Article pubs.acs.org/JPCA
In Silico Studies to Explore the Mutagenic Ability of 5‑Halo/Oxy/LiOxy-Uracil Bases with Guanine of DNA Base Pairs Kalyanashis Jana†,‡ and Bishwajit Ganguly*,†,‡ †
Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR−Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India ‡ Academy of Scientific and Innovative Research, CSIR−CSMCRI, Bhavnagar, Gujarat 364002, India S Supporting Information *
ABSTRACT: DNA nucleobases are reactive in nature and undergo modifications by deamination, oxidation, alkylation, or hydrolysis processes. Many such modified bases are susceptible to mutagenesis when formed in cellular DNA. The mutagenesis can occur by mispairing with DNA nucleobases by a DNA polymerase during replication. We have performed a study of mispairing of DNA bases with unnatural bases computationally. 5-Halo uracils have been studied as mispairs in mutagenesis; however, the reports on their different forms are scarce in the literature. The stability of mispairs with keto form, enol form, and ionized form of 5-halo-uracil has been computed with the M06-2X/6-31+G** level of theory. The enol form of 5-halo-uracil showed remarkable stability toward DNA mispair compared to the corresponding keto and ionized forms. FU-G mispair showed the highest stability in the series and HaloUenol/ionized-G mispair interactions energies are more stable than the natural G-C basepair of DNA. To enhance the stability of DNA mispairs, we have introduced the hydroxyl group in the place of halogen atoms, which provides additional hydrogenbonding interactions in the system while forming the 5-membered ring. The study has been further extended with lithiated 5-hydroxymethyl-uracil to stabilize the DNA mispair. CH2OLiUionized-G mispair has shown the highest stability (ΔG = −32.4 kcal/mol) with multi O−Li interactions. AIM (atoms in molecules) and EDA (energy decomposition analysis) analysis has been performed to examine the nature of noncovalent interactions in such mispairs. EDA analysis has shown that electrostatic energy mainly contributes toward the interaction energy of mispairs. The higher stability achieved in these studied mispairs can play a pivotal role in the mutagenesis and can help to attain the mutation for many desired biological processes.
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the nucleic acid systems.17−24 It has been reported that the mispair formation of the halouracil can be enhanced with an increase in the pH of the solution.24 The presence of electronwithdrawing fluorine or chlorine atoms at the 5 position of the pyrimidine ring facilitates the ionization and enolization of FU/ Cl U in DNA or RNA, which leads to mispairing with guanine during replication or transcription.14,23 The selective incorporation of the FU in nucleic acids of malignant cells might be helpful to inhibit the growth of tumor cells.17,21,22 Due to smaller size of fluorine, FU is mimicking 2′-deoxyuridine 5′monophosphate and it could be easily removed from DNA by uracil-glycosyase enzymes.25−27 However, BrU can replace thymine in dsDNA, but BrU are repaired only by a few uracil glycosylases.25−29 ClU could be an alternate mispair unit of the F U and BrU, due to its intermediate size; however, ClU in dsDNA causes chromosomal abnormalities and shows toxicity.30,31 Halogenated uracil molecules present in keto, enol, and ionized forms depend upon the pH of the solution; at lower pH of the solution, they exist either in keto form or in enol form. When the pH of halogenated uracil solution is
INTRODUCTION The structure of DNA plays an essential role to govern replication and gene expression.1−3 It is known that hydrogen bonding and stacking interactions are chiefly responsible to control the structure of DNA.4 The effect of substitution at any position in DNA base-pairs can alter the stability and other properties.5−13 The stabilities of DNA can also be influenced with unnatural/substituted bases. Such interactions alter the typical base-pair in DNA and are termed as mutation.5−13 5Bromouracil (BrU) has been extensively studied as mutant with the nucleic acid system and shown significant effect.5−13 BrU influences to alter patterns of transcription, enhances the binding of the lac repressor to its operator, increases the affinity of chromosomal proteins for BrU-containing DNA, inhibits the expression of differentiated functions, and causes alterations in membrane properties.14 The mutagenic properties of the BrU has now been widely accepted and frequently observed during the DNA replication process.15,16 Mutagenicity is apparently determined by the concentration of BrU to which the cells are exposed rather than the amount of BrU in DNA. Such results were obtained due to the induction of ouabain resistance and thioguanine resistance as markers for mutagenesis.15,16 The studies with fluorouracil and chlorouracil are limited in the literature; however, these unnatural bases can mispair with © 2014 American Chemical Society
Received: July 25, 2014 Revised: September 18, 2014 Published: September 19, 2014 9753
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Scheme 1. Hydrogen-Bonding Interactions in A-T, G-C Basepairs, and 5-Substituted Uracila
a
The H-bonding interaction distances were taken from the M06-2X/6-31+G** level of theory optimized structures. (Distances are given in angstroms.).
Table 1. Interaction Energies Were Calculated with Different Methods for the G-C Base Pair and
a
Halo
U-G Mispaira
name of the pair
ΔEM06‑2X/6‑31+G**
ΔGM06‑2X/6‑31+G**
ΔEMP2/aug‑cc‑pVDZ
ΔEBSSE(M06‑2X/6‑31+G**)
G-C Br Uketo-G Br Uenol-G Br Uion-G Cl Uketo-G Cl Uenol-G Cl Uion-G F Uketo-G F Uenol-G F Uion-G
−28.6 −18.5 −31.3 −31.8 −16.5 −30.2 −29.9 −16.8 −30.6 −30.6
−15.6 −4.9 −18.6 −17.9 −4.8 −18.5 −17.7 −4.9 −18.6 −18.1
−30.5 −19.0 −31.2 −31.4 −18.9 −31.2 −31.5 −19.1 −31.2 −32.0
−30.7 −17.6 −38.7 −30.5 −17.5 −38.6 −31.0 −17.9 −39.2 −31.7
All the energy values are given in kilocalories per mol.
