A novel guanlne-guanine base pairing: crystal structure of a complex between 7-methylguanosine and its iodide

Abstract

7-Methylguanosine, one of the biologically important minor nucleosides, could be crystallized as a complex of its zwitterionic form and its iodide, and the crystal structure was determined by the X-ray diffraction method. The crystals belong to the triclinic space group P1 with the unit cell dimensions: a = 7.678(1), b = 18.094(3), and c = 5.711(1) A, alpha = 79.32(1), beta = 80.14(1) and gamma = 76.90(1) degrees. The structure was solved by the heavy atom method and refined by the least-squares method to give a final R index of 0.075. The novel reverse Watson-Crick type base pairing observed between a positively charged molecule and a deprotonated one indicates that the deprotonation at the N(1) position promoted by the alkylation at the N(7) position may interrupt the formation of the normal Watson-Crick type GC base pair. The conformations about the glycosidic bond and the sugar puckering are quite different between the two molecules: the former has anti and C(4')-exo,C(3')-endo and the latter syn and C(1')-exo-C(2')-endo.

Additive CHARMM force field for naturally occurring modified ribonucleotides

“…In crystal structures protonated m 7 G is reported to be in an anti ‐ C3'endo conformation and NMR experiments indicate that it is a mixture of syn and anti in solution with anti highly related to C3'endo . The trend in the simulations was consistent with the PES prediction and experimental data.…”

“…Also the χ torsion distribution was more narrow than in G and shifted to ∼190°, and the pucker was north / west of C3'endo (Fig. d), which coincides with the C3'endo‐C4'exo conformation ( χ = 181° and P = 40°) in the crystal structure . Here the west pucker ( P ≈ 50°) was related to the syn ‐ C3'endo conformation, while it was still north ( P ≈ 18°) in anti .…”

Structure of 7-methyl-8-oxo-7,8-dihydroguanosine monohydrate

“…The bond lengths in the aglycon are within two e.s.d. 's of those observed in the structure of the cationic molecule of 7-methylguanosine (Yamagata, Fukumoto, Hamada, Fujiwara & Tomita, 1983); however, that structure exhibited average e.s.d. 's of 0.024 )~.…”

“…2. The O5'...N3 intramolecular hydrogen bond is moderately strong in light of its geometrical parameters [d(O5'.--N3) = 2.939 (2) A], but apparently weaker than those found in 8-bromo- (Tavale & Sobell, 1970), 8-chloro-(Birnbaum et al, 1984), 8-methyl-(Hamada et al, 1985 and 7-methylguanosine (Yamagata et al, 1983) (2.860, 2.845, 2-839 and 2.79 A, respectively). The base moieties are nearly parallel to the bc plane [dihedral angle: 3-50 (2) °] and stacked around the 21 screw axes parallel to the a axis.…”

(N7)-Platination and its effect on (N1)H-acidification in nucleoside phosphate derivatives

“…For N7-methylguanine bases (N9 position blocked), which have pK a values of ca. 7, self-pairing at physiological pH is well established [103,104].…”