Alternative Structures of DNA

The structure of DNA comprises a series of flat aromatic heterocyclic bases attached to a hydrophilic, negatively charged sugar-phosphate backbone. The backbone is relatively flexible and can relax to accommodate structural alternation caused by variation in base-base interactions. Three main kinds of interactions govern most of the structural changes observed in DNA  

The charged phosphate groups of the backbone are mutually repulsive, and this sets limits on the extent of structural variation that is possible. These electrostatic 

Hydrogen bonding between bases is the driving force for the formation of mutis-tranded structures. 

The bps exert short-range attractive interactions on each other, leading to stacking interactions between the flat surfaces. 

These properties lead to the adoption of the normal double-stranded structure of DNA comprising the charged backbone on the outside and the stacked bps on the inside. Adjustments in the structural relationship between adjacent bps can be achieved through several operations. These include  

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Examples of some known alternative structures of DNA duplexes are illustrated in Table 4.6. Importantly, these subtle differences in structure may be another factor that contributes to the selective recognition of the DNA heUx by proteins or small molecules. They may also determine the extent to which the structure may be altered as follows ... 

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