bonding interactions. Further, employing lithiated-5-hydroxymethyluracil (CH2OLiU) as a unit of mispair, the stability was augmented significantly compared to halogenated uracils.42−47
around the value of pKa of the corresponding halogenateduracil, the ionization of such uracils takes place via deprotonation of the N3-H unit.24 Hydrogen-bonding interaction is known to play an important role in stabilizing the DNA or RNA and helping to form different forms of DNA or RNA.4 The natural base pairs (A-T) and (G-C) form very strong hydrogen bonds with each other in DNA or RNA. A number of computational studies contributed to our knowledge of nucleic acids base pairing including their interactions and stability.32−35 It is known that the H-bonding stabilization energy of the G-C base pair is greater (∼12.0 kcal/ mol) than the A-T base pair.32−35 The greater stability of the G-C base pair is achieved via additional H-bonding interaction compared to the A-T base pair (Scheme 1). The H-bonding interaction energies calculated for the G-C base pair using RIMP2/aug-cc-pVTZ → RI-MP2/aug-cc-pVQZ Helgaker’s extrapolated energy is −28.2 kcal/mol and seems to be fairly accurate.32 We have performed DFT calculations using M062X/6-31+G** level of theory to examine the H-bond energy of the G-C base-pair.36−40 The calculated results suggest that the hydrogen-bonding interaction energy of G-C is −28.6 kcal/ mol, and the BSSE41 corrected energy at the M06-2X/631+G** level of theory is −30.7 kcal/mol (Table 1). These results are in good agreement with the earlier reports.32−35 We have extended our study using the M06-2X/6-31+G** level of theory to examine the interactions of the unnatural mutants with guanine of DNA. In this article, we have systematically examined the mispairing of halogenated uracils (FU, ClU, and BrU) with the guanine base of DNA. There are reports on the interactions of mutagenic mispair of halogenated uracil with the guanine; however, the detailed understanding is limited in the literature.5−31 We have exploited the stability pattern of mispairs of 5-susbtituted uracils 5-hydroxyuracil (OHU) and 5hydroxymethyluracil (CH2OHU) with additional hydrogen-
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COMPUTATIONAL METHODS All the structures of halogenated, hydroxy, hydroxymethyl, and lithiated-hydroxymethyl uracil have been optimized in gas phase with the M06-2X36 DFT functional and 6-31+G**39,40 Pople basis set. We have performed the frequency calculations at the same level of theory to confirm minima of optimized geometries with no imaginary frequencies. The M06-2X is one of the best functional for the organic system and even for the anionic systems.37,38 The interactions energy of these mispair were calculated using the following equation ΔEA ‐ B = EA ‐ B − (EA + E B)
(1)
Where EA‑B is interaction energy of A-B mispair, EA and EB is the interaction energy of individual A and B base molecules, and ΔEA‑B is the difference in the interaction energies. We have calculated the free energies using similar equations for mispair interactions. The M06-2X/6-31+G** level of theory optimized geometries were taken for single point energy calculations with MP2/aug-cc-pVDZ.48−50 We have calculated the basis set superposition error (BSSE) corrected energy with the Counterpoise method using the M06-2X/6-31+G** level optimized structures.41 The BSSE corrected binding energies were calculated, in which, it is considered that there is no structural change of monomers in complex geometry. We have performed aqueous phase (ε = 78.8) calculation using SMD salvation model with M06-2X/6-31+G** level of theory.51 Natural bond orbital (NBO) analysis has been carried out to investigate charge distribution of the 5-hydroxyuracil molecule.52,53 All calculations were performed using the G09 package.54 9754
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Figure 1. Hydrogen bonding interactions of keto, enol, and ionized forms of HaloU-G are represented in the above figure, optimized with M06-2X/631+G** level of theory. All interaction distances are given in angstroms (Gray: C; blue: N; white: H; red: O; brown: Br; green: Cl; cyan: F).
pKa in this series.23 The deprotonation energies calculated for these halo-uracils with the M06-2X/6-31+G** level of theory using the SMD solvation model in aqueous phase also show the similar trend as observed by the experimental pka values (Table S1 of the Supporting Information). The keto, enol, and ionized forms of BrU have been complexed with the guanine of DNA (Figure 1). The calculated results show that the keto form of the BrU interacts weakly (ΔG = −4.9 and ΔE = −17.6 kcal/mol) with guanine nucleobase compared to the BrUenol-G mispair (ΔG = −18.6 and ΔE = −38.7 kcal/mol). The better interaction of BrUenol with guanine nucleobase is due to the additional hydrogen bonding present in this case (Figure 1). The geometrical analyses show that the hydrogen bonds are strong in both cases. The H-bond interaction distances in BrUketo-G are 1.77 Å for the (N−H--O) interaction and 1.90 Å for the (O---H−N) interaction. The Br Uenol-G mispair (O---H−N) interaction is 1.97 Å, N---H−N is 1.77 Å, and the additional (O−H---O) interaction is 1.41 Å. The ionized BrUion mispair with guanine has also been calculated at the M06-2X/6-31+G** level of theory. The calculated results suggest that the interaction energy of BrUion-G is −30.5 kcal/mol and free energy is −17.9 kcal/mol, which is significantly higher than the corresponding keto form of BrU (Table1). However, the energies calculated with the ionized Br Uion mispair is comparable to the energies calculated for the Br Uenol-G mispair. The effect of substituents on uracil as mispair was further examined with the FU-G and ClU-G forms. The influence of electronegativity of halo-substituents on the Hbond interactions of these mispairs was observed (Table 1 and Figure 1). The increase in interaction energies have been seen with the most electronegative fluoro substituent (Table 1). Further, the 5-substitued halo-uracils in their enol and ionized forms yield higher interaction energies with guanine compared to the typical G-C base pair. We have also performed single
AIM calculation were performed with AIM2000 package, where we have used the M06-2X/6-31+G** level of theory generated wave functions.55−58 Finally, we have carried out localized molecular orbital energy decomposition analysis (LMOEDA) using the GAMESS package.59,60 In EDA method, total interaction energy decomposes into electrostatic energy (ES), exchange energy (EX), repulsion energy (REP), polarization energy (POL), and DFT dispersion energy (DISP).
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RESULTS AND DISCUSSION 5-HaloUracil. The mutation study was carried out with 5substituted uracil [i.e., 5-bromouracil (BrU), 5-chlorouracil (ClU), 5-fluorouracil (FU), 5-hydroxyuracil (OHU), 5-methylhydroxyuracil (CH2OHU), and lithiated-5-methylhydroxyuracil (CH2OLiU) with nucleobase guanine]. The optimized structures were taken to analyze the hydrogen-bonding interactions, depending upon the substitution at the 5 position of uracil. It is to note that the electron-withdrawing substituents at the 5position facilitate the ionization of the 5-substituted halo-uracil with an increase of the solution pH.24 It has been demonstrated experimentally that the degree of mispairing of the halouracil could be increased with an increase in solution pH, consistent with the ionized base pair model.23,24 The reports reveal that the formation of tautomeric enol forms of such halo-uracils is generally disfavored in enzyme-catalyzed mispair formation.24 Nevertheless, this disfavored tautomeric enol forms of halouracils cannot be ruled out.24 We have considered all forms of halo-uracils to examine their interactions with guanine base of DNA. The M06-2X/6-31+G** level of theory shows that the Br Uketo is more stable by −9.5 kcal/mol compared to the tautomeric BrUenol (Figure S1 of the Supporting Information). The experimentally determined pKa values for these 5substitued halo-uracils show that the FU possess the lowest 9755
