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J. Phys. Chem. B 2008, 112, 150-157
Tautomeric Equilibrium, Stability, and Hydrogen Bonding in 2′-Deoxyguanosine Monophosphate Complexed with Mg2+ Dmytro Kosenkov,† Leonid Gorb,†,‡ Oleg V. Shishkin,§ Jirı´ Sˇ poner,| and Jerzy Leszczynski*,† Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State UniVersity, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, Institute of Molecular Biology and Genetics, Department of Molecular Biophysics, National Academy of Sciences of Ukraine, 150 Zabolotnoho, KieV, Ukraine 03143, STC “Institute for Single Crystals”, National Academy of Sciences of Ukraine, 60 Lenina AVenue, KharkiV 61001, Ukraine, and Institute of Biophysics, Academy of Sciences of the Czech Republic, V.V.i., Kra´ loVopolska´ 135, 612 65 Brno, Czech Republic ReceiVed: July 26, 2007; In Final Form: September 26, 2007
The tautomeric equilibrium and hydrogen bonding in nucleotide 2′-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O‚Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O‚Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the PdOfMg and MgrN7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O‚Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.
Introduction experimental1-8
Nucleotides have been subjected to extensive and theoretical studies1-2,9 due to their biological and chemical significance. Nucleotides participate in a number of biochemical pathways and serve as building blocks of nucleic acids and constituents of enzyme cofactors.1-2,10 The nucleotides consist of three fragments: nucleic acid (NA) base, furanose sugar moiety, and phosphate groups. Very often, the single nucleobases are considered the simplest model to understand chemical properties of NA constituents.11-25 The specific molecular interactions between nucleobases (stacking and base pairing) constitute the most fundamental forces in nucleic acids. Another interesting feature of nucleobases is their capability to tautomerize. Actually, a long time ago Watson and Crick hypothesized that “rare” tautomeric forms of DNA bases could give rise to mispairing of purines and pyrimidines.26 In the DNA double helix, the canonic form of guanine (G) pairs only with cytosine (C), and the canonic form of adenine forms hydrogen bonds only with thymine in order to keep the genetic information intact.26 In principle, mispairing of nucleobases with “rare” tautomers could contribute to formation of point mutations where the AT base pair replaces * Author to whom correspondence should be addressed. E-mail: jerzy@ ccmsi.us. Mailing Address: Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, MS, 39217, USA, Tel: (601) 9793723 Fax: (601) 979-7823. † Jackson State University. ‡ Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine. § Institute for Single Crystals, National Academy of Sciences of Ukraine,. | Institute of Biophysics, Academy of Sciences of the Czech Republic.
the GC base pair on the replicated DNA helix. Nevertheless, this tautomeric hypothesis yet remains to be proven, as it is well-established that evolution has selected only those nucleobases that do not readily tautomerize in polar environments. (The gas phase and polar solvent condensed phase tautomeric equilibria are very different.) Rare tautomers of natural DNA bases have never been detected in biochemically relevant environments. According to the experimental data,11-17,27 all DNA bases in polar solvents and in crystals exist exclusively in the canonic form. These findings do not rule out that transient formation of tautomers may contribute to the mutations. It is important to highlight that the concentration (or probability of formation) of such transient “rare” tautomer forms in DNA would be extremely small (certainly outside of the detection limits of modern analytical methods and equipments), but transient tautomer species could still cause mutations. In particular, transient occurrence of rare tautomers in the growing strand could induce point mutations during DNA replication. We also would like to mention that occurrence of DNA tautomers is not the only mechanism of formation of DNA point mutations. Among such postulated mechanisms are involvement of cytosine deamination, oxidative damage, and so forth.27-29 In contrast to the biochemical environments, several cytosine and guanine tautomers were unambiguously shown to coexist in argon matrix and gas-phase experiments,11-17,30,31 although the relative population of these gas-phase tautomers and the assignment of IR and UV transitions are still disputed.11,30-33 Recently, we investigated tautomeric properties of different forms of DNA bases in the gas phase and analyzed the corresponding Gibbs free energies and the equilibrium constants
10.1021/jp075888t CCC: $40.75 © 2008 American Chemical Society Published on Web 12/11/2007
Tautomeric Equilibrium in 4H2O•Mg[dGMP]
Figure 1. Conformations of 2′-deoxy-guanosine-monophosphate. (a) north/anti; (b) north/syn; (c) south/anti; (d) south/syn. X ) H2PO4, HPO4-, PO42-, 4H2O‚(MgHPO4)+.
