Figure 1. Chemical structure of adenosine triphosphate (ATP), a nucleotide. All nucleotides consist of a base, a sugar and a phosphate ester. These constituent parts are shown for ATP, where the base is adenine (shown in green), the sugar is -d-ribose (shown in purple), and the phosphate is triphosphate (shown in orange). The base-and-sugar moiety is referred to as a nucleoside (termed adenosine for the nucleoside shown). The positions of atoms in the base and sugar are numbered. Purine bases contain atoms numbered 1–9 as shown, and pyrimidine bases are numbered 1–6 (see Figure 2). Atoms within the sugar (identified by the prime mark) are numbered similarly for all nucleotides containing -d-ribose. Bond lengths are not drawn to scale.

Figure 2. Structures and tautomeric equilibria of the DNA bases. Atoms within bases are numbered, with N1 of pyrimidines and N9 of purines being bonded to C1’ of the sugar in nucleosides and nucleotides. Tautomeric forms shown to the left are the major ones and the imino and enol forms shown to the right are present in very small amounts. Participation in hydrogen bonds is shown by the arrows: hydrogen bond donors are shown by arrows directed away from the atom, acceptors are shown by arrows directed towards the atom.

Figure 3. Conformations of nucleotides. (a) Torsion angle notation (IUPAC definitions) for a polynucleotide. A conventional representation showing the torsion angles relative to atom number of the nucleotide. See Table 4 for a complete description of the atoms defining each angle. (b) Representation of puckering modes of furanose sugar. Three twist (T) forms are shown in which three ring atoms (C4¢, O4¢, C1¢) are planar and the other two (C2¢, C3¢) lie on opposite sides of this plane. ‘Base’ refers to any purine or pyrimidine base. (c) Anti and syn conformations of the glycosolic bonds for a purine or pyrimidine base. The arrow indicates which base atoms lie above the furanose sugar ring. For purine nucleotides: R¹ = H or OH; R² = NH₂ or O; R³ = H or double bond to C6¢; R⁴ = H or  NH₂. For pyrimidine nucleotides: R¹ = H or OH; R² = H or double bond to C4; R³ =  NH₂ or O; R⁴ = H or  CH₃. (d) Preferred nucleotide conformations at C4¢–C5¢ and C3¢–O3¢. The structures show synclinal (sc) and antiperiplanar (ap) rotamers of the C4¢–C5¢ bond and the typical antiperiplanar/anticlinal (ap/-ac) conformation of the C3¢–O3¢ bond.