J. Phys. Chem. A 2010, 114, 11231–11237
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Microhydration of the Guanine-Guanine and Guanine-Cytosine Base Pairs† Shu-hei Urashima,‡ Hiroya Asami,‡ Masashi Ohba,§ and Hiroyuki Saigusa*,‡ Graduate School of Arts and Sciences, Yokohama City UniVersity, Yokohama 236-0027, Japan and Yokohama College of Pharmacy, Yokohama 245-0066, Japan ReceiVed: April 1, 2010; ReVised Manuscript ReceiVed: May 3, 2010
Monohydration structures of the guanine-guanine and guanine-cytosine base pairs have been elucidated by IR-UV double resonance spectroscopy combined with ab initio calculations. The systems studied consist of the homodimer of 9-methylguanine and the heterodimer of 9-methylguanine and 1-methylcytosine in which the methyl group is introduced to mimic the presence of the sugar-phosphate backbone and to block specific tautomerization. The monohydrate of the homodimer is identified as that of the most stable symmetric structure formed by the keto tautomers of guanine, which demonstrates that the base pair structure is not influenced by the hydration. It is also shown that at least two structural isomers, one of which retains the Watson-Crick GC pair structure, contribute the monohydrated cluster of the heterodimer. Although stacked base pairs are suggested to be significantly stabilized by the addition of water, the result shows no clear indication for the presence of stacked monohydrates in either homodimer or heterodimer case. 1. Introduction Whereas the supramolecular structure of DNA is stabilized mainly by hydrogen-bonding and stacking interactions between the nucleic acid bases, the degree of hydration plays a key role in their secondary and tertiary structure.1 Structural analyses of DNA by X-ray crystallography revealed that water molecules occupy well-defined positions at the surface to form a primary hydration shell.2-5 However, it is difficult to elucidate microscopic solvation effects on the conformation of DNA by separating from base interactions, and thus the theoretical investigations of these systems have outpaced the experiments so far.6-10 Furthermore, most theoretical calculations suggested that stacked structures of the base pairs are stabilized upon the addition of water molecules with respect to the planar hydrogenbonded base pairs. Studying clusters of the DNA base pairs isolated in the gas phase enables us to investigate pairing and stacking interactions in the absence and presence of water molecules. Recently, AboRiziq et al.11 reported the structures of hydrated clusters of guanine base pairs formed by laser-desorption and supersonicjet cooling method. The result of IR-UV double resonance measurements indicated the presence of two different planar structures for the dimer,12 each consisting of the N7H-keto and N9H-keto tautomers of guanine and thus revealing an asymmetric structure. It was also demonstrated that one of the base pairs is preferred by the addition of a single water molecule. Nevertheless, the base pair of the symmetric structure that is calculated to be the lowest in energy was not observed. It was also demonstrated that the base pair cluster formed between 9-ethylguanine and 1-methylcytosine (1MC) corresponds to the most stable Watson-Crick (WC) base structure.13 Here we investigate the microhydration effects on the base pair formation of guanine-guanine and guanine-cytosine by utilizing the methylated compounds, 9-methylguanine (9MG) †
Part of the “Klaus Mu¨ller-Dethlefs Festschrift”. * To whom correspondence should be addressed. Fax: +81 45 787 2413. E-mail:
[email protected]. ‡ Yokohama City University. § Yokohama College of Pharmacy.
and 1MC. The use of these methyl compounds is two-fold. The methylation prevents the N9H-N7H tautomerization in unsubstituted guanine and the keto-enol tautomerization in unsubstituted cytosine. It can be used to mimic the presence of DNA backbones composed of the sugar and phosphate groups. Previous theoretical calculation9 suggested that three stable monohydrated structures are formed for the 9MG-1MC base pair, two of which are based on the WC form and one is of a stacking structure. Experimental investigations on the homodimers of 9MG and their hydrates have not been reported so far. 2. Theoretical Calculations A. Methods. Stable structures of isolated base pairs and their solvated clusters were obtained at the MP2/6-31++G(d,p) level. However, it is known that the MP2 method tends to overestimate the stability of stacked base pairs, and thus single-point calculations were performed at the CCSD/6-31++G(d,p) level to improve the accuracy of the energetic ordering of the isomers. Harmonic vibrational frequencies were calculated at the MP2/ 6-31++G(d,p) for the base pairs consisting of unsubstituted bases, namely, N9H-guanine (9HG) and N1H-cytosine (1HC), and scaled by a factor of 0.940. B. (9MG)2 Base Pair. The two most stable structures of 9MG base pairs obtained in this study are shown in Figure 1a. The lowest energy structure corresponds to the planar form with the two 9MG-keto tautomers symmetrically double hydrogen bonded together (pl-GG). This structure agrees with the result based on the MD/Q method reported by Kabela´cˇ and Hobza.14 The stacked base pair structure (st-GG) is calculated to be the second most stable isomer. In the case of unsubstituted guanine, there are some other stable structures composed of the N7Hketo and N9H-keto tautomers. Other planar and stacked structures including those of the enol tautomer are less stable by >20 kJ/mol with respect to the lowest energy structure, and thus they are not considered in this study. Figure 1b shows low-energy monohydrate structures of the 9MG dimer, (9MG)1W1 (W)H2O). It can be seen that the two most stable structures, pl-Wg2g6 and st-Wg12g6, correspond
10.1021/jp102918k 2010 American Chemical Society Published on Web 05/13/2010
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J. Phys. Chem. A, Vol. 114, No. 42, 2010
Urashima et al.