at room temperature. Currently, these data are available for guanine, cytosine, their mono- and dihydrated forms, and all protonated DNA bases.23 We also addressed the kinetics of tautomerization using a recently developed approximate instanton approach,23 which can describe the proton-transfer dynamics in model systems of biological importance. These results were applied to explain the frequency of spontaneous mutations in E. coli, for which reliable experimental data are available.34 A logical extension of these investigations is to study whether the DNA backbone is able to modulate the tautomeric properties of nucleobases. Such a study was reported in our recent paper9,35 and revealed that the influence of a DNA backbone is quite complex and depends on the conformation of nucleotide (Figure 1) and the value of its uncompensated charge (Figure 2) in the gas-phase environment. The charge of the phosphate group also influences the relative stability of the conformers. In neutral nucleotides, conformers with syn orientation (Figure 1b,d) of the nucleobase is significantly stabilized by intramolecular Os H‚‚‚O, NsH‚‚‚O, and OsH‚‚‚N hydrogen bonds. The relative energy of these conformers depends on the strength of the formed H-bonds. The most stable conformer is north/syn (Figure 1b) in neutral pdG. Among conformers with an anti orientation (Figure 1a,c) of the nucleobases, the south/anti (Figure 1c) conformer has the lowest energy in the monoanionic pdG. Deprotonation of the phosphate group leads to south/syn (Figure 1d) conformers as being the most stable in monoanions of pdG. The most striking changes are observed for dianions of nucleotides. There are no local minima on the potential energy surface corresponding to the syn orientation of the nucleobase, and the north/anti (Figure 1a) conformer is the most stable. The next important observation concerns the tautomeric properties of 2′-deoxyribonucleotides. According to the obtained results,35 the tautomeric properties of isolated DNA bases and anti conformers of 2′-deoxyribonucleotides are virtually the same. They do not depend on the amount of the uncompensated negative charge. Therefore, only 2′-deoxyribonucleotides, pos-
J. Phys. Chem. B, Vol. 112, No. 1, 2008 151 sessing south/anti and north/anti conformations (Figure 1c,a) containing guanine and cytosine, could contribute significantly to the rate of spontaneous point mutations due to the formation of biologically relevant amounts of “rare” tautomers. The current paper extends this study in the following way. We replace the proton that had compensated the negative charge in our previous models by a hydrated Mg2+ cation which certainly represents a considerably more realistic system. Mg2+ is an abundant physiological cation known to often interact with the anionic nucleic acids, and actually magnesium cations are present in an active site of DNA polymerase.36 Interactions of divalent cations with nucleotides and the DNA backbone have been reported in several recent papers.37-39 In these studies, the nucleotide was assumed to have a formal charge of -1. The nucleotide had a 5′-guanosine monophosphate anion (5′GMP-) with the 3′-end phosphate oxygen blocked by a hydrogen. This results in assumption of a formal nucleotide charge of -1, corresponding to the charge distribution in nucleic acid chains and the total charge (+1) of the studied nucleotidecation systems. In the present paper, we assume inner-shell coordination interactions of Mg2+ with the nucleotide (Figure 3), while the nucleotide has its formal charge of -2 (5′GMP2-). The Mg2+ cation directly binds to two nucleotide atoms (including at least one anionic phosphate oxygen), while its first ligand shell is completed by four water molecules to obtain the correct hexacoordination of magnesium. This model system has some substantial advantages: (i) Since the whole system is neutral, the uncompensated ionic effects that often entirely bias gas-phase calculations are reduced. Thus, the present calculations can be more easily extrapolated to the polar solvent situation where all long-range ionic effects are typically annihilated.40-42 (ii) In the current study, overall charge distribution corresponds to the ion-binding mode of nucleotides observed in biological systems. Recent crystallographic studies have shown that the functional RNA molecules like the Thi-box riboswitch and glmS ribozyme recognize their monophosphorylated ligands in the following way. The phosphate group interacts via innershell binding with Mg2+, and the ligand is subsequently bound to the RNA mainly through the water molecules completing the coordination shell of the cation. In other words, the phosphorylated ligands are recognized in their complexes with Mg2+. This is exactly the same binding mode of Mg2+ considered in the current study, and it thus appears to represent a common interaction pattern of Mg2+ with nucleotides and similar phosphorylated molecules under the physiological conditions.43-47 The following questions are addressed in this study regarding the structure and energies of different conformers of 2′deoxyguanosine-monophosphate (dGMP2-). Does the interaction with the hydrated cation result in any significant changes in chemical structure of 2′-deoxyguanosine monophosphate in comparison to either its charge-neutralized model structure (charge compensated by protons) or its dianionic forms? What is the free energy difference between different conformers of 2′-deoxyguanosine monophosphate? Does it depend on the type of negative charge compensation? Are the south/ anti or north/anti conformations (Figure 1c,a) dominating in different DNAs the lowest energy minima among the considered forms?
