Canonical and unconventional pairing schemes between bis(nucleobase) complexes of trans-a₂Pt^II: Artificial nucleobase quartets and C—H…N bonds

Abstract

If two nucleobases are crosslinked by trans-a₂Pt^II, self-association via H bonding may take place either through individual bases or jointly through both bases. Due to the blockage of an acceptor site by the metal, the number of feasible pairing patterns can be reduced, and the preferred ones altered. If the metalated base pair as a whole undergoes association, base quartets can form. Various scenarios resulting from the application of guanine, hypoxanthine, and cytosine model nucleobases are discussed. Unconventional C—H…N hydrogen bonding has been observed in several instances.

The existence of cyclic guanine (G) quartets and the association of poly(G) and poly(I) into four-stranded structures have been known for quite some time (1, 2). Proof of the formation of G quartets in telomere sequences (3) and their existence in human cells (4), new insights on the structure of human telomeric DNA (5, 6), and, above all, implications that G quartets are potential drug targets for the chemotherapy of cancer, on the one hand, and can play a dysfunctional role, on the other (7), have made the field of DNA quadruplex structures a booming area. From an inorganic chemistry point of view, the involvement of metal ions in the formation and stabilization of G₄ structural elements is of particular interest. That these cations, K⁺ and Na⁺ under physiological conditions and many other cations under nonphysiological conditions, are absolutely essential for maintaining the G₄ structure elements has been recognized at an early stage. Moreover, it is now clear that a stem of G₄ quartets stabilizes other quartet structures, including those between dimers of Watson–Crick pairs, e.g., [GC]₂ (C, cytosine) (8).

Small molecules that bind specifically to quadruplex DNA, thereby interfering with the enzyme telomerase or inhibiting expression of a crucial gene, are believed to be useful for chemotherapeutic applications. Among these, cationic porphyrins such as tetra-(N-methyl-4-pyridyl)porphine are particularly promising (4, 9, 10). Our interest in this area stems from our experience with metal–nucleobase complexes representing artificial base quartets that are cationic and flat and that have dimensions compatible with the natural base quartets. Because of their shape and charge, these compounds can be expected to have a natural affinity for tetra-stranded DNA in general and telomere sequences in particular. The use of metal ions (M) displaying linear coordination geometries and the fact that purine nucleobases, on simultaneous metal binding to N1 and N7, provide 90° angles between their M-N vectors and hence represent angular building blocks of squares and rectangles have enabled the construction of a variety of artificial M-base quartets (11–16). Examples are given in Scheme . Depending on the metal ions applied and the degree of crosslinking, these quartets can be kinetically labile or robust, also occasionally assembled by remarkably strong H bonds, even in solution. It will be our ultimate goal to probe the interaction of these quartets or fragments thereof with naturally occurring DNA quadruplexes. Our work relates to the early findings of Shin and Eichhorn (17), who have demonstrated that poly(I) arranges into a tetra-stranded structure in the presence of Ag⁺ ions; and to reports of Houlton and coworkers (18) on artificial M-guanine quartets on the basis of chelate-tethered guanines; as well as to the work of Mingos and coworkers (19) on self-assembly processes of metal complexes via H bond formation. Finally, our work relates to our findings on the spontaneous dimerization of two parallel-stranded DNA fragments containing crosslinks of trans-(NH₃)₂Pt^II with terminal G bases (20). Among others, it was these observations that prompted the work reported here, which also originated from the more general question of how platinated model nucleobases such as 9-methylguanine (9-MeGH), 9-ethylguanine, 9-methylhypoxanthine (9-MeHxH), and 1-methylcytosine (1-MeC) organize via H bonds in the solid state and in solution. As will be reported, H bond formation between aromatic protons of nucleobases and endocyclic N atoms is observed in several instances, a feature still extremely rare in nucleic acid chemistry (14, 21, 22).

Scheme 1.

Comparison of natural guanine quartet (Left) and artificial M quartets as verified by x-ray analysis: I (11), II (11), III (12), IV (13), V (14), VI (15). For IV, a linkage isomer has likewise been obtained (16). A, 9-methyl/ethyladenine; C, 1-methylcytosine; H, 9-methylhypoxanthine; G, 9-methylethylguanine; U, 1-methyluracil. G⁻, G²⁻, etc., denote deprotonated bases.

