BIOINORGANIC CHEMISTRY A Short Course Second Edition

50 BIOCHEMISTRY FUNDAMENTALS

This is described as an antiparallel arrangement. This arrangement allows the
two chains to fi t together better than if they ran in the same direction (parallel
arrangement). A sequence illustrating complimentarity is shown in Figure
2.15.
In forming the double - helix polymeric DNA structure, the two sugar –
phosphate backbones twist around the central stack of base pairs, generating
a major and minor groove. Several conformations, known as DNA polymorphs,
are possible. The classical form, B DNA, exhibits well - defi ned major and minor
grooves: C 2 ′ - endo deoxyribose sugar puckers (see Figure 2.16 ) and parallel
stacked base pairs perpendicular to the helix axis. A and B DNA form right -
handed helices, while Z DNA forms a left - handed helix. Usually, DNA adopts
the B conformation; but in high salt or organic solvent conditions, the Z con-
formation may be found. Sequences containing alternating GC nucleotides
favor the Z DNA conformation. Several different base - sequence - dependent
DNA polymorphs may exist within a given genome. Double - stranded RNA
or RNA – DNA hybrids normally form the A DNA conformer. Visualizations
of all forms are found on the Jena image library of biological molecules site
at http://www.imb-jena.de/IMAGE_DNA_MODELS.html. DNA conforma-
tions are dependent on a number of parameters, including the type of pucker
found in the nonplanar ribose sugar ring, the syn or anti conformation of the
nucleobase relative to the sugar moiety, and the orientation about the C 4 ′ – C 5 ′
bond. Figure 2.16 , as adapted from references 14 and 15 , illustrates some of
the possibilities. 14,15
The differing conformations of the ribose have been named with respect to
that ring atom which puckers out of the plane given by the other ring atoms.
The most prominent conformations are C 2 ′ - endo in B - helices and C 3 ′ - endo in
A - helices. At room temperature, both conformers are in a dynamic equilib-
rium. Intermediates between C 2 ′ - endo and C 3 ′ - endo are found in several (time -

Figure 2.14 Watson – Crick base pairing in DNA.

N

N NH

N

N

HN N

O

O

H

H H

1

(^67)
9
adenine, A
2
4
1
thymine, T
(^13)
4
cytosine, C
5
HN N
N
O
N
N NH
N
O
N
H
H
H
H
H
1 guanine, G
3
(^67)
9
points of attachment to the ribose-phosphate backbone