The crystal and molecular structure of 2′:-deoxy-2′:-fluoroinosine monohydrate

Abstract

The structure of the hydrate of 2'-deoxy-2'-fluoroinosine has been determined by single-crystal x-ray diffraction. The nucleoside crystallizes in space group P2 12 121 with unit cell dimensions, a = 33.291, b = 10. 871, c = 6.897A. There are two nucleosides and two water molecules in the asymmetric unit. The structure was solved by direct methods and refined to a residual R = 0.095. The two independent nucleosides in the asymmetric unit show different conformations about the glycosidic bond, while other structural details are similar.

2-Amino-8-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)imidazo[1,2-a][1,3,5]triazin-4(8H)-one monohydrate, a 2′-deoxyguanosine analogue with an altered Watson–Crick recognition site

“…In contrast, for ribonucleoside (IIIb) a Àgauche conformation about the C4 0 -C5 0 bond was reported, which corresponds to ap (gauche, trans) according to Saenger (1984). The F2 0 -C2 0 length of (Ia) is 1.398 (2) Å , similar to the C-F bonds found in other 2 0 -fluoro 'up' nucleosides (Birnbaum et al, 1982;He et al, 2003;Seela et al, 2006) and 2 0 -fluoro 'down' nucleosides (Suck et al, 1974;Hakoshima et al, 1981). Moreover, the F2 0 -C2 0 bond length is notably close to the C2 0 -O2 0 distance observed in the parent compound, (IIIb) [1.400 (4) Å ; Kojić-Prodić et al, 1982].…”

Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn,

“…Hence, whereas the 4WJ structure would readily accommodate either modification (Figure 5C, red arrow), the minimal ribozyme structures suggest that this modification would result in more than the loss of a single H-bond. The associated reduction in ribozyme activity would be due to the proximity of the essential residue A38, which base stacks on this motif, succumbing to the preference of the 2′-deoxy-2′-fluoro adduct to adopt a C3′-endo furanose conformation (56). Interestingly, the sugar puckers at A38 also differ between the minimal and 4WJ structures (Figure 5B versus 5C, black arrow).…”

Properties of 2'-fluorothymidine-containing oligonucleotides: interaction with restriction endonuclease EcoRV

“…More recently (Herdewijn et al, 1989), a number of sugar-fluorinated nucleosides have been synthesized by employing the fluorinating agent DAST (Card, 1985). We have used this reagent for an improved and convenient synthesis of 2'-fluorothymidine from ribofuranosylthymine as shown in Figure 1.…”

“…A compared to 1.20 A) but an electronegativity more akin to that of a hydroxyl group. The 2'-deoxy-2'-fluoro analogues of uridine (Codington et al, 1964), cytidine (Doerr & Fox, 1967), thymidine (Codington et al, 1964), adenosine (Ikehara & Miki, 1978), and guanosine (Ikehara & Imura, 1981) have all been prepared, and the crystal structures reveal that a 3'-endo conformation is adopted by these analogues (Hakoshima et al, 1981;Marck et al, 1982b;Suck et al, 1974). NMR1 data (Catlin & Guschlbauer, 1975;Cushley et al, 1968;Guschlbauer & Janikowski, 1980) indicate that this same conformational preference exists in solution, often resulting in more than 90%…”