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Figure 2. The structural formulas and molecular structures of the considered systems: (a) neutral form,9,48 (b) monoanion form,9,48 (c) dianion,9,48 (d) monoanion complexed with hydrated magnesium.61
Figure 3. Atom numeration for of 2′-deoxyguanosine monophosphate (dGMP2-) in complex with 4H2O‚Mg2+ (north/anti conformation). Dashed lines represent hydrogen bonds.
Methods of Calculation The nucleotide 2′-deoxyguanosine monophosphate complexed with a hydrated magnesium cation (4H2O‚Mg[dGMP]) (Figures 3 and 4) was considered. All starting geometries have been designed from the optimized geometry9 of dGMP2-coordinated by hydrated Mg2+ and forming two covalent bonds with O2P and O3P atoms (see Figure 3). The numeration of atoms is shown in Figure 3. The minimal number of water molecules was selected to saturate coordinate bonding of Mg2+. In the same way as previously,9,35,48 the current investigation considers conformations with syn and anti orientations of guanine with respect to the 2′-deoxyribose ring1 and north (C3′-endo) and south (C2′-endo) conformations of the 2′-deoxyribose ring. These conformations of the nucleotide are found to be the most common in nucleic acid structures.1 Among all possible tautomeric states of 2′-deoxyguanosine monophosphate, only the
hydroxo-amino form was considered, since it is assumed that only this form could play the role in formation of GC f AT point mutations26 and, in addition, this is the low-energy form for gas-phase guanine tautomers23 (see Figure 4). The hydroxo-amino form of guanine is represented by two rotamers: O6-hydroxo-syn-amino- (hereinafter hydroxo-s) and O6-hydroxo-anti-amino-guanine (hereinafter hydroxo-a). These forms correspond to different orientations of the hydroxyl group with respect to the amino group of the guanine nucleobase (Figure 4). Quantum chemical calculations were carried out using the Gaussian03 program.49 The molecular structure of the nucleotide was calculated using density functional theory (DFT)50,51 with Becke’s three-parameter exchange functional52,53 and the gradient-corrected functional of Lee, Yang, and Parr (B3LYP).54 Standard Dunning’s correlation consistent basis set cc-pVDZ55 was used for optimization of the molecular geometries. Local minima were verified by establishing that the matrix of energy second derivatives (Hessian) had only positive eigenvalues. The vibration frequencies, the energy of zero-point vibrations, and temperature corrections to the Gibbs free energy were calculated in the framework of harmonic approximation at the level of geometry optimization. The Gibbs free energies and equilibrium constants were estimated at T ) 298.15 K using the standard expressions: ∆G ) ∆H - T∆S and Keq ) exp(-∆G/RT). The total energies of all conformers were also calculated at the MP2/cc-pVDZ and B3LYP/aug-cc-pVTZ levels using a reference B3LYP/cc-pVDZ geometry. A topological analysis of the electron density distribution was carried out within Bader’s Atoms in Molecules (AIM) approach56 in the AIM2000 program57 using the wavefunction obtained at the B3LYP/cc-pVDZ level of theory. The existence of intramolecular hydrogen bonds in different conformers of 2′-deoxyguanosine monophosphate was identified using geometrical and Atoms in Molecules (AIM, Bader’s theory) criteria. The existence of intramolecular hydrogen bonds was established on the basis of the presence of a bond (3, -1) critical point (BCP) between two covalently nonbonded atoms
Tautomeric Equilibrium in 4H2O•Mg[dGMP]
J. Phys. Chem. B, Vol. 112, No. 1, 2008 153
Figure 4. Tautomeric forms of 2′-deoxyguanosine monophosphate in complex with 4H2O‚Mg2+ (4H2O‚Mg[dGMP]).