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G mispair as observed with the interaction energies calculated at the same level of theory (Table 2, Figure 2, and Figure S2 of the Supporting Information). Further, we have extended our study to decompose the Hbond interaction energies in these mispairs. Localized Molecular Orbital Energy Decomposition Analysis (LMOEDA) has been employed to decompose the interaction energy to electrostatic energy (ES), exchange energy (EX), repulsion energy (REP), polarization energy (POL), and DFT dispersion energy (DISP).52,53 EDA is a very useful method to analyze the interaction energies in noncovalent interactions. The decomposition energies using EDA method for these mispairs are given in Table 3. The calculated decomposition energies suggest that the electrostatic, exchange, polarization, and DFT dispersion energies contribute to the interaction energy; however, the contribution of electrostatic energy in the Hbonding interactions is predominant in these mispairs. The calculations performed with M06-2X/6-31+G** level of theory for the guanine-cytosine base base pairs of DNA show that the interaction energy is comparable to BrUion-G mispairs; however, lower than the BrUenol-G mispair (Table 3). The EDA analysis performed for FU-G and ClU-G mispairs also show very similar trends of energy decomposition as obtained with BrU-G mispair (Table 3 and Table S2 of the Supporting Information). Electrostatic energy mainly contributes to the interaction energy for FU-G and ClU-G mispairs also. The higher interaction energies for FU-G among the halide-substituted uracils were also reflected in the electrostatic energy contributions obtained from EDA analysis. (Table 3 and Table S2 of the Supporting Information). These results suggest that the ionized form of HaloU can favorably lead toward the mutation of DNA compared to the native BrUketo-form.24 5-OxyUracil. The DFT calculations performed with the halide-substituted uracils suggest that mutations in DNA structures can be achieved under certain experimental conditions as the neutral keto form of such uracils are weaker in terms of interaction with the DNA basepair (guanine). The Uionized forms of halo-uracils can be generated with experimental manipulations; however, the calculated results suggest that mispair formed with such uracils are marginally preferred over the G-C basepair. Therefore, to enhance the mispair interactions, we have examined some oxy-substituted uracils with the guanine base of DNA. To improve the strength of hydrogen-bonding interactions, we have substituted the halogen atoms of 5-halo-uracils with the hydroxyl group (Figure 3). The role of the substituted hydroxyl group is to enhance the hydrogen-bonding ability of the N−H group of uracil with G via intramolecular H-bond. The five-membered intramolecular H-bond formed in OHUketo can make the carbonyl group electron deficient, which in turn can make the N−H hydrogen more electropositive for the interaction with G (Figure 3). Furthermore, the intramolecular hydrogen bond can make the −OH group more electron-rich and hence in turn can make the N3−H hydrogen more electron-rich through resonance effect for the interaction with guanine. To examine this, we have modeled the 5-hydroxy uracil, where the intramolecular hydrogen bonding is not possible (Figure S5 of the Supporting Information). The natural bond orbital analysis (NBO) suggests that the N3−H hydrogen possess similar charge in both the H-bonded and non-H-bonded structures. Therefore, the resonance effect from the −OH group to N3−H of 5-hydroxy uracil is not very significant in this case. A similar effect can also be seen with the OHUenol for
point energy calculations using the MP2/aug-cc-pVDZ level of theory and observed similar trends as obtained with the M06− 2X/6-31+G** level of theory (Table 1). We have examined the strength of the H-bond in these studied mispair with AIM and EDA analysis. To calculate the strength of noncovalent interaction, we have performed the AIM analysis.55−58,61,62 We have measured the electron density, ρ(rc), Laplacian of electron density ∇2ρ(rc), densities of kinetic energy, G(rc), and potential energy, G(rc), at the bond critical point. The electron density value is the direct measure of the noncovalent bond strength at the bond critical point (BPC), whereas the nature of the bond is described by the Laplacian. When the G(rc) > V(rc), |V(rc)/G(rc)| < 1, then the interaction is closed shell type and when the ratio is greater than 2, the interaction is known to be as the shared type.57 Shared type interactions indicate the covalency nature of the bond and when the ratio falls between the 1 and 2, the interaction known as the intermediate which are partially covalent and electrostatic in nature. The electron density calculations at the bond critical points have been shown in Table 2. The measured electron density, Table 2. Topological Analysis of Noncovalent Hydrogen Bonding Interactions for the G-C Base Pair and HaloU-G Mispair Calculated Using the M06-2X/6-31+G** Level of Theory Obtained Wave Function pair G-C
Br
Uketo-G
Br
Uenol-G
Br
Uion-G
Cl
Uketo-G
Cl
Uenol-G
Cl
Uion-G
F
Uketo-G
F
Uenol-G
F
Uion-G
bonds
Rho[ρ(rc)]
∇2(rc)
|V(rc)/G(rc)|
O---H−N N---H−N N−H---O O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O---H−N N−H---O N−H---O N−H---N O---H−O O---H−N N---H−N O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N
0.02691 0.03252 0.03689 0.03395 0.03610 0.02303 0.04400 0.09037 0.03257 0.03275 0.03334 0.03542 0.02342 0.04369 0.08882 0.03322 0.03216 0.03429 0.03509 0.02313 0.04431 0.09031 0.03415 0.03203
0.085 0.085 0.119 0.111 0.114 0.071 0.107 0.110 0.099 0.082 0.110 0.113 0.072 0.107 0.113 0.101 0.080 0.113 0.111 0.071 0.108 0.108 0.104 0.080
0.996 1.024 0.981 0.979 0.981 1.013 1.086 1.581 1.013 1.039 0.977 0.978 1.011 1.083 1.561 1.011 1.037 0.976 0.979 1.013 1.088 1.584 1.011 1.038
ρ(rc), and the calculated |V(rc)/G(rc)| suggest that the interactions in the BrUionized-G and BrUenol-G mispair are stronger than the BrUketo-G (Table 2). On the basis of these AIM analysis, BrUketo-G appears to be a closed shell interaction; however, BrUion-G is an intermediate interaction (Table 2). The AIM analysis also revealed the strongest interaction with the BrUenol-G form in these mispairs and also falls under intermediate interaction. The atoms in molecules analysis of FU-G and ClU-G mispairs shows that the | V(rc)/G(rc)| ratio is greater for the FU-G mispair than the ClU9756
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Figure 2. Molecular graph of the BrU-G and ClU-G mispair where the red points are the bond critical points. All these figures were obtained using the AIM2000 package.
Table 3. Decomposition of Total Interaction Energy of the G-C Base Pair and BrUenol-G Mispair Calculated by LMOEDA Method at M06-2X/6-31+G** Level of Theorya
a
name of the pair
electrostatic energy
exchange energy
repulsion energy
polarization energy
DFT dispersion energy
total interaction energy
G-C Br Uketo-G Br Uenol-G Br Uion-G
−43.0 −27.3 −58.2 −35.0
−25.7 −17.7 −44.5 −20.4
75.0 53.1 127.8 57.4
−20.6 −14.1 −43.9 −19.6
−16.3 −11.5 −20.0 −12.9
−30.7 −17.5 −38.6 −30.5
All the energy values are given in kilocalories per mol.
Figure 3. Hydrogen-bonding interactions of OHU-G and CH2OHU-G and CH2OLiU-G. Keto, enol, and ionized forms are represented, respectively, optimized with a M06-2X/6-31+G** level of theory. All the interaction distances are given in angstroms (gray: C; blue: N; white: H; red: O; and violet: Li).
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Table 4. Interactions Energies Were Calculated with Different Methods for the Oxy-Substituted Mispairsa name of the pair OH
Uketo-G OH Uenol-G OH Uion-G CH2OH Uketo-G CH2OH Uenol-G CH2OH Uion-G CH2OLi Uketo-G CH2OLi Uenol-G CH2OLi Uion-G a
ΔEM06‑2X/6‑31+G**
ΔGM06‑2X/6‑31+G**
ΔEMP2/aug‑cc‑pVDZ
ΔEBSSE(M06‑2X/6‑31+G**)
−17.7 −32.9 −30.9 −16.8 −26.3 −30.2 −18.2 −36.3 −46.2
−6.0 −20.2 −18.5 −4.7 −10.2 −17.9 −6.2 −23.7 −32.4
−20.1 −33.4 −32.3 −19.1 −42.9 −31.8 −20.7 −36.3 −47.8
−19.1 −43.4 −32.2 −17.9 −40.2 −31.4 −19.5 −48.3 −52.3
All the energy values are given in kilocalories per mol.