Experimental Procedures

9-MeHxH and 9-MeGH were purchased from Chemogen (Konstanz, Germany). The following compounds were prepared according to published methods: 1-MeC (23), trans-(NH₃)₂PtCl₂ (24), trans-(CH₃NH₂)₂PtCl₂ (25), and trans-[(CH₃NH₂)₂Pt(1-MeC)Cl]Cl (26).

Syntheses.

trans-[(NH₃)₂Pt(9-MeGH)₂]X₂⋅nH₂O [X₂ = SiF₆, n = 2 (1a); X = CF₃SO₃, n = 2.45 (1b)] and trans-[(NH₃)₂Pt(9-MeHxH)₂](ClO₄)₂ (2) were prepared in water from trans-(NH₃)₂PtCl₂ and the respective purine with the help of AgX or anion exchange. trans-[(CH₃NH₂)₂Pt(1-MeC)(9-MeHxH)]X₂·nH₂O [X = NO₃, n = 0.5 (3a); X = ClO₄, n = 0 (3b); X = CF₃SO₃, n = 1 (3c)] was prepared in water from trans-[(CH₃NH₂)₂Pt(1-MeC)Cl]Cl, 9-MeHxH, and AgX. trans-[(CH₃NH₂)₂Pt(1-MeC)(9-MeHx)]X⋅nH₂O [X = NO₃, n = 1.5 (4a)] was obtained from 3a at pH 10.7. The corresponding salts with X = ClO₄ (4b) and CF₃SO₃ (4c) contained NaX. Details of preparations, elemental analysis data, and NMR chemical shifts (¹H, ¹⁹⁵Pt) can be found in Supporting Text, which is published as supporting information on the PNAS web site, www.pnas.org.

NMR Spectroscopy.

¹H NMR spectra were recorded on a Bruker 200 instrument (Billerica, MA). Sodium 3-(trimethylsilyl)-propanesulfonate (δ = 0.00 ppm) was used as an internal standard in aqueous solutions, whereas spectra recorded in DMSO-d₆ were calibrated to the signal of partially deuterated solvent. Spectra recorded in dimethylformamide-d₇ were likewise referenced against solvent peaks. ¹⁹⁵Pt NMR spectra were recorded on a Bruker AM-300 FT NMR spectrometer by using sodium hexachloroplatinate (δ = 0 ppm) as external standard. 2D rotating-frame Overhauser effect spectroscopy spectra were recorded on a Bruker DRX 400 at 296 K with a mixing time of 300 ms.

Acidity Constants.

pK_a values of 9-MeHxH and of the mixed cytosine–hypoxanthine complex 3 were determined by pH-dependent ¹H NMR measurements in D₂O. The measured pH values (= uncorrected pH*), determined by a glass electrode, were converted into pD values by adding 0.4 units to the meter reading. The changes in chemical shifts of aromatic protons as a function of pD were evaluated by a Newton-G nonlinear least-squares curve-fitting procedure as reported (27). The pK_a values (D₂O) obtained this way were then converted to pK_a values in H₂O (28).

Association Constant.

The association constant of 4c was determined by concentration-dependent ¹H NMR measurements in DMSO-d₆ as described (14). The triflate salt was used for solubility reasons. The presence of NaCF₃SO₃ was considered in determining the concentration of cation 4. Because the mixtures studied contained residual water, the value determined is to be considered a lower limit.

Electrospray Ionization–MS.

Mass spectra were recorded on a Finnigan-MAT 90 spectrometer (San Jose, CA) by using an electrospray source (Finnigan) at an acceleration potential of +5,000 V and an infusion pump E540101 (Harvard Apparatus). A fused silica capillary (inner diameter 75 μm) was used. The 2-propanol sheath flow was 5–10 μl⋅min⁻¹, and the sample flow rate was 0.5 μl⋅min⁻¹. Cations were registered.

X-Ray Crystallography.

