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  • Print publication year: 2015
  • Online publication date: March 2015

1 - DNA structures


Chemical structure and conformational flexibility of single-stranded DNA

Single-stranded DNA (ssDNA) is the building base for the double helix and other DNA structures. All these structures are formed due to noncovalent interactions between the components of ssDNA. ssDNA consists of a backbone of repeating units and bases that are attached to each unit as side chains (Fig. 1.1).

An isolated part of the repeating unit that consists of a base and the sugar is called a nucleoside. If a phosphate group is added to the nucleoside, it becomes a 3′- or 5′- nucleotide, depending on where the phosphate group is bound. Each repeating unit of the backbone consists of sugar and phosphate and has six skeletal bonds. The backbone has clear directionality, and the method of numbering of carbon atoms of the sugar, shown in Fig. 1.1, identifies 3′–5′ or 5′–3′ directions. It is common to assume a 5′–3′ direction of the polynucleotide chain when presenting a sequence of bases.

There is an important degree of freedom in isolated nucleosides that is related to rotation around the bond connecting the sugar and a base, the β-glycosidic bond. The rotation angle, χ, is measured with reference to the orientation of O1′–C1′ and N9–C8 bonds for purines and to the orientation of O1′–C1′ and N1–C6 bonds for pyrimidines. Although many different values of χ are sterically allowed, two major rotational isomers, called anti and syn, are particularly important. For the anti conformation χ is close to 0°, and for syn χ is around 210°. The conformations are diagramed in Fig. 1.2.

The bond lengths and the angles between the adjacent bonds do not change notably. The remarkable conformational flexibility of ssDNA is due to six rotation angles in each repeating unit of the backbone. Of course, the rotation angles cannot accept just any values, since there are many potential steric clashes between chemical groups of the unit.

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