Nucleoside torsion angles

Another nucleoside linked to the imidazo[l,2- ][l,3,5]triazine ring system 58 in a monohydrate form has also been investigated by X-ray crystallography <2002AXC142>. The obtained data reveal that the compound adopts a high //-conformation, and the N(8)—C(7) and C(a)-C(J3) bonds are nearly eclipsed (the torsion angle is 30.3°). 

Diester methods have been used to synthesize analogues of the initiator codon ApUpG in which the adenine residue has a fixed torsion angle, as for instance in (78),132 and triester methods have been used to prepare dinucleoside phosphates and codon analogues133 134 containing the hydroxyalkyl nucleosides 9-(4 -hydroxybutyl)-adenine (80), 9-(3 -hydroxypropyl)adenine (81), and 1 -(3 -hydroxypropyl)uracil (82), with a view to determining the effect of the achiral residues on the c.d. spectra. 

P2i Z = 2 Dx = 1.577 R = 0.033 for 1,041 intensities. The compound is a hydrolysis product of 5-azacytidine. The conformation of the D-ribose part is 4E, with C-4 endo, similar to that observed for some a-nucleosides. The oxazolidine ring is planar. The dihedral angle between the two planes, as defined by the torsion angle 0-4-C-l-C-2-0-2 about the common C-l-C-2 bond, is +111°. The orientation of the primary alcohol group is gauche /gauche. 

Fig. 13. Schematic representations of the syn and anti conformational ranges in nucleosides, as expressed by the torsion angle %...

In nucleosides and nucleotides, the base can adopt two main orientations about the glycosyl CT-N link, called anti and syn and defined by the torsion angle y, which is the OT-Cl -N9-C4 torsion angle for... 

The nucleoside 8-azaadenosine (monohydrate) was found to have a conformation intermediate between syn and anti (with a torsion angle of 104°) around the glycosyl - nitrogen bond, apparently stabilized by an electrostatic attraction between N-8 and C-2. Adenosine deaminase, which can not deaminate any analogs with a syn conformation, has only a feeble action on this nucleoside. ... 

Conformation 2.42, P = 175°, is rather close to The maximum torsion angle is still between 2 and 3, -42°. The fact that the same molecule can have two different conformations in the same crystal is in itself indicative of their small energy difference. All the same it is unusual and nucleosides/nucleotides are divided equally between 0° < P < 36° and 144° < P < 180° with few exceptions. 

This notation will be explained by an example taken from the chemistry of nucleosides/nucleotides, by far the most important family of furanosides (see Section 3.4). The nucleosides are glycosidic combinations with a heterocyclic base and a /3-D-ribofuranosyl or 2-deoxy-)3-D-cryr/iro-pentofuranosyl residue. The example chosen is the synthetic nucleoside 5-iodouridine. We can observe two different conformations of this molecule in the crystalline form, close to 72 (2.41) and Tj (2.42), respectively. The maximum torsion angle is between the 2 and 3 positions. In order for P to be close to 0, we will therefore choose T2 = Oq (Fig. 2.10) and consequently for 0. .. 0, the values T3, T4, Tq, and Ti, respectively. Knowledge of the two torsion angles allows us to calculate and P. The P angle has the character of a phase and is a measure of the flattening of the... 

Figure 7 Schematic diagrams of human telomeric quadruplex folding topologies. (A) The fold determined by NMR spectroscopy of the intramolecular G-quadruplex formed by d(AG3(T2AG3)s) in solution with only Na ions. Gray rectangles represent nucleosides with syn glycosidic torsion angles. For clarity, only G-bases are represented. (B) The G-quadruplex fold, with parallel GGG elements and external loops, as determined by X-ray crystallography for the same sequence crystallized in the presence of ions ...

---