Intensity data of 1a, 1b, 2, 3a, and 3b were collected on a κ charge-coupled device (Mo-Kα, λ = 0.71069 Å, graphite monochromator; Enraf-Nonius, Delft, The Netherlands). Frames were integrated and corrected for Lorentz and polarization effects by using denzo (29). The scaling, as well as the global refinement of crystal parameters, was performed by using scalepack (29). Structures were solved by standard Patterson methods (30) and refined by full-matrix least-squares methods based on F² by using the SHELXTL-PLUS (Siemens, Madison, WI) and SHELXL-93 programs (University of Göttingen, Göttingen, Germany). The positions of all nonhydrogen atoms were deduced from difference Fourier maps and refined anisotropically. Exceptions are the carbon and fluorine atoms of the triflate anions in 1b, which were treated isotropically only, as well as the oxygen atoms of the water molecules in the same compound. According to the values of the anions, these oxygens were given fixed isotropic displacement factors of 0.3. Unrestrained refinement yielded occupancy factors of 0.5–1.0, resulting in a total of 4.9 water molecules per asymmetric unit distributed over seven positions. Hydrogen atoms were in calculated positions and refined with isotropic displacement factors according to the riding model. Exceptions are the water protons in 1a, as well as the aromatic protons of the nucleobases and the methyl protons of 1-MeC in 3b, which were located in difference Fourier maps and refined isotropically without restraints. Experimental details and crystal data are summarized in Table 1. Crystallographic data for the structures reported in this article have been deposited with the Cambridge Crystallographic Data Centre (CCDC 195464–195468).

Table 1.

Crystallographic data for compounds 1a, 1b, 2, 3a, and 3b

	1a	1b	2	3a	3b
Empirical formula	C12H24N12O4PtSiF6	C14H24.9N12O10.45PtS2F6	C12H18N10O10PtCl2	C13H24N11O8.5Pt	C13H23N9O10PtCl2
Formula weight	737.62	901.77	728.36	665.52	731.39
λ(Mo Kα), Å	0.71069	0.71069	0.71069	0.71069	0.71069
Temp, K	293	293	293	293	173
Space group	P-1	P21	P21/n	Pccn	P21/n
a, Å	6.399 (1)	7.988 (2)	5.240 (1)	17.159 (3)	11.867 (2)
b, Å	8.437 (2)	27.481 (5)	15.707 (3)	18.304 (4)	15.242 (3)
c, Å	10.745 (2)	13.897 (3)	13.431 (3)	14.253 (3)	13.821 (3)
α, deg	77.66 (3)
β, deg	76.03 (3)	95.03 (3)	90.38 (3)		107.93 (3)
γ, deg	85.93 (3)
V, Å3	549.8 (2)	3038.9 (11)	1105.4 (4)	4477 (2)	2378.5 (8)
Z	1	4	2	8	4
R1 (obs. data)*	0.0507	0.0492	0.0338	0.0224	0.0255
wR2 (obs. data)†	0.1207	0.0866	0.0662	0.0326	0.0495

^*R₁ = ∑/| |F_o| − |F_c| |/∑|F_o|.

^† wR₂ = [∑w(F − F)²/∑w(F)²]^1/2.

Results

Bis(Purine) Complexes of trans-a₂Pt^II.

Apart from reactivity aspects of the bis(guanine) crosslink of trans-(NH₃)₂PtCl₂, our main interest relevant to the topic of this work was whether an association of trans-[a₂Pt(purine)₂]ⁿ⁺ units into discrete dimeric entities could be realized. We were aware that, unlike in squares V and VI (Scheme ), where the bis(nucleobase) units are self-complementary, neither M(G-N7)₂ nor M(hypoxanthine-N7)₂ displays this feature. Still, there is precedence for such dimerization scenarios: In [Pt(NH₃)(9-MeGH-N7)₃]²⁺, self-association of the two transoriented guanine bases is observed that utilizes those four sites of the bis(guanine) unit that are complementary, resulting in a purine quartet (31) with the shape of a parallelogram. In other words, the cations slide past each other until they become locked in complementary H bonding (Scheme ). This situation is supported by four attractive secondary electrostatic interactions within the AADD sequence (A, acceptor; D, donor). H bond lengths are normal, 2.79(1) Å for N2…O6 and 2.89(1) Å for N1…O6. The latter is rather similar to the one between two guanines in a metalated nucleobase sextet [2.882(9) Å] (15). With the bis(hypoxanthine-N7) complex of trans-a₂Pt^II, an arrangement as observed (32, 33) for the silver complex [Ag(9-MeHxH-N7)₂]⁺ is feasible, i.e., dimerization with inclusion of two solvent (H₂O) molecules (Scheme ).

Scheme 2.

Association pattern of (a) two trans-[PtXY(9-MeG-N7)₂]²⁺ cations (X = 9-MeG-N7; Y = NH₃) with attractive secondary electrostatic interactions indicated (31) and (b) two trans-[Ag(9-MeHxH-N7)₂]⁺ cations via H₂O molecules (32).