and the value of electron density (F) in a bond critical point in the range (1.5-3.5) × 10-2 e/au3 (refs 48, 58, 59) and Laplacian of electron density (∇2F) in a bond critical point in the range (4.4-13.9) × 10-2 e/au5 (refs 48, 58, 59). Following ref 48, the distance between RCP (ring critical point) and BCP was considered to be LRCP > 1.5 a.u. for strong H-bonds and LRCP > 1.1 a.u. for weak H-bonds of CsH‚‚‚O or CsH‚‚‚N types. The ellipticity ( ) λ1/λ2 - 1) provides a measure of the extent where the charge is preferentially accumulated in the given plane.60 According to ref 48, if the hydrogen bond exists the ellipticity should be < 0.09 for strong and < 0.22 for weak H-bonds.48 To describe conformations of 4H2O‚Mg[pdG], the standard geometrical parameters were used. The torsion angle χ ) O(4′) - C(1′) - N(9) - C(4) characterizes the relative orientation of the nucleobase and the ribose ring. The puckering of the sugar ring was described by the pseudorotation angle P and the degree of puckering νmax: tan(P) ) {(ν4 + ν1) - (ν3 + ν0)}/{2ν2[sin(36°) + sin (72°)]}, νmax ) ν2/cos(P), where ν0, ν1, ..., ν4 are internal dihedral angles of the sugar ring.1 The deviation from the planar form (pyramidality) of the amino groups in the nucleobase47 was measured as π ) 360 θ, where θ is the sum of all valence angles centered on the nitrogen of the amino group. Results and Discussion Structure of the Nucleotide. The molecular structure of 2′deoxyguanosine monophosphate coordinated by the hydrated magnesium cation is drawn in Figures 3 and 5. Basic geometrical parameters are collected in Table 1. The corresponding Cartesian coordinates for all considered conformations of 4H2O‚Mg[dGMP] can be found in the Supporting Information. The most important feature of the considered structures compared to the data presented in refs 9 and 35 is the presence of a hydrated magnesium cation. As we already mentioned, we consider innershell coordination of the Mg2+ cation which forms six coordinate bonds with surrounding water molecules and electron-donor parts of dGMP2-. The water molecules occupy four coordination sites in all the considered conformations. In both syn conformations, two other coordination vacancies are occupied by oxygens
of the phosphate group. However, in the north/anti and south/ anti conformations, two other coordination sites are occupied by the N7 atom of the nucleobase and by oxygen of the phosphate group. Thus, in these conformations, in addition to electrostatic interaction, the hydrated magnesium cation polarizes the DNA nucleobase by direct involvement of the N7 lone pair. Hydrogen bonds found in 4H2O‚Mg[dGMP] are listed in Table SI of the Supporting Information. Obviously, the presence of the hydrated Mg2+ cation leads to an increase of the total number of H-bonds and rearrangement of the intramolecular hydrogen bonds in comparison to neutral, anion, and dianion nucleotides.9,48,61 The structures of these neutral, anion, and dianion nucleotides are sketched in Figure 2. Indeed, the number of OsH‚‚‚O and OsH‚‚‚N bonds greatly increases due to the presence of water molecules playing the role of donors in these H-bonds. In conformers with anti orientation of the base, the C(8)s H‚‚‚O5′ hydrogen bond is present in all considered forms independently of the phosphate group charge and the presence of magnesium cation. The water molecules of the Mg2+ hydration shell also form several additional hydrogen bonds with the base and phosphate group (Figure 5). Conformers with syn orientation of the base are stabilized by the N(2)sH‚‚‚O(2P) hydrogen bond. The cation hydrated shell also plays the role of bridge between phosphate group and guanine, due to formation of the OsH‚‚‚O and OsH‚‚‚N hydrogen bonds. Several weak CsH‚‚‚O and CsH‚‚‚N hydrogen bonds exist in both syn and anti conformations that contribute to their stabilization. The tautomerization does not influence significantly the conformation of the 2′-deoxyribose ring due to a relatively long separation between nucleobase and 2′-deoxyribose in the anti conformation. In syn conformers with the south conformation of the 2′-deoxyribose ring, the conformation is quite stable and does not change significantly under tautomerization. The presence of the Mg2+ cation could result in some changes of geometrical parameters comparing to the structures considered in the previous studies.9,22,23 Thus, we compared four parameters, which describe common features of nucleotide geometry (Table 1). Two of them are related to the nucleobase: the orientation of the nucleobase with respect to the sugar ring χ and
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Figure 5. The conformations of the 2′-deoxyguanosine monophosphate in complex with hydrated Mg2+ (4H2O‚Mg[dGMP]). Dashed lines represent hydrogen bonds.