2X/6-31+G** level for CH2OLiUion-G is −32.4 kcal/mol. Note that the lithium present in CH2OLiUion can extend its stable coordination up to 4 with different ligands.69 We have also examined the four coordination of Li with water molecules considered as a solvent. The tetra-coordinated Li of CH2OLi Uionized-G mispair yields the interaction energy −65.6 kcal/mol, which is significantly higher than typical G-C base-pair of DNA (Figure S4 of the Supporting Information). The higher interaction energy of CH2OLiUionized-G mispair than G-C has also been observed in the aqueous phase as calculated with the same level of theory, which suggests that the CH2OLiUionized can induce the stability in the DNA mispair under physiological conditions (Table S5 of the Supporting Information). Importantly, the deprotonation energy calculated for CH2OLi Uionized is lowest in the studied systems and hence the formation of the ionized mispair with guanine base would be facile (Table S1 of the Supporting Information). The CH2OLiUionized-G mispair has shown much higher interaction energy among the mispair calculated because of the additional coordination of Li and oxygen [O−Li---O− C(G), 1.97 Å] (Figure 3). This additional coordination of Li altered the H-bonding arrangement in this case compared to corresponding interactions in Uionized-G mispairs in other cases (Figures 1 and 2). We have also performed gas phase single point energy calculations using MP2/aug-cc-pVDZ level of theory and observed similar trends as obtained with M06−2x/ 6-31+G** level of theory (Table 4). The topological analysis corroborates the interaction distances observed in the M06-2X/6-31+G** level optimized geometry for these oxy-substituted mispairs. The better binding ability of OHU-G mispairs than the HaloU-G mispairs has been found to be in good agreement with the |V(rc)/G(rc)| ratios obtained for respective forms (Table 5). Similar trends were also observed with CH2OHU-G and CH2OLiU-G mispairs (Table 5 and Table S3 and Figure S3 of the Supporting Information). The energy decomposition analysis (EDA) has been carried out to examine the contributions of different energies in such H-bond interactions for these oxy mispairs. The EDA analysis shows that the electrostatic energy contributes chiefly in all cases to stabilize the interaction of mispairs similar to halosubstituted uracils (Table 6).
effective interaction with the guanine base of DNA (Figure 3). The M06-2X/6-31+G** level of theory calculated results show that the OHUketo-G and OHUenol-G mispairs interact more strongly than the halo-substituted uracils with guanine (Tables 1 and 4). The OHUionized form, however, is not significantly better in terms of its interaction with G compared to the corresponding halo-uracils (Table 1). In this case, an additional acidic proton is available in the 5-position. The pKa values observed for this acidic proton is lower than the N3−H proton.63 Therefore, it appears that the effective interaction of the OHUionized-G mispair can be achieved at a higher pH condition. The deprotonation energies calculated with the M06-2X/6-31+G** level of theory, however, revealed that the role of solvation is important in this case. The N−H deprotonation is relatively lower in energy compared to the OH deprotonation in 5-hydroxy uracil. The implicit solvation model (SMD) and the involvement of explicit water molecule, however, showed that the deprotonation energy gap is reduced for the abstraction of N−H and O−H protons from 5-hydroxy uracil (Table S4 of the Supporting Information). These results presumably suggest that more solvent molecules may be needed for direct comparison with the observed pka values in this case. We have further extended the model study of mispair interactions with the −CH2OH group as a substituent at the 5position of uracil. The −CH2OH group can help to form more stable 6-membered rings by intramolecular hydrogen bonding (Figure 3).64−66 The M06-2X/6-31+G** level of theory calculated results show that the mispair interactions of CH2OH U with G is energetically lower than the OHU (Table 4). The intramolecular hydrogen bonding is weaker due to the presence of the electron-releasing methylene group of −CH2OH and the nonplanarity of the 6-membered ring formed in this case. The geometrical constraints avoid the 6membered ring to achieve planarity for CH2OHU with G (Figure 3).67 We have exploited the structural advantage of CH2OH using the electropositive lithium (Li) in place of the OH hydrogen atom. The electropositive lithium (Li) can make the mispair interactions even stronger by additional coordination with neighboring functional groups (Figure 3). We have considered lithium because it is highly electropositive in nature, multicoordination property and lithium salts have been extensively and successfully used for the treatment of manic depression and other neurological and psychiatric disorders.68 The calculated results suggest that the CH2OLiU-G mispair interactions enhanced significantly for CH2OLiUenol-G and CH2OLiUionized-G mispairs (Table 4). The calculated free energy with the M06-
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CONCLUSIONS In this work, we have reported the mutagenic property of substituted uracils with the DNA base. The halo-substituted uracils have been examined computationally with guanine of DNA base pairs. The halouracils, in particular BrU, have been extensively studied by experimentalists; however, their toxicity 9758
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Table 5. Topological Analysis of Noncovalent HydrogenBonding Interactions Calculated by the M06-2X/6-31+G** Level of Theory Obtained Wave Function pair OH
Uketo-G
OH
Uenol-G
OH
Uion-G
CH2OH
Uion-G
CH2OLi
Uion-G
bonds O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O−H---O(CH2OH--O) N---H−N O---H−N O−Li---O−C(G) O−Li---O−C(U)
Rho[ρ(rc)]
∇2(rc)
|V(rc)/ G(rc)|
0.03610 0.03647 0.02390 0.04796 0.09846 0.03572 0.03173 0.02872 0.03362 0.03275 0.02591
0.119 0.115 0.073 0.111 0.078 0.109 0.079 0.098 0.102 0.081 0.080
0.978 0.984 1.014 1.121 1.721 1.010 1.035 1.020 1.011 1.039 1.051
0.03267 0.06758 0.02613 0.02824
0.082 0.159 0.175 0.202
1.042 1.223 0.780 0.776
Article
ASSOCIATED CONTENT
S Supporting Information *
Experiemental pKa values and deprotonation energies and free energies, AIM analyzed data, molecular graph generated by AIM2000 package, EDA energies, M06-2X/6-31+G** level of theory optimized Cartesian coordinates of all these mispairs, and NBO charge analysis. This material is available free of charge via the Internet at http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
*E-mail: [email protected]. Tel: +91-278-2567760, ext 6770. Fax: (+91)-278-2567562. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS CSMCRI communication no: 089/2014. K.J. is thankful to UGC, New Delhi, India, for awarding a junior research fellowship. K.J. acknowledges AcSIR for his Ph.D. enrolment. B.G. thanks MSM, SIP (CSIR, New Delhi), and BRNS, Mumbai, for financial support. We thank the reviewer’s for their valuable comments/suggestions that have helped us to improve the paper.
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or size factor limits them to be good mutagenic agents. We have examined the interaction energies of halouracil-guanine mispairs and compared with the guanine-cytosine DNA base pairs. The easily accessible Uionized forms of substituted uracil with G are energetically slightly better than the G-C basepair. The remarkable stability of U with hydroxyl substituents has been achieved in the studied mispairs. CH2OLiUionized-G mispair has shown the highest stability (−52.3 kcal/mol) among the mispairs studied here. The advantage of multicoordination of electropositive lithium and the contribution of higher electrostatic interaction energy augments the stability of this mispair. Lithium is not expected to bioaccumulate, and it does not show higher toxicity in the human body. The DFT calculated results have been further corroborated by AIM and EDA analyses. The electrostatic interactions contribute mainly toward the hydrogen-bonding interactions in such mispairs. The stability of mispair is considered to be one of the important criteria in mutagenesis, and these results would encourage the researchers to design similar unnatural bases to achieve the mutagenetic process. We are further pursuing the mutagenic study with other DNA basepairs and will report in the future.