Figure 1. Low-energy structures of (9MG)2 and (9MG)2W1 calculated at the CCSD/6-31++G(d,p) level. The relative energies are indicated in kJ/mol. The numbers used for labeling the monohydrated structures refer to the sites of the guanine moieties (g) linked by water (W). The dotted lines indicate the formation of hydrogen bonding revealed by NBO analyses. The hydrogen-bond distances are in angstroms.
TABLE 1: Vibrational Frequencies and IR Intensities Calculated for (9HG)2 Base Pairs and Their Solvated Clustersa,b assignment N1H N1H(S)c sNH2(S)c sNH2 sOH(S)d N9H aNH2(S)c aNH2
pl-GG 2975.9 (0.0001) 3029.9 (3489.9)
pl-Wg2g6
st-Wg12g6
st-Wg2g67
pl-Mg2g6
3392.0 (29.2) 3392.5 (110.9)
2891.8 (1988.1)
3400.9 (181.7)
3401.4 (81.2)
2887.1 (1941.3)
3131.5 (1247.4) 3280.3 (847.2) 3404.4 (146.5)
3285.7 (170.9) 3355.1 (183.1) 3347.5 (62.7)
3398.3 (60.4) 3183.0 (561.6) 3360.7 (78.2)
3129.3 (1091.9) 3217.4 (1298.1) 3404.2 (144.1)
3442.6 (715.0) 3483.3 (111.0) 3485.0 (98.9) 3507.6 (77.1) 3540.4 (108.4)
3405.8 (553.7) 3480.7 (41.9) 3482.8 (116.9) 3512.4 (96.0) 3464.9 (39.5)
3503.5 (200.1) 3479.6 (45.9) 3481.1 (143.6) 3472.1 (60.2) 3471.7 (38.2)
3455.8 (820.0) 3482.8 (106.6) 3484.8 (99.8) 3505.3 (66.8) 3540.1 (107.4)
3711.0 (136.1)
3708.4 (165.7)
3584.8 (85.9)
3401.7 (0.6) 3403.2 (274.9)
3345.1 (13.4) 3346.1 (153.8)
3484.2 (217.3) 3484.3 (0.01)
3479.7 (18.2) 3480.5 (157.2)
3538.6 (55.8) 3538.8 (165.1)
3472.4 (44.0) 3472.5 (42.0)
aOH(W)e a
st-GG
-1
Vibrational frequency values (in cm ) scaled by a factor of 0.940. IR intensities values (in km/mol) in parentheses. c Vibrational modes in proximity to the solvent S (S ) W or MeOH). d Bridge OH stretch of solvent. e Antisymmetric stretch of water.
to the monohydrates of bare pl-GG and st-GG dimers shown in Figure 1a. The letters “W” and “g” refer to water and 9MG, respectively, and the numbers indicate the sites of the guanine moiety linked by the water. The third monohydrate st-Wg2g67 arises from the bare dimer pl-GG with water bridging the O6 and N7 atoms of one moiety. This planar structure is calculated to be unstable and converted to the stacked form with the water linking to the N2H atom of the other moiety. In the pl-GG structure, neither NH2 group is involved in the hydrogen bonding, and thus this symmetric structure can accommodate a water molecule around the NH2 group to form the stable monohydrate pl-Wg2g6. The CCSD calculation was also performed for methanol clusters, which indicates that the analogous planar geometry pl-Mg2g6 (M)MeOH) is slightly less stable (1.7 kJ/mol) than the stacked geometry st-Mg12g6. The harmonic frequencies of the stable guanine dimers and their solvated clusters calculated for nonmethylated guanine (N9H-keto) are listed in Table 1. C. (9MG)1(1MC)1 Base Pair. The lowest-energy structures calculated for the base pair of 9MG and 1MC are shown in Figure 2a. The WC form wc-GC is found to be more stable (32 kJ/mol) than the stacked pair st-GC. The result agrees well with their stabilization energies calculated at the CCSD(T) level by Jurecˇka and Hobza.15
b
Monohydrated structures of the 9MG-1MC dimer, (9MG)1(1MC)1W1, displayed in Figure 2b are found to be low in energy (34 200 cm-1, was found to give rise to narrow UV spectral features at irregular intervals superimposed on the broad background. The anomalous intensity distribution was used to infer that significant geometry changes of the amino-keto form still occur in the excited state. Furthermore, the occurrence of such excited-state dynamics specific to the amino-keto form can be rationalized by theoretical calculations on unsubstituted 9H-guanine,25-27 which suggested that out-of-plane distortions of the six-membered purine ring at the C2 position occurs in the excited state. A similar explanation can be provided for the broad UV spectra of the guanine-cytosine WC base pair. In contrast, Abo-Riziq et al.13 suggested that the broad UV spectra are associated with the occurrence of an ultrafast excited-state lifetime on the order of