TABLE 1: Selected Calculated Parameters Describing the Geometry of 2′-Deoxyguanosine Monophosphatea conformation
south /syn
north /syn
south /anti
north /anti
molecular forms
Mg2+ a
neutral neutral neutral formb anionb dianionb Mg2+ a formb anionb dianionb Mg2+ a formb anionb dianionb Mg2+ a neutralb anionb dianionb
χ, deg P, deg νmax, deg π, deg
77.5 154.6 33.3 28.2
73.2 164.8 33.3 13.5
69.4 159.7 37.5 12.6
-
64.4 37.3 38.5 28.5
66.3 29.7 37.9 11.8
58.1 42.3 28.3 15.0
-
-167.4 -133 -111 -90 -175.4 -145 -163 -102 187.5 174.3 148.9 196.3 -0.5 18.5 31.1 8.5 26.8 32.9 41.9 31.4 41.1 34.0 30.8 39.1 16.1 17.4 24.9 31.6 15.5 18.0 24.1 30.4
a The four conformations of the nucleotide (syn/south, syn/north, anti/south, anti/north) are considered. b Complex with hydrated magnesium Mg2+, current study. c B3LYP/6-31G* calculations from ref 9. χ ) O(4′) - C(1′) - N(9) - C(4) - torsion angle which characterizes different orientations of the nucleobase with respect to the 2′-deoxyribose ring; P ) angle of pseudorotation of 2′-deoxyribose furanose ring; νmax ) maximum out-of-plane pucker; π ) deviation from the planar form (pyramidality).
pyramidality of the NH2 group. Other two parameters P and νmax describe pseudorotation of the sugar ring. Table 1 suggests that the geometry of the amino group in south/syn and north/ syn species is changed most significantly compared to systems
without Mg2+ (refs 9 and 35). In fact, pyramidality of the NH2 group in 4H2O‚Mg[dGMP] complexes is comparable to the pyramidality in dianions. The possible reasons for the enhanced pyramidalization include a change in hybridization of the
Tautomeric Equilibrium in 4H2O•Mg[dGMP]
J. Phys. Chem. B, Vol. 112, No. 1, 2008 155
TABLE 2: Relative Stabilities and Relative Gibbs Free Energies of 2′-Deoxyguanosine Monophosphate Canonic (oxo) Forms, kcal/mol
north/anti south/anti north/syn south/syn a
B3LYP/ 6-31G* aniona
B3LYP/ 6-31++G** anionb
B3LYP/ 6-31G* neutral forma
B3LYP/ 6-31G* dianiona
B3LYP/ cc-pVDZ Mg2+ c
MP2/cc-pVDZ// B3LYP/cc-pVDZ Mg2+ c
B3LYP/aug-cc-pVTZ// B3LYP/cc-pVDZ Mg2+ c
17.18 9.53 4.04 0.0
5.60 10.02 4.51 0.0
9.50 8.83 0.0 5.01
0.0 10.22 -
0.0 9.29 11.95 19.24
0.0 12.08 13.14 20.89
0.0 8.10 10.03 16.97
Calculations from ref 9. b Calculations from ref 48. c Complex with hydrated magnesium Mg2+, current study.