REFERENCES
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Table 6. Decomposition of Total Interaction Energy of the Oxy-Substituted Mispairs Calculated by LMOEDA Method at M062X/6-31+G** Level of Theorya Name of the Pair OH
Uketo-G OH Uenol-G OH Uion-G CH2OH Uketo-G CH2OH Uenol-G CH2OH Uion-G CH2OLi Uketo-G CH2OLi Uenol-G CH2OLi Uion-G a
Electrostatic Energy
Exchange Energy
Repulsion Energy
Polarization Energy
DFT Dispersion Energy
Total Interactions Energy
−29.4 −63.8 −37.1 −27.4 −60.3 −36.1 −29.6 −68.8 −71.2
−18.8 −48.9 −21.4 −17.4 −45.4 −20.9 −18.5 −51.2 −40.9
56.0 140.1 59.9 52.0 130.2 58.6 55.3 146.1 116.5
−15.1 −49.9 −20.7 −13.8 −44.5 −20.2 −14.9 −53.1 −36.6
−11.8 −20.8 −12.9 −11.3 −20.2 −12.8 −11.8 −21.3 −20.1
−19.1 −43.4 −32.2 −17.9 −40.2 −31.4 −19.5 −48.3 −52.3
All the energy values are given in kilocalories per mol. 9759
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(7) Kaufman, E. R.; Davidson, R. L. Bromodeoxyuridine Mutagenesis in Mammalian Cells: Mutagenesis Is Independent of the Amount of Bromouracil in DNA. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 4982− 4986. (8) Hwang, G. T.; Hari, Y.; Romesberg, F. E. The Effects of Unnatural Base Pairs and Mispairs on DNA Duplex Stability and Salvation. Nucleic Acids Res. 2009, 37, 4757−4763. (9) Litman, R. M.; Pardee, A. B. Production of Bacteriophage Mutants by a Disturbance of Deoxyribonucleic Acid Metabolism. Nature 1956, 178, 529−531. (10) Hill, B. T.; Tsuboi, A.; Baserga, R. Effect of 5-Bromodeoxyuridine on Chromatin Transcription in Confluent Fibroblasts. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 455−459. (11) Kotzin, B. L.; Baker, R. F. Selective Inhibition of Genetic Transcription in Sea Urchin Embryos. Incorporation of 5-Bromodeoxyuridine into Low Molecular Weight Nuclear DNA. J. Cell Biol. 1972, 55, 74−81. (12) Lin, S. Y.; Riggs, A. D. Lac Operator Analogues: Bromodeoxyuridine Substitution in the lac Operator Affects the Rate of Dissociation of the lac Repressor. Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 2574−2576. (13) Silagi, S.; Bruce, S. A. Suppression of Malignancy and Differentiation in Melanotic Melanoma Cells. Proc. Natl. Acad. Sci. U.S.A. 1970, 66, 72−78. (14) Freese, E. The Specific Mutagenic Effect of Base Analogues on Phage T4. J. Mol. Biol. 1959, 1, 87−105. (15) Baker, R. M.; Brunette, D. M.; Mankovitz, R.; Thompson, L. H.; Whitmore, G. F.; Siminovitch, L.; Till, J. E. Ouabain-Resistant Mutants of Mouse and Hamster Cells in Culture. Cell 1974, 1, 9−21. (16) Spandidos, D. A.; Siminovitch, L. Transfer of Codominant Markers by Isolated Metaphase Chromosomes in Chinese Hamster Ovary Cells. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 3480−3484. (17) Heidleberger, C.; Chaudhuri, N. K.; Danneberg, P.; Mooren, D.; Griesbach, L.; Duschinsky, R.; Schnitzler, R. .J.; Pleven, E.; Scheiner, J. Fluorinated Pyrimidines. A New Class of Tumor-Inhibitory Compounds. Nature (London) 1957, 179, 663−666. (18) Wilkinson, D. S.; Crumley, J. Metabolism of 5-fluorouracil in sensitive and resistant Novikoff hepatoma cells. J. Biol. Chem. 1977, 252, 1051−1056. (19) Kufe, D. W.; Major, P. P.; Egan, E. M.; Loh, E. 5-Fluoro-2′Deoxyuridine Incorporation in L1210 DNA. J. Biol. Chem. 1981, 256, 8885−8888. (20) Kremer, A. B.; Mikita, T.; Beardsley, G. P. Chemical Consequences of Incorporation of 5-Fluorouracil into DNA as studied by NMR. Biochemistry 1987, 26, 391−397. (21) Pinedo, H. M.; Peters, G. F. J. Fluorouracil-Biochemistry and Pharmacology. J. Clin. Oncol. 1988, 6, 1653−1664. (22) Kovach, J. S.; Beart, R. W. Cellular Pharmacology of Fluorinated Pyrimidines Invivi in Man. Invest. New Drugs 1989, 7, 13−25. (23) Theruvathu, J. A.; Kim, C. H.; Darwanto, A.; Neidigh, J. W.; Sowers, L. C. pH-Dependent Configurations of a 5-ChlorouracilGuanine Base Pair. Biochemistry 2009, 48, 11312−11318. (24) Yu, H.; Eritja, R.; Bloom, L. B.; Goodman, M. F. Ionization of Bromouracil and Fluorouracil Stimulates Base Mispairing Frequencies with Guanine. J. Biol. Chem. 1993, 268, 15935−15943. (25) Bennett, M. T.; Rodgers, M. T.; Hebert, A. S.; Ruslander, L. E.; Eisele, L.; Drohat, A. C. Specificity of Human Thymine DNA Glycosylase Depends on N-Glycosidic Bond Stability. J. Am. Chem. Soc. 2006, 128, 12510−12519. (26) Darwanto, A.; Theruvathu, J. A.; Sowers, J. L.; Rogstad, D. K.; Pascal, T.; Goddard, W. A., III; Sowers, L. C. Mechanisms of Base Selection by Human Single-Stranded Selective Monofunctional UracilDNA Glycosylase. J. Biol. Chem. 2009, 284, 15835−15846. (27) Morgan, M. T.; Bennett, M. T.; Drohat, A. C. Excision of 5Halogenated Uracils by Human Thymine DNA Glycosylase. Robustactivity for DNA Contexts Other Than CpG. J. Biol. Chem. 2007, 282, 27578−27586. (28) Brennan, C. A.; Van Cleve, M. D.; Gumport, R. I. The Effects of Base Analogue Substitutions on the Cleavage by the EcoRI Restriction
Endonuclease of Octadeoxyribonucleotides Containing Modified EcoRI Recognition Sequences. J. Biol. Chem. 1986, 261, 7270−7278. (29) Petruska, J.; Horn, D. Sequence-Specific Responses of Restriction Endonucleases to Bromodeoxyuridine Substitution in Mammalian DNA. Nucleic Acids Res. 1983, 11, 2495−2510. (30) Michishita, E.; Kurahashi, T.; Suzuki, T.; Fukuda, M.; Fujii, M.; Hirano, H.; Ayusawa, D. Changes in Nuclear Matrix Proteins during the Senescence-Like Phenomenon Induced by 5-Chlorodeoxyuridine in HeLa Cells. Exp. Gerontol. 2002, 37, 885−890. (31) Brandon, M. L.; Mi, L. J.; Chaung, W. R.; Teebor, G.; Boorstein, R. J. 5-Chloro-2′-Deosyuridine Cytotoxicity Results from Base Excision Repair of Uracil Subsequent to Thymidylate Synthase Inhibition. Mutat. Res. 2000, 459, 161−169. (32) Sponer, J.; Jurecka, P.; Hobza, P. Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs. J. Am. Chem. Soc. 2004, 126, 10142−10151. (33) Dabkowska, I.; Gonzalez, H. V.; Jurecka, P.; Hobza, P. Stabilization Energies of the Hydrogen-Bonded and Stacked Structures of Nucleic Acid Base Pairs in the Crystal Geometries of CG, AT, and AC DNA Steps and in the NMR Geometry of the 5′-d(GCGAAGC)3′ Hairpin: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels. J. Phys. Chem. A 2005, 109, 1131−1136. (34) Otero-Navas, I.; Seminario, J. M. Molecular Electrostatic Potentials of DNA Base−base Pairing and Mispairing. J. Mol. Model. 2012, 18, 91−101. (35) Bebenek, K.; Pedersen, L. C.; Kunkel, T. A. Replication Infidelity via a Mismatch with Watson−Crick Geometry. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 1862−1867. (36) Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, And Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functional. Theor. Chem. Acc. 2008, 120, 215−241. (37) O’Reilly, R. J.; Karton, A.; Radom, L. Effect of Substituents on the Preferred Modes of One-Electron Reductive Cleavage of N−Cl and N−Br Bonds. J. Phys. Chem. A 2013, 117, 460−472. (38) Yu, H.-Z.; Yang, Y.-M.; Zhang, L.; Dang, Z.-M.; Hu, G.