Applying x-ray crystallography, we have characterized two examples of bis(guanine) complexes of trans-(NH₃)₂Pt^II, trans-[(NH₃)₂Pt(9-MeGH-N7)₂]SiF₆⋅2H₂O (1a) and trans-[(NH₃)₂Pt(9-MeGH-N7)₂](CF₃SO₃)₂·2.45H₂O (1b) and one example of a bis(hypoxanthine) complex, trans-[(NH₃)₂Pt(9-MeHxH-N7)₂](ClO₄)₂ (2). To make the story short, in none of the three cases was there an intermolecular association leading to discrete purine base quartets. In 1a, the two bases adopt a head-to-tail orientation, which automatically excludes formation of a discrete base quartet. Water molecules as well as SiF⁻ anions are H bonded to nucleobase sites of the Watson–Crick edge and prevent any direct base–base contact, although maintaining a dimer structure (Figs. 6–8, which are published as supporting information on the PNAS web site). Whereas in 1b the two guanine bases are indeed arranged head-to-head, interbase hydrogen bonding involves the N3 and N(2)H₂ sites (the so-called sugar edge) and leads to a tape structure (Fig. 1). H bond lengths vary between 2.99(2) and 3.07(2) Å (two crystallographically independent molecules) and are thus at the lower end of similar H bonds in other examples of Pt^II guanine complexes (14, 34). Adjacent tapes display partial stacking of the purine rings and are connected by intermolecular H bonds between NH₃ ligands and O6 sites of the guanine ligands (see Figs. 9–11, which are published as supporting information on the PNAS web site). Finally, in 2, the two hypoxanthine bases are head-to-tail, and cations are involved in H bonds between pairs of N3 and C(2)H sites of 3.29(2) Å, which leads to a tape structure as well (Fig. 2). The significance of the involvement of the aromatic proton H2 in H bonding will be discussed below. Again, these tapes are layered on top of each other and held together by H bonds between NH₃ ligands and O6 [2.89(1) Å] as well as H bonds mediated by an oxygen atom of a perchlorate anion (see Fig. 12, which is published as supporting information on the PNAS web site). There are no unusual structural features in cations of 1a, 1b, and 2, which is why we do not wish to discuss any further details (see Tables 2–4, which are published as supporting information on the PNAS web site). Still, the relatively short intramolecular contact between the O6 sites in 1b [3.11(1) and 3.10(1) Å] deserves mentioning. Mutual repulsion of these atoms is eased by their involvement in two intermolecular H bonds to NH₃ ligands of adjacent cations.

Fig 1.

Intermolecular association of cations of 1b along the z axis with H bonds involving N3 and N(2)H₂ sites.

Fig 2.

Intermolecular association of cations of 2 with H bonds involving N3 and the aromatic proton H2.

Concentration-dependent ¹H NMR spectra of 1 and 2 were recorded in DMSO-d₆. They did not reveal shifts of resonances that could have been interpreted in terms of any cation association in this solvent.

Mixed Cytosine–Hypoxanthine Complexes.

The mixed cytosine–hypoxanthine complex trans-[(CH₃NH₂)₂Pt(1-MeC-N3)(9-MeHxH-N7)]X₂ (3) was isolated as three different salts, with counter ions being NO, ClO, and CF₃SO. Crystals suitable for x-ray analysis were obtained for the nitrate (3a) and the perchlorate salt (3b) only, which crystallize in different space groups. Although similar [head-to-tail orientation of two bases with respect to positions of exocyclic oxygen atoms and intermolecular H bond between O6 of 9-MeHxH and N(4)H₂ of 1-MeC], there are numerous minor geometrical differences (dihedral angles between nucleobases, angles about Pt, and internal H bond lengths; see Fig. 13 and Tables 5 and 6, which are published as supporting information on the PNAS web site) and a major one in the packing pattern. Both cations undergo dimer association through intermolecular H bonding between NH₂ of methylamine ligands and exocyclic oxygen atoms of the nucleobases. In 3a, this is the O6 of hypoxanthine [2.954(5) Å], whereas in 3b, it is the O2 site of cytosine [2.905(3) Å]. Partial stacking of the base planes (3.11 Å) is observed in 3a. A unique feature of the packing of 3a is the formation of H bonds involving N3 and C(2)H sites [3.179(7) Å] leading to a dimer structure in which the two purine bases are at a substantial angle of almost 34° (Fig. 3).

Fig 3.

Association of cations 3a via C(2)H…N (3)H bonds [3.179(7) Å]. (Upper) Top view. (Lower) Side view.

