.97 degrees for the example chosen.

To measure the dihedral angle as shown:

  1. Select the view "Sugar (deoxyribose)"
  2. Click on the dihedral angle tool at the far right of the toolbar.
  3. Click on the 4 consecutive carbon atoms of the sugar ring, beginning next to the oxygen atom.
  4. Note the dihedral angle in the information box below the molecule.

The Biology Project
University of Arizona
Modified: May 27, 1997
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