-H. Quantum-Chemical Predictions of pKa’s of Thiols in DMSO. J. Phys. Chem. A 2014, 118, 606−622. (39) Hariharan, P. C.; Pople, A. Accuracy of AH Equilibrium Geometries by Single Determinant Molecular-Orbital Theory. J. Chem. Phys. 1974, 27, 209−214. (40) Hariharan, P. C.; Pople, J. A. Influence of Polarization Functions on Molecular-Orbital Hydrogenation Energies. Theor. Chem. Acc. 1973, 28, 213−222. (41) Boys, S. F.; Bernardi, F. Calculation of Small Molecular Interactions by Differences of Separate Total Energies: Some Procedures with Reduced Errors. Mol. Phys. 1970, 19, 553−566. (42) Luke, T. L.; Jacob, T. A.; Mohan, H.; Destaillats, H.; Manoj, V. M.; Manoj, P.; Mittal, J. P.; Hoffmann, M. R.; Aravindakumar, C. T. Properties of the OH adducts of hydroxy-, methyl-, methoxy-, and amino-substituted pyrimidines: Their dehydration reactions and endproduct analysis. J. Phys. Chem. A 2002, 106, 2497−2504. (43) Zarakowska, E.; Gackowski, D.; Foksinski, M.; Olinski, R. Are 8Oxoguanine (8-oxoGua) and 5-Hydroxymethyluracil (5-hmUra)oxidatively Damaged DNA Bases or Transcription (Epigenetic) Marks? Mutat. Res., Genet. Toxicol. Environ. Mutagen. 2014, 764− 765, 58−63. (44) El Safadi, Y.; Paillart, J.-C.; Laumond, G.; Aubertin, A.-M.; Burger, A.; Marquet, R.; Vivet-Boudou, V. 5-Modified-2′-dU and 2′dC as Mutagenic Anti HIV-1 Proliferation Agents: Synthesis and Activity. J. Med. Chem. 2010, 53, 1534−1545. (45) Park, Y.; Peoples, A. R.; Madugundu, G. S.; Sanche, L.; Wagner, J. R. Side by-Side Comparison of DNA Damage Induced by LowEnergy Electrons and High-Energy Photons with Solid TpTpT Trinucleotide. J. Phys. Chem. B 2013, 117, 10122−10131. (46) Pfaffeneder, T.; Spada, F.; Wagner, M.; Brandmayr, C.; Laube, S. K.; Eisen, D.; Truss, M.; Steinbacher, J.; Hackner, B.; Kotljarova, O.; 9760
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In Silico Studies to Explore the Mutagenic Ability of 5‑Halo/Oxy/LiOxy-Uracil Bases with Guanine of DNA Base Pairs Kalyanashis Jana†,‡ and Bishwajit Ganguly*,†,‡ †
Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR−Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India ‡ Academy of Scientific and Innovative Research, CSIR−CSMCRI, Bhavnagar, Gujarat 364002, India S Supporting Information *
ABSTRACT: DNA nucleobases are reactive in nature and undergo modifications by deamination, oxidation, alkylation, or hydrolysis processes. Many such modified bases are susceptible to mutagenesis when formed in cellular DNA. The mutagenesis can occur by mispairing with DNA nucleobases by a DNA polymerase during replication. We have performed a study of mispairing of DNA bases with unnatural bases computationally. 5-Halo uracils have been studied as mispairs in mutagenesis; however, the reports on their different forms are scarce in the literature. The stability of mispairs with keto form, enol form, and ionized form of 5-halo-uracil has been computed with the M06-2X/6-31+G** level of theory. The enol form of 5-halo-uracil showed remarkable stability toward DNA mispair compared to the corresponding keto and ionized forms. FU-G mispair showed the highest stability in the series and HaloUenol/ionized-G mispair interactions energies are more stable than the natural G-C basepair of DNA. To enhance the stability of DNA mispairs, we have introduced the hydroxyl group in the place of halogen atoms, which provides additional hydrogenbonding interactions in the system while forming the 5-membered ring. The study has been further extended with lithiated 5-hydroxymethyl-uracil to stabilize the DNA mispair. CH2OLiUionized-G mispair has shown the highest stability (ΔG = −32.4 kcal/mol) with multi O−Li interactions. AIM (atoms in molecules) and EDA (energy decomposition analysis) analysis has been performed to examine the nature of noncovalent interactions in such mispairs. EDA analysis has shown that electrostatic energy mainly contributes toward the interaction energy of mispairs. The higher stability achieved in these studied mispairs can play a pivotal role in the mutagenesis and can help to attain the mutation for many desired biological processes.
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the nucleic acid systems.17−24 It has been reported that the mispair formation of the halouracil can be enhanced with an increase in the pH of the solution.24 The presence of electronwithdrawing fluorine or chlorine atoms at the 5 position of the pyrimidine ring facilitates the ionization and enolization of FU/ Cl U in DNA or RNA, which leads to mispairing with guanine during replication or transcription.14,23 The selective incorporation of the FU in nucleic acids of malignant cells might be helpful to inhibit the growth of tumor cells.17,21,22 Due to smaller size of fluorine, FU is mimicking 2′-deoxyuridine 5′monophosphate and it could be easily removed from DNA by uracil-glycosyase enzymes.25−27 However, BrU can replace thymine in dsDNA, but BrU are repaired only by a few uracil glycosylases.25−29 ClU could be an alternate mispair unit of the F U and BrU, due to its intermediate size; however, ClU in dsDNA causes chromosomal abnormalities and shows toxicity.30,31 Halogenated uracil molecules present in keto, enol, and ionized forms depend upon the pH of the solution; at lower pH of the solution, they exist either in keto form or in enol form. When the pH of halogenated uracil solution is
INTRODUCTION The structure of DNA plays an essential role to govern replication and gene expression.1−3 It is known that hydrogen bonding and stacking interactions are chiefly responsible to control the structure of DNA.4 The effect of substitution at any position in DNA base-pairs can alter the stability and other properties.5−13 The stabilities of DNA can also be influenced with unnatural/substituted bases. Such interactions alter the typical base-pair in DNA and are termed as mutation.5−13 5Bromouracil (BrU) has been extensively studied as mutant with the nucleic acid system and shown significant effect.5−13 BrU influences to alter patterns of transcription, enhances the binding of the lac repressor to its operator, increases the affinity of chromosomal proteins for BrU-containing DNA, inhibits the expression of differentiated functions, and causes alterations in membrane properties.14 The mutagenic properties of the BrU has now been widely accepted and frequently observed during the DNA replication process.15,16 Mutagenicity is apparently determined by the concentration of BrU to which the cells are exposed rather than the amount of BrU in DNA. Such results were obtained due to the induction of ouabain resistance and thioguanine resistance as markers for mutagenesis.15,16 The studies with fluorouracil and chlorouracil are limited in the literature; however, these unnatural bases can mispair with © 2014 American Chemical Society
Received: July 25, 2014 Revised: September 18, 2014 Published: September 19, 2014 9753
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Scheme 1. Hydrogen-Bonding Interactions in A-T, G-C Basepairs, and 5-Substituted Uracila
a
The H-bonding interaction distances were taken from the M06-2X/6-31+G** level of theory optimized structures. (Distances are given in angstroms.).
