8-Methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures

Abstract

This paper concerns the Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) structural studies of the quadruple helix arrangements adopted by three tailored oligodeoxyribonucleotide analogues, namely d(TGMeGGT), d(TGGMeGT) and d(TGGGMeT), where dGMe represents a 8-methyl-2′-deoxyguanosine residue. The results of this study clearly demonstrate that the effects of the incorporation of dGMe instead of a dG residue are strongly dependant upon the positioning of a single base replacement along the sequence. As such, d(TGMeGGT), d(TGGMeGT) have been found to form 4-fold symmetric quadruplexes with all strands parallel and equivalent to each other, each more stable than their natural counterpart. NMR experiments clearly indicate that [d(TGMeGGT)]4 possesses a GMe-tetrad with all dGMe residues in a syn-glycosidic conformation while an anti-arrangement is apparent for the four dGMe of [d(TGGMeGT)]4. As the two complexes show a quite different CD behaviour, a possible relationship between the presence of residues adopting syn-glycosidic conformations and CD profiles is briefly discussed. As far as d(TGGGMeT) is concerned, NMR data indicate that at 25°C it exists primarily as a single-strand conformation in equilibrium with minor amounts of a quadruplex structure.

The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands

“…NMR data for T12 and F12 are compatible with the formation of tetramolecular parallel quadruplex structures characterized by an all- syn tetrad at the 5′ end and two (for T12 ) or three (for F12 ) all- anti tetrads for the other purines (Figure 5). These results are in agreement with those obtained for monosubstituted TG 3 T and TG 4 T in the first and second positions, folding in quadruplex structures in which the modified guanosines form all- syn tetrads only if positioned at the 5′-end side (33,34).

Figure 5.Schematic representation of the quadruplexes formed by T12, T13, F12, F13, F14 and F24 .

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“…This arrangement is consistent with that of the quadruplex structures adopted by the monosubstituted ODNs TMGGGT and TGGGMT, in which the M residues form an all- syn tetrad in both cases (33). …”

“…The CD profile of T12 exhibits two positive bands at 246 and 295 nm and two negative ones at 230 and 266 nm. According to the NMR results the proposed structure is characterized by one heteropolar (HH) and one homopolar (HT) stacking (Figure 5), as for quadruplex structures formed by ODNs TBGGT (tetramolecular, B = 8-bromo-2′-deoxyguanine) (39), TMGGT (tetramolecular) (33) and G 3 T 4 G 3 (bimolecular) (40–42) that show quite similar CD profiles (38).

Figure 7.CD spectra of ODNs ( A ) TG 3 T (solid lines), T12 (dotted lines) and T13 (dashed lines); (B) TG 4 T (solid lines), F12 (dotted lines) and F14 (dashed lines); (C) TG 4 T (solid lines), F13 (dotted lines) and F24 (dashed lines) at 20°C, strand concentration 0.1 mM, 10 mM KH 2 PO 4 /K 2 HPO 4 , 70 mM KCl and 0.2 mM EDTA, pH 7.0.

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Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs

“…It has been reported that the inclusion of two 8-methyl-2′-deoxyguanosine (M) residues in d(TMGMGT) promotes the formation of an unprecedented antiparallel tetra-stranded G4 in which two adjacent strands run in the same direction (59). Since a bromine atom has a similar size as a methyl group and the 8-bromoguanine residue has the same tendency to promote a syn glycosidic conformation (7,60–62), we investigated the assembly properties of d(TG Br GG Br GAC 7 ), where G Br indicates an 8-bromoguanine residue. Figure 3B shows that under acidic conditions d(TG Br GG Br GAC 7 ) forms tetrameric ions with three NH 4 + ions corresponding to tetramolecular G4 structures ([4M + 3NH 4 ] 8− at m/z 2032.45; [4M + 3NH 4 ] 7− at m/z 2322.97).…”

Flipping a G‐Tetrad in a Unimolecular Quadruplex Without Affecting Its Global Fold

“…[9] Interestingly, tetramolecular all-trans quadruplexes [TG [3][4] T] 4 lacking intervening loop sequences are often prone to changes in tetrad polarity through the introduction of syn-favoring 8-Br-dG or 8-Me-dG analogues. [10] By changing the polarity of the ODN 5'-terminal tetrad, the antiparallel G-tract and each of the three parallel G-tracts exhibit a non-alternating all-syn and all-anti array of glycosidic torsion angles, respectively. This particular glycosidicbond conformational pattern is unique, being unreported in any known quadruplex structure, expanding the repertoire of stable quadruplex structural types as defined previously.…”