TABLE 3: Relative Tautomerization Energies (∆G298, kcal/mol) and Equilibrium Constants (Keq) of hydroxo-s and hydroxo-a Tautomeric Forms of 4H2O‚Mg[dGMP], dGMP 2-, and Guanine at T ) 298 K hydroxo-s
hydroxo-a
∆G298 north/anti 4H2O‚Mg[dGMP] south/anti 4H2O‚Mg[dGMP] north/syn 4H2O‚Mg[dGMP] south/syn 4H2O‚Mg[dGMP] north/anti dGMP 2south/anti dGMP 2guanine a
a
6.05 (7.42) 5.56 (6.51) -0.6 (0.16) 0.51 (0.90) 0.49 0.75 0.95 (1.01)
Keq b
3.7 × 10 (3.64 × 10 ) 8.4 × 10-5 (1.70 × 10-5) 2.80 (7.58 × 10-1) 4.2 × 10-1 (2.18 × 10-1) 4.4 × 10-1 2.8 × 10-1 2.0 × 10-1 (1.81 × 10-1) -5
-6
∆G298
Keq
8.22 (10.91) 7.13 (9.93) -0.25 (-0.07) 0.65 (0.81) 1.50 (1.43)
9.4 × 10 (1.0 × 10-8) 6.0 × 10-6 (5.23 × 10-8) 1.50 (1.13) 3.3 × 10-1 (2.6 × 10-1) 0.8 × 10-1 (9.0 × 10-2) -7
MP2/cc-pVDZ//B3LYP/cc-pVDZ calculations. b B3LYP/aug-cc-pVTZ //B3LYP/cc-pVDZ calculations.
nitrogen atom and electrostatic attraction between positively charged hydrogen atoms and negatively charged oxygen atoms. For the syn structures complexed with the cation (Table 1), the significant change of pyramidality occurs due to the direct participation of both nitrogen and hydrogen atoms of the NH2 group in hydrogen bond formation. In other words, the amino group simultaneously acts as an H-bond donor and amino acceptor, and the latter interaction is significant, as it involves a polarized water molecule from the cation hydration shell.62,63 We also would like to point out that the other parameters (χ, P, νmax) did not change significantly after addition of a hydrated magnesium cation. In particular, one may conclude that the orientation of the nucleobase in the south/syn and north/syn conformations is approximately the same as in the species where negative charge is compensated by a proton (called neutral in Table 1). The conformation of the sugar ring belongs to 2E and 3E structural types, similar to that described in ref 9. Relative Stability. It was shown previously48 that an application of the extended basis set with diffuse functions for geometry optimization leads only to slight changes in geometry of the nucleotide. Therefore, in Tables 2 and 3 we present the data obtained using the same method with different basis sets for comparison with our results. As we already mentioned, recently published data35 suggest that relative stability of the considered nucleotides depends on the value of the uncompensated negative charge located on the phosphate group (Table 2). The syn-oriented forms dominate in the case of all neutral (compensated by proton) and single negatively charged deoxyribonucleotides except 2′-deoxythymidine phosphate. The only anti conformations are present in the case of dianions. We believe that this behavior is due to an increase of repulsive interaction between the negative charge of the phosphate group and π or n-electrons of the DNA bases. Due to the presence of the Mg2+cation, the considered case is similar to the case assumed for the dianions from our previous study.35 There is full predominance of the north/anti conformer over all others. Similar to the data presented in ref 35, one may notice a large energetic gap between the north/anti and south/ anti conformations of 4H2O‚Mg[dGMP]. This result could be explained by formation of the coordinate PdOfMg and MgrN7 bonds in the anti conformations. In addition, multiple
H-bonds are formed among the water shell of the Mg2+, the phosphate group, and the nucleobase. These interactions contribute to stabilization of anti conformations of 4H2O‚Mg[dGMP]. Thus, in spite of energetic similarity of dianions and 4H2O‚Mg[dGMP], the reasons for this similarity are different. However, in contrast to the data presented in ref 35 for dianions, we found that the north/syn and south/syn conformers are highenergy local minima. They most probably are stabilized by electrostatic interaction (to a greater extent than in the case of the dianions) between the NH2 group of syn oriented nucleobase and the hydrated Mg2+ cation. Previously, we found35 that the north/anti conformation is significantly more stable then the south/anti one. This is confirmed by the results of the present study. We also would like to mention that this result assures one that the model of dGMP2- with Mg2+ better mimics the biologically relevant structure where the nucleotides exist in anti conformations. The north/anti conformation belongs to the A form of DNA and the south/anti one to the B form. It is known that DNA in the B form requires more water molecules per nucleotide and it spontaneously transforms to the A form when there are not enough water molecules to stabilize the B form.1 It is reasonable to assume that in our case the north/anti conformation is more stable due to the fact that water