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Non-canonical Backbone Shapes in DNA Duplex
As described in Chapter 1, natural DNAs form antiparallel B-type duplex, which is
often designated as B-DNA, while natural RNA forms A-type duplex
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5)
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However, it has been pointed out that
the crystallization conditions of high alcohols commonly used in oligonucleotide
crystallography may be factors that provide the A-DNA duplexes
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5 Structures of A-type (PDB ID: 3V9D)
(a) and Z-type (PDB ID: 4OCB) (b) DNA duplexes
formed in GC-rich sequence
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(b)

causes a query whether the A-DNA is the functional structure in biological systems
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The B-A transition is actually occurring in the cell nucleus, suggesting that A-DNA duplex
would contribute to gene regulation in response to the molecular environment
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5)
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Phosphate backbone of ZDNA forms a distinct zigzag pattern, which is an origin of its name, whereas that of B-DNA and ADNA is uniformly wound to form the helix
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Guanine
nucleotides in Z-DNA show C3′-end conformation in its sugar puckering and syn orientation in its
glyosidic bond angle
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Z-DNA has a structure feature that the
distance between phosphate groups at interstrand is shorter than B-DNA and A-DNA that results
in stronger electrostatic repulsion
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It is also known that the Z-DNA is
stabilized under the condition with a negative twist when the sequence is incorporated in plasmid
DNA and applied in a supercoil state
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Substantial number of Z-DNA-binding proteins has been identified in various
organisms including eukaryotes, prokaryotes, and viruses [10]

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