Chemistry Reference
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Figure 9.1 The three most important DNA secondary structure families in side view (top) and
along the helix axis (bottom). A-DNA features a right-handed double helix with the strongly
tilted base pairs aligned around a central hollow cavity. It is found for DNA at low humidity
and the most common RNA duplex structure. B-DNA is the predominant conformation of dou-
ble-stranded DNA. It is a right-handed helix of parallel-stacked Watson-Crick base pairs with
one full helical twist every ten base pairs. Z-DNA features a left-handed helix with pair wise
clustered base pairs and is mainly found in CpG alternating sequences. The less common C-,
D- and E-DNA families, triple helical structures and quadruplexes are not presented here.
This twisting is an inherent feature of the double-strand having its origins in the shape,
connectivity, conformation and electronic properties of the phosphate backbone, the 2
0
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deoxyribose sugar and the hydrogen-bonded and p-stacked nucleobases [4]. External
influences such as temperature and ionic strength can have a tremendous effect on the
adopted helix structure, as does the base pair sequence. Interestingly, not only double-
stranded oligonucleotides show a pronounced secondary structure; single-stranded DNA
was also found to show a helical ordering based on its sugar-phosphate backbone struc-
ture and p-stacking between neighboring bases [5]. Forming linear double-strands, how-
ever, is not the end of the line when regarding the degree of structural complexity
implemented by oligonucleotides. DNA can form structures termed hairpins and bulges
as well as three- or even four-way junctions, which were shown to have tremendous bio-
logical significance in the process of homologous recombination of paternal and maternal
genes in the process of inheritance [2]. Even more so, RNA is able to adopt a great variety
of secondary and tertiary structures with implications in the regulation of gene expression.
Furthermore, complex folded RNA structures in the form of tRNA and ribosomal subunits
are the basis of gene translation [2]. The control and nanotechnological exploitation of
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