Deoxyribose

 

The sugar

Sugars are polyalcohols, i.e. organic molecules with multiple hydroxyl groups. Ribose is a five carbon sugar, and in the cyclic furanose form seen here would have hydroxyl groups at carbons 1, 2, 3, and 5. Deoxyribose (the D in DNA) is ribose with the hydroxyl group at carbon 2 deleted and replaced by hydrogen. The lack of a hydroxyl group at C2 is actually important, e.g. it increases the chemical stability of the phosphodiester backbone.


The sugar as part of DNA

The 3' and 5' carbons are linked by ester bonds to phosphate (when in DNA, the carbon numbers are primed to distinguish them from the carbons of the bases). The 1' carbon is linked to a nitrogen of one of the four heterocyclic bases. The C1'- base bond is not an ester, because the base is not an acid. The bond goes by the rather generic name "glycosidic", which merely says the compound is a derivative of a sugar. Deoxyribose is thus a structural node, it is part of the phosphodiester backbone, and ties the bases to that backbone.

Thus, the phosphodiester backbone of DNA has six bonds per nucleotide, and a 5'-3' or 3'-5' polarity due to the sugar structure. When writing a sequence of nucleotides, the convention is to put the 5' end on the left.


Geometry of the deoxyribose ring

There is a continuum of configurations for the sugar ring, but the planar geometry is the least favorable. The energies differ by 2-6 kcal/mole and depend on the substituents on C1' and C5'. Molecules probably pass from one form to another without passing through the planar geometry.

The nomenclature is based on an edge view with the 2' and 3' carbons toward the viewer, and the oxygen at the back. The 3' carbon is to the left of the 2' carbon. In some configurations the four carbons are almost in a plane, and if the oxygen is above this plane the configuration is called O endo, if below it is O exo. In other configurations the back three atoms, C4'-O-C1' are in a plane, and then the configuration is named for the relative positions of C2' and C3' with respect to this plane. While these structures represent valleys in the energy landscape, there is a continuum of intermediate structures. In solution there appears to be rapid equilibrium between the C-endo and C-exo forms.

However, when part of a DNA molecule, the sugar ring configuration can have a substantial effect on structure. In particular note the large change in the angle of the C1'-N glycosidic bond (indicated by the arrow) with the C4'-C5' in the O endo compared to the O exo ring.

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