molecules hydrate only magnesium cation and do not hydrate sugar and DNA base. It means that there are not enough intermolecular interactions that could stabilize the south/anti conformation of the nucleotide to make the B form of the DNA more stable. Stabilization of Tautomeric Forms. Let us now qualitatively comment on the tautomeric equilibria. From the obtained results, the tautomeric behaviors of north/anti and south/anti conformations of 4H2O‚Mg[dGMP] are the most important, because these conformations are found in the right-handed DNA double helices. The data presented in Table 3 suggest a dramatic difference in the tautomeric properties of the considered nucleotides comparing to isolated DNA bases and dGMP2-. The tautomeric properties of north/anti and south/anti tautomers of 4H2O‚Mg[dGMP] are shifted by 4 orders of magnitude (ca. 5 kcal/mol) in favor of the canonic form. The close proximity of the cation to the O6 group certainly reduces the probability that the H1(G) hydrogen would move to the O6. In other words, the most likely mode of Mg2+ binding to the guanine anti-
156 J. Phys. Chem. B, Vol. 112, No. 1, 2008 nucleotide is by suppressing the tautomerization of guanine. In our opinion, the reason for this stabilization involves direct participation of oxo and hydroxo groups of guanine in hydrogen bonding with the hydrated Mg2+ (see Figure 5). This also explains the virtually unchanged tautomeric properties (compared to isolated bases) found for syn-4H2O‚Mg[dGMP] species. In these structures, the oxo and hydroxo groups are not involved in hydrogen bonding (see Figure 5). Despite the fact that our models are still quite far from those structures involved in DNA synthesis (hydrated or partially hydrated triphosphonucleotides, coordinated by two Mg2+ cations), we would like to mention that the tautomeric properties of north/anti and south/anti 4H2O‚Mg[dGMP] species correspond to biologically relevant situations much better than the tautomeric properties of an isolated guanine molecule. We believe that the qualitative trend emerging from our calculations, namely, the stabilization of the canonical tautomer, is correct. The above results, namely, the values of the equilibrium constants collected in Table 3, should be considered in the context of the frequency of point mutations in DNA in vivo (10-8-10-10) and in vitro (10-6-10-5) (refs 64 and 65). It is well-known that the hydration of DNA bases contributes to the preferable stabilization of the canonic nucleobase form.34,66 Our study shows that interaction of guanine with Mg2+ also contributes to suppression of tautomeric properties of guanine. The binding of Mg2+, therefore, would decrease the frequency of point mutations of DNA, provided they are related to transient nucleobase tautomerism during replication. In other words, coordination of physiological cations in the course of replication could, as a secondary effect, contribute to fidelity of replication by stabilizing the canonical form of guanine. Conclusions The interaction of 2′-deoxyguanosine monophosphate with the hydrated Mg2+ cation was studied by ab initio calculations. From a structural point of view, the most important difference comparing with the structure considered earlier9,48,61 is direct formation of several hydrogen bonds between hydrated Mg2+ and guanine. We also found a very significant influence of the presence of hydrated Mg2+ on pyramidalization of the amino group. From an energetic point of view, we found the same order of stability that was previously observed for isolated dianions of 2′-deoxyribonucleotides. However, syn forms also exist, but they possess high energy. We found that, in the case of north/ anti and south/anti conformers, the interaction of the hydrated magnesium cation with the guanine backbone increases the tautomerization energy of the guanine significantly. This changes the tautomeric equilibrium by about 4 orders of magnitude. We speculate that this interaction is also important for biological processes where 2′-deoxyguanosine monophosphate occurs in its syn conformation. Acknowledgment. The authors thank the Mississippi Centre for Supercomputer research for generous allotment of computer time. We also thank Ms. Yana Kholod for helpful discussion. This study was supported by NSF-CREST grant no. HRD0318519 and ONR grant No. 00014-03-1-0498. J.S. acknowledges the support by the following grants: GA203/05/0009 and 203/05/0388 by the Grant Agency of the Czech Republic, research project AVOZ50040507 and grants LC06030 and MSM0021622413 by Ministry of Education of the Czech Republic, and grant 1QS500040581 by the Internal Grant Agency of the Academy of Sciences.
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