Table 1. Interaction Energies Were Calculated with Different Methods for the G-C Base Pair and
a
Halo
U-G Mispaira
name of the pair
ΔEM06‑2X/6‑31+G**
ΔGM06‑2X/6‑31+G**
ΔEMP2/aug‑cc‑pVDZ
ΔEBSSE(M06‑2X/6‑31+G**)
G-C Br Uketo-G Br Uenol-G Br Uion-G Cl Uketo-G Cl Uenol-G Cl Uion-G F Uketo-G F Uenol-G F Uion-G
−28.6 −18.5 −31.3 −31.8 −16.5 −30.2 −29.9 −16.8 −30.6 −30.6
−15.6 −4.9 −18.6 −17.9 −4.8 −18.5 −17.7 −4.9 −18.6 −18.1
−30.5 −19.0 −31.2 −31.4 −18.9 −31.2 −31.5 −19.1 −31.2 −32.0
−30.7 −17.6 −38.7 −30.5 −17.5 −38.6 −31.0 −17.9 −39.2 −31.7
All the energy values are given in kilocalories per mol.
bonding interactions. Further, employing lithiated-5-hydroxymethyluracil (CH2OLiU) as a unit of mispair, the stability was augmented significantly compared to halogenated uracils.42−47
around the value of pKa of the corresponding halogenateduracil, the ionization of such uracils takes place via deprotonation of the N3-H unit.24 Hydrogen-bonding interaction is known to play an important role in stabilizing the DNA or RNA and helping to form different forms of DNA or RNA.4 The natural base pairs (A-T) and (G-C) form very strong hydrogen bonds with each other in DNA or RNA. A number of computational studies contributed to our knowledge of nucleic acids base pairing including their interactions and stability.32−35 It is known that the H-bonding stabilization energy of the G-C base pair is greater (∼12.0 kcal/ mol) than the A-T base pair.32−35 The greater stability of the G-C base pair is achieved via additional H-bonding interaction compared to the A-T base pair (Scheme 1). The H-bonding interaction energies calculated for the G-C base pair using RIMP2/aug-cc-pVTZ → RI-MP2/aug-cc-pVQZ Helgaker’s extrapolated energy is −28.2 kcal/mol and seems to be fairly accurate.32 We have performed DFT calculations using M062X/6-31+G** level of theory to examine the H-bond energy of the G-C base-pair.36−40 The calculated results suggest that the hydrogen-bonding interaction energy of G-C is −28.6 kcal/ mol, and the BSSE41 corrected energy at the M06-2X/631+G** level of theory is −30.7 kcal/mol (Table 1). These results are in good agreement with the earlier reports.32−35 We have extended our study using the M06-2X/6-31+G** level of theory to examine the interactions of the unnatural mutants with guanine of DNA. In this article, we have systematically examined the mispairing of halogenated uracils (FU, ClU, and BrU) with the guanine base of DNA. There are reports on the interactions of mutagenic mispair of halogenated uracil with the guanine; however, the detailed understanding is limited in the literature.5−31 We have exploited the stability pattern of mispairs of 5-susbtituted uracils 5-hydroxyuracil (OHU) and 5hydroxymethyluracil (CH2OHU) with additional hydrogen-
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COMPUTATIONAL METHODS All the structures of halogenated, hydroxy, hydroxymethyl, and lithiated-hydroxymethyl uracil have been optimized in gas phase with the M06-2X36 DFT functional and 6-31+G**39,40 Pople basis set. We have performed the frequency calculations at the same level of theory to confirm minima of optimized geometries with no imaginary frequencies. The M06-2X is one of the best functional for the organic system and even for the anionic systems.37,38 The interactions energy of these mispair were calculated using the following equation ΔEA ‐ B = EA ‐ B − (EA + E B)
(1)
Where EA‑B is interaction energy of A-B mispair, EA and EB is the interaction energy of individual A and B base molecules, and ΔEA‑B is the difference in the interaction energies. We have calculated the free energies using similar equations for mispair interactions. The M06-2X/6-31+G** level of theory optimized geometries were taken for single point energy calculations with MP2/aug-cc-pVDZ.48−50 We have calculated the basis set superposition error (BSSE) corrected energy with the Counterpoise method using the M06-2X/6-31+G** level optimized structures.41 The BSSE corrected binding energies were calculated, in which, it is considered that there is no structural change of monomers in complex geometry. We have performed aqueous phase (ε = 78.8) calculation using SMD salvation model with M06-2X/6-31+G** level of theory.51 Natural bond orbital (NBO) analysis has been carried out to investigate charge distribution of the 5-hydroxyuracil molecule.52,53 All calculations were performed using the G09 package.54 9754
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Figure 1. Hydrogen bonding interactions of keto, enol, and ionized forms of HaloU-G are represented in the above figure, optimized with M06-2X/631+G** level of theory. All interaction distances are given in angstroms (Gray: C; blue: N; white: H; red: O; brown: Br; green: Cl; cyan: F).
pKa in this series.23 The deprotonation energies calculated for these halo-uracils with the M06-2X/6-31+G** level of theory using the SMD solvation model in aqueous phase also show the similar trend as observed by the experimental pka values (Table S1 of the Supporting Information). The keto, enol, and ionized forms of BrU have been complexed with the guanine of DNA (Figure 1). The calculated results show that the keto form of the BrU interacts weakly (ΔG = −4.9 and ΔE = −17.6 kcal/mol) with guanine nucleobase compared to the BrUenol-G mispair (ΔG = −18.6 and ΔE = −38.7 kcal/mol). The better interaction of BrUenol with guanine nucleobase is due to the additional hydrogen bonding present in this case (Figure 1). The geometrical analyses show that the hydrogen bonds are strong in both cases. The H-bond interaction distances in BrUketo-G are 1.77 Å for the (N−H--O) interaction and 1.90 Å for the (O---H−N) interaction. The Br Uenol-G mispair (O---H−N) interaction is 1.97 Å, N---H−N is 1.77 Å, and the additional (O−H---O) interaction is 1.41 Å. The ionized BrUion mispair with guanine has also been calculated at the M06-2X/6-31+G** level of theory. The calculated results suggest that the interaction energy of BrUion-G is −30.5 kcal/mol and free energy is −17.9 kcal/mol, which is significantly higher than the corresponding keto form of BrU (Table1). However, the energies calculated with the ionized Br Uion mispair is comparable to the energies calculated for the Br Uenol-G mispair. The effect of substituents on uracil as mispair was further examined with the FU-G and ClU-G forms. The influence of electronegativity of halo-substituents on the Hbond interactions of these mispairs was observed (Table 1 and Figure 1). The increase in interaction energies have been seen with the most electronegative fluoro substituent (Table 1). Further, the 5-substitued halo-uracils in their enol and ionized forms yield higher interaction energies with guanine compared to the typical G-C base pair. We have also performed single
AIM calculation were performed with AIM2000 package, where we have used the M06-2X/6-31+G** level of theory generated wave functions.55−58 Finally, we have carried out localized molecular orbital energy decomposition analysis (LMOEDA) using the GAMESS package.59,60 In EDA method, total interaction energy decomposes into electrostatic energy (ES), exchange energy (EX), repulsion energy (REP), polarization energy (POL), and DFT dispersion energy (DISP).