Pt^II binding to the N7 position of 9-MeHxH in 3 causes the expected acidification of the proton at N1. pH*-dependent ¹H NMR spectra of 3 in D₂O were recorded and compared with those of free 9-MeHxH. A pK_a of 8.13 ± 0.13 (D₂O) (corresponding to 7.56 ± 0.13 in H₂O) was found with 3, which compares with 9.77 ± 0.07 (D₂O) and 9.18 ± 0.07 (H₂O) for the free nucleobase. The acidifying effect is of the expected magnitude (35). We have subsequently isolated the deprotonated form of 3, trans-[(CH₃NH₂)₂Pt(1-MeC-N3)(9-MeHx-N7)]X (4) on a preparative scale, with X = NO₃ (4a), ClO₄ (4b), and CF₃SO₃ (4c). Unfortunately, crystals suitable for x-ray analysis could not be obtained. As a consequence of deprotonation of the N1 position of 9-MeHxH, several ¹H NMR resonances of 4 (in DMSO-d₆) occur upfield with respect to the parent compound 3, e.g., H8 (Δδ, −0.38 ppm), H2 (Δδ, −0.27 ppm), and N-CH₃ (Δδ, −0.11 ppm). On the other hand, the amino protons of the 1-MeC base are shifted downfield and split. Interestingly, the chemical shifts of both these NH₂ resonances and the H5 doublet of 1-MeC are concentration-dependent, with one of the amino proton resonances and H5 being shifted downfield with increasing concentrations (Fig. 4). The behavior of 4 is thus similar to that of trans-[(NH₃)₂Pt(1-MeC-N3)(9-EtG-N7)]⁺, which has been demonstrated to form a stable base quartet structure both in solution and in the solid state (14). Therefore, we propose that 4 adopts a similar structure and consists of two +1 cations, with pairs of intermolecular hydrogen bonds holding them together (Scheme ). Of these H bonds, two are between the aromatic H5 protons of 1-MeC and the deprotonated N1 positions of the 9-MeHxH. The other two intermolecular H bonds involve one of the two amino protons (denoted with an asterisk in Scheme ; see also Fig. 4) and either O6 or O6 and N1 (bifurcated). Thus the metalated quartet displays at the same time four primary and four attractive secondary H bonding interactions (36) as a consequence of the DDAA sequence. This arrangement is supported by ¹H,¹H rotating-frame Overhauser effect spectroscopy experiments carried out with DMSO-d₆ and dimethylformamide-d₇ solutions of 4. In addition to the expected crosspeaks between the H6 and H5 doublets of the 1-MeC ligand, crosspeaks between H5 and the NH* proton of the exocyclic amino group of 1-MeC, as well as between H5 of 1-MeC and H2 of 9-MeHx, are observed. The latter crosspeak (Fig. 5) confirms that these two protons are spatially close to each other, thereby further corroborating our proposal.

Fig 4.

Concentration dependence of proton resonances of 4 in DMSO-d₆.

Scheme 3.

Proposed association pattern of 4 based on ¹H NMR data (concentration dependence, ¹H,¹H rotating-frame Overhauser effect spectroscopy). Nuclear Overhauser effect crosspeaks (see Fig. 6) are indicated.

Fig 5.

Section of ¹H,¹H rotating-frame Overhauser effect spectroscopy spectrum of 4b in DMSO-d₆ (2.8⋅10⁻² M) with crosspeaks of H5 (1-MeC) with H6 and N(4)H* (1-MeC) as well as with H2 (9-MeHx) (see also Scheme ).

From the concentration dependence of the cytosine H5 and NH* signals, an association constant of 7.8 ± 4 M⁻¹ (2 σ) was calculated for the dimer. This value is clearly smaller than that of the 9-EtG system (44.1 ± 3.2 M⁻¹) (14) but comparable with that of the Watson–Crick pair of 1-MeC and 9-ethylguanine under identical conditions (DMSO-d₆, 6.9 ± 1.3 M⁻¹) (37). That the DMSO-d₆ samples contained residual water most likely accounts for a reduction in dimer association (36).

The existence of the platinated nucleobase quartet has been confirmed by electrospray ionization–MS with mass peaks of the dimer (m/z = 1,061.2). Its Na⁺ (m/z = 1,083.2) adduct, as well as the ClO (m/z = 1,163.1) and NaClO₄ (m/z = 1,182.0) adducts, is also clearly discernible. The calculated mass distributions of these peaks are in agreement with the experimentally observed ones (Fig. 14, which is published as supporting information on the PNAS web site).

