Biochemistry - The Chemical Reactions of Living Cells, Volume 1 - D. Metzler 1980

The Molecules We Are Made Of
Nucleic Acids
Nucleotide Conformations

The ribose and deoxyribose furanose rings can adopt a wide range of Conformations, such as envelope and other non-planar puckered conformations. Typically, either the C-2' or C-3' atom is displaced from the plane of the other four ring atoms. If this carbon atom lies above the ring—meaning on the same side as the base—the ring conformation is designated as endo; conversely, if it lies below the ring, it is termed an exo-conformation (Fig. 2-22, A). Free NUCLEOTIDES predominantly exist in the C(2')-endo and C(3')-endo conformations; however, the B-form of DNA likely adopts the C(3')-exo conformation [65]. Puckered conformations of the C(2')-endo-C(3')-exo type (Fig. 2-22, A) and envelope conformations readily interconvert [66, 67].

The orientation of the base relative to the sugar is defined by the value of the torsion angle % (Fig. 2-22, B and C). A unified system of nomenclature for torsion angles in nucleotides is currently lacking, nor is there a universal consensus on which angles should be designated as 0°. For instance, the angle % can be defined in at least two ways, as shown in Fig. 2-22. It is frequently assumed that the angle equals 0° when the conformation is such that the C(2)—N(1) bond of a pyrimidine or the C(4)—N(9) bond of a purine is cis relative to the C(1')—O(1') bond of the sugar [66], with The values of the angle (denoted as χ′ in Fig. 2-22, B) ranging from 0 to 360°. In another approach, a zero angle corresponds to the cis-position of the aforementioned bond in the base relative to the C(1')—C(2') bond in the sugar; in this case, the angle χ varies between −180° and +180° (Fig. 2-22, C) [65].

The measured values of the angle χ vary among different nucleotides, with ~127° being the most typical value. In this anti-conformation, the CO and NH groups at the 2nd and 3rd positions of the pyrimidine ring (or positions 1, 2, and 6 of the purine ring) are directed away from the sugar ring, whereas in the syn-conformation (corresponding to a 180° rotation), these groups are positioned above the ring. Both in the free state and within Nucleic Acids, nucleotides predominantly reside in the anti-conformation.

Defining the conformation of the polynucleotide backbone requires an additional five torsion angles [65–70] (Fig. 2-22, D). The angles ω, ξ, and θ determine the spatial arrangement of groups within the nucleotide molecule, while φ and ψ have the same meaning as in polypeptide and polysaccharide chains. The range of values that the angles ω, ξ, and θ can adopt is extremely limited. Another torsion angle, σ, is located within the sugar ring (Fig. 2-22, D) and determines THE POSITION OF the C-3' atom. In the C(3')-endo conformation, σ = 80±10°, whereas in the C(3')-exo conformation of B-form DNA, it is approximately ~156°.

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FIG. 2.22. Conformational properties of nucleosides. A. Several possible conformations of the ribose or deoxyribose ring of a nucleoside [66]. B. View of a nucleoside along the N—C bond axis connecting the pyrimidine base to the sugar ring. The angle χ′ can take values from 0 to 360°. Syn-conformations refer to those in which χ falls within the values highlighted by the bold semicircle [66]. C. An alternative convention for defining the torsion angle relative to the glycosidic C—N bond. The angle χ ranges from 0 to ±180°. The anti-conformation of the nucleoside is shown. D. Designation of the backbone conformational angles of a polynucleotide [68]. (Note that at least four other systems of nomenclature exist for these angles [70].)