Tautomerism and conformation of the promutagenic analogueN⁶-methoxy-2′,3′,5′-tri-O- methyladenosine⁺

Abstract

N6-Methoxy-2',3',5'-tri-O-methyladenosine crystallizes in space group P2(1)2(1)2(1) with cell dimensions a = 4.693, b = 11.412, c = 31.741 A. Least-squares refinement of diffractometer data converged at R = 0.038. The location of a hydrogen atom at N1 and the observed bond lengths and bond angles indicate unequivocally the imino tautomer of the adenine moiety. The N6-methoxy group is oriented syn to N1 and the glycosidic torsion angle XCN is -3.6 degrees, i.e. in the anti range. The furanose ring has a C2'-exo/C3'- endo pucker (P = 0.9 degrees) and is unusually flattened (tau m = 30.0 degrees). The conformations of the O-methyl groups of the ribose ring are compared with those of monomethylated nucleosides, including the biologically important 2'-O-methyl nucleosides. Evidence is presented for the existence of C-H ... N intermolecular hydrogen bonds between adenine moieties. Bearing in mind that N6-methoxyadenosine is a promutagenic analogue, the results are compared with those for the corresponding promutagenic N4-methoxycytidine. They are also discussed in relation to the tautomerism, the conformation of the N6-methoxy group, and the associated base-pairing abilities in the absence and presence of polymerases.

Crystallographic studies on damaged DNAs. I. an N6-methoxyadenine residue forms a watson-crick pair with a cytosine residue in a B-DNA duplex

“…The second striking feature is that both methoxy groups adopt an anti conformation to the N 1 atom around the C 6 -N 6 bond. This conformation is quite different from those found previously in N 6 -methoxyadenine derivatives (Birnbaum et al, 1984;Fujii et al, 1990). In the latter crystals, the derivatives are in a syn conformation, forming a hydrogenbonded ribbon involving C-H Á Á ÁO and C-H Á Á ÁN interactions.…”

“…bonds, the chemical structure of the methoxylated adenine base must be the imino form, as shown in Figure 6, since it is known that the cytosine base exists only in the amino form (Pieber et al, 1973). This is consistent with the structures found in N 6methoxyadenine derivatives (Birnbaum et al, 1984;Fujii et al, 1990), which take the imino form. Although many types of base-pairs have been reported, only the wobble base-pairing has been found between cytosine and adenine bases in the protonated form (Schuerman et al, 1998;Hunter et al, 1986).…”

“…Crystallographic studies have been reported on the structural properties of methoxylated adenine. Two crystal structures of N 6 -methoxyadenine derivatives, N 9 -benzyl-N 6 -methoxyadenine (Fujii et al, 1990) and N 6 -methoxy-2 H ,3 H ,5 H -tri-O-methyl-adenosine (Birnbaum et al, 1984), indicate that the N 6 -methoxylated base prefers the imino form. This fact is consistent with the results from proton nuclear magnetic resonance (Stolarski et al, 1984(Stolarski et al, , 1987, and ultraviolet and infrared spectroscopy studies (Fujii et al, 1987).…”

“…In the crystals, the methoxy groups take a syn conformation around the N 6 -C 6 bond to the N 1 atom, so that the two purine moieties are associated through three hydrogen bonds including a C-HÁ Á ÁN interaction. From these results, Birnbaum et al (1984) proposed that mo 6 A with a syn conformation pairs with a 2 Hdeoxycytidine through two hydrogen bonds, between N 1 (mo 6 A) and N 3 (C) and between the methoxy oxygen atom and N 4 (C). The geometry of the base-pair, however, will be largely distorted from that of the regular Watson-Crick pairing.…”

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo6AATCCGCG) containing 2′-deoxy-N 6-methoxyadenosine: change in crystal packing with different humidity

“…It was also demonstrated that when the triphosphate of 2 H -deoxy-N 6 -methoxyadenosine derivatives was used as a reactant, it incorporated dATP and dGTP in a similar way (Hill et al, 1998). The two crystal structures of the component N 6 -methoxyadenine derivatives, N 6 -methoxy-2 H ,3 H ,5 H -tri-O-methyladenosine (Birnbaum et al, 1984) and 9-benzyl-N 6 -methoxyadenine (Fujii et al, 1990), indicate that this modi®ed base prefers an imino form (see Fig. 1) with the methoxyl group in the syn conformation to the N(1) atom around the C(6)ÐN(6) bond.…”