Discussion

Four different self-association patterns of N9-blocked guanine nucleobases exist that pair through two cyclic H bonds each (38). These are (i) N(1)H…O6′ and N(1′)H…O6, (ii) N(1)H…O6′ and N(2)H₂…N7′, (iii) N(2)H₂…O6′ and N(1)H…N7′, and (iv) N(2)H₂…N3′ and N(2′)H₂…N3. All these possibilities have been verified by x-ray structural analysis either in RNA structures (39) or G,G mismatches of DNA (40). If extended beyond the dimer level, iii results in a polymeric ribbon structure, as does a combination of i and iv (41). There is also the possibility of generating a cyclic structure, the G quartet, if pattern ii is doubled and the four bases become connected by four pairs of cyclic H bonds (see Scheme 6, which is published as supporting information on the PNAS web site). With the N9-blocked hypoxanthine (or the nucleoside inosine), the number of pairing patterns is reduced to one (i), unless the involvement of the aromatic proton H2 in base pairing is allowed. If so, an identical number of different pairing schemes is to be expected. There is presently no evidence that this is indeed the case. The tetra-stranded structure of poly(rI) (42) is believed to contain four single H bonds between N(1)H and N7′ sites (43).

Blockage of the N7 sites of guanine or hypoxanthine by a metal ion reduces the number of possible association patterns to two for guanine (i, iv) while not affecting the number in the case of hypoxanthine (i). Examples of Pt^II guanine complexes displaying either of these patterns have been reported (14, 15). Findings with the hypoxanthine complexes 2 and 3a, reported in this work, suggest that N7 metal coordination may “activate” the H2 proton in such a way as to become involved in H bonding and base association. That we find this type of interaction in two complexes (of only three studied by us) can be considered accidental, but maybe it is not. The C—H…N bond lengths observed in 2 and 3a are in agreement with expectations (refs. 44 and 45; ref. 46 and references therein).

The apparent reduction in the number of possible self-pairing patterns of N7 metalated 6-oxopurine compounds is compensated for if a crosslinked nucleobase X is included and/or if the purine undergoes deprotonation at the N1 position (Scheme ). Thus, Scheme a is an example for the involvement of a second nucleobase (X = guanine) in self-association (v in Scheme ), as are compounds V (14) and VI (15) in Scheme . Moreover, on deprotonation of the guanine base (vi in Scheme ), self-pairing can occur via N1 and N(2)H₂ sites (47). Finally, hemideprotonation of the guanine ligand results in complementary pairing between a neutral and an anionic guanine with three sites involved in H bond formation (vii in Scheme ). This pair by far exceeds the normal G,C Watson–Crick pair in strength (47–50).

Scheme 4.

H bonding edges in trans-[M(G)X]ⁿ⁺ (Left) and trans-[M(G⁻)X]^(n-1)+ (Right) cations, with X being a second nucleobase.

A convincing example of the significance of the involvement of a second nucleobase X in self-association is realized in compound 4 (Scheme ). There can be little doubt that the H bond between the aromatic H5 proton of the 1-MeC ligand and N1 of the hypoxanthinate anion is strong. If it were just a secondary interaction as a consequence of another much stronger interaction, one would have to rationalize the considerable stability of the quartet 4 on the basis of two H bonds only, between N(4)H₂ of 1-MeC and O6 of 9-MeHx, a rather unlikely situation. The same arguments apply to the related quartet containing a guanine anion instead of hypoxanthine (14). A comparison of the artificial Pt^II-containing base quartet 4 with the natural base quartet consisting of two cytidine and two inosine bases (Scheme ) reveals the overall similarity in shape and orientation of the glycosidic bonds in the two quartets, and at the same time points out the differences. In 4, cytosine and hypoxanthinate are connected by coordinative and H bonds, as opposed to H bonds only in the case of the natural quartet. From molecular dynamics simulations, it is concluded (43) that the ICIC quartet, like the corresponding GCGC quartet (8), is stable in a tetra-stranded DNA only if a G₄ stem is formed and the appropriate cations (K⁺, Na⁺) are present. There can be no doubt that the artificial base quartet 4 does not require these factors.

Scheme 5.

Comparison of natural base quartet HCHC (Left) and artificial metalated quartet 4 (Right). In nature, the hypoxanthine (H) ring is part of the nucleoside inosine (I).

Abbreviations

• 9-MeGH, 9-methylguanine

• 9-MeHxH, 9-methylhypoxanthine

• 1-MeC, 1-methylcytosine