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RESULTS AND DISCUSSION 5-HaloUracil. The mutation study was carried out with 5substituted uracil [i.e., 5-bromouracil (BrU), 5-chlorouracil (ClU), 5-fluorouracil (FU), 5-hydroxyuracil (OHU), 5-methylhydroxyuracil (CH2OHU), and lithiated-5-methylhydroxyuracil (CH2OLiU) with nucleobase guanine]. The optimized structures were taken to analyze the hydrogen-bonding interactions, depending upon the substitution at the 5 position of uracil. It is to note that the electron-withdrawing substituents at the 5position facilitate the ionization of the 5-substituted halo-uracil with an increase of the solution pH.24 It has been demonstrated experimentally that the degree of mispairing of the halouracil could be increased with an increase in solution pH, consistent with the ionized base pair model.23,24 The reports reveal that the formation of tautomeric enol forms of such halo-uracils is generally disfavored in enzyme-catalyzed mispair formation.24 Nevertheless, this disfavored tautomeric enol forms of halouracils cannot be ruled out.24 We have considered all forms of halo-uracils to examine their interactions with guanine base of DNA. The M06-2X/6-31+G** level of theory shows that the Br Uketo is more stable by −9.5 kcal/mol compared to the tautomeric BrUenol (Figure S1 of the Supporting Information). The experimentally determined pKa values for these 5substitued halo-uracils show that the FU possess the lowest 9755
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G mispair as observed with the interaction energies calculated at the same level of theory (Table 2, Figure 2, and Figure S2 of the Supporting Information). Further, we have extended our study to decompose the Hbond interaction energies in these mispairs. Localized Molecular Orbital Energy Decomposition Analysis (LMOEDA) has been employed to decompose the interaction energy to electrostatic energy (ES), exchange energy (EX), repulsion energy (REP), polarization energy (POL), and DFT dispersion energy (DISP).52,53 EDA is a very useful method to analyze the interaction energies in noncovalent interactions. The decomposition energies using EDA method for these mispairs are given in Table 3. The calculated decomposition energies suggest that the electrostatic, exchange, polarization, and DFT dispersion energies contribute to the interaction energy; however, the contribution of electrostatic energy in the Hbonding interactions is predominant in these mispairs. The calculations performed with M06-2X/6-31+G** level of theory for the guanine-cytosine base base pairs of DNA show that the interaction energy is comparable to BrUion-G mispairs; however, lower than the BrUenol-G mispair (Table 3). The EDA analysis performed for FU-G and ClU-G mispairs also show very similar trends of energy decomposition as obtained with BrU-G mispair (Table 3 and Table S2 of the Supporting Information). Electrostatic energy mainly contributes to the interaction energy for FU-G and ClU-G mispairs also. The higher interaction energies for FU-G among the halide-substituted uracils were also reflected in the electrostatic energy contributions obtained from EDA analysis. (Table 3 and Table S2 of the Supporting Information). These results suggest that the ionized form of HaloU can favorably lead toward the mutation of DNA compared to the native BrUketo-form.24 5-OxyUracil. The DFT calculations performed with the halide-substituted uracils suggest that mutations in DNA structures can be achieved under certain experimental conditions as the neutral keto form of such uracils are weaker in terms of interaction with the DNA basepair (guanine). The Uionized forms of halo-uracils can be generated with experimental manipulations; however, the calculated results suggest that mispair formed with such uracils are marginally preferred over the G-C basepair. Therefore, to enhance the mispair interactions, we have examined some oxy-substituted uracils with the guanine base of DNA. To improve the strength of hydrogen-bonding interactions, we have substituted the halogen atoms of 5-halo-uracils with the hydroxyl group (Figure 3). The role of the substituted hydroxyl group is to enhance the hydrogen-bonding ability of the N−H group of uracil with G via intramolecular H-bond. The five-membered intramolecular H-bond formed in OHUketo can make the carbonyl group electron deficient, which in turn can make the N−H hydrogen more electropositive for the interaction with G (Figure 3). Furthermore, the intramolecular hydrogen bond can make the −OH group more electron-rich and hence in turn can make the N3−H hydrogen more electron-rich through resonance effect for the interaction with guanine. To examine this, we have modeled the 5-hydroxy uracil, where the intramolecular hydrogen bonding is not possible (Figure S5 of the Supporting Information). The natural bond orbital analysis (NBO) suggests that the N3−H hydrogen possess similar charge in both the H-bonded and non-H-bonded structures. Therefore, the resonance effect from the −OH group to N3−H of 5-hydroxy uracil is not very significant in this case. A similar effect can also be seen with the OHUenol for
point energy calculations using the MP2/aug-cc-pVDZ level of theory and observed similar trends as obtained with the M06− 2X/6-31+G** level of theory (Table 1). We have examined the strength of the H-bond in these studied mispair with AIM and EDA analysis. To calculate the strength of noncovalent interaction, we have performed the AIM analysis.55−58,61,62 We have measured the electron density, ρ(rc), Laplacian of electron density ∇2ρ(rc), densities of kinetic energy, G(rc), and potential energy, G(rc), at the bond critical point. The electron density value is the direct measure of the noncovalent bond strength at the bond critical point (BPC), whereas the nature of the bond is described by the Laplacian. When the G(rc) > V(rc), |V(rc)/G(rc)| < 1, then the interaction is closed shell type and when the ratio is greater than 2, the interaction is known to be as the shared type.57 Shared type interactions indicate the covalency nature of the bond and when the ratio falls between the 1 and 2, the interaction known as the intermediate which are partially covalent and electrostatic in nature. The electron density calculations at the bond critical points have been shown in Table 2. The measured electron density, Table 2. Topological Analysis of Noncovalent Hydrogen Bonding Interactions for the G-C Base Pair and HaloU-G Mispair Calculated Using the M06-2X/6-31+G** Level of Theory Obtained Wave Function pair G-C
Br
Uketo-G
Br
Uenol-G
Br
Uion-G
Cl
Uketo-G
Cl
Uenol-G
Cl
Uion-G
F
Uketo-G
F
Uenol-G
F
Uion-G
bonds
Rho[ρ(rc)]
∇2(rc)
|V(rc)/G(rc)|
O---H−N N---H−N N−H---O O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O---H−N N−H---O N−H---O N−H---N O---H−O O---H−N N---H−N O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N
0.02691 0.03252 0.03689 0.03395 0.03610 0.02303 0.04400 0.09037 0.03257 0.03275 0.03334 0.03542 0.02342 0.04369 0.08882 0.03322 0.03216 0.03429 0.03509 0.02313 0.04431 0.09031 0.03415 0.03203
0.085 0.085 0.119 0.111 0.114 0.071 0.107 0.110 0.099 0.082 0.110 0.113 0.072 0.107 0.113 0.101 0.080 0.113 0.111 0.071 0.108 0.108 0.104 0.080
0.996 1.024 0.981 0.979 0.981 1.013 1.086 1.581 1.013 1.039 0.977 0.978 1.011 1.083 1.561 1.011 1.037 0.976 0.979 1.013 1.088 1.584 1.011 1.038
ρ(rc), and the calculated |V(rc)/G(rc)| suggest that the interactions in the BrUionized-G and BrUenol-G mispair are stronger than the BrUketo-G (Table 2). On the basis of these AIM analysis, BrUketo-G appears to be a closed shell interaction; however, BrUion-G is an intermediate interaction (Table 2). The AIM analysis also revealed the strongest interaction with the BrUenol-G form in these mispairs and also falls under intermediate interaction. The atoms in molecules analysis of FU-G and ClU-G mispairs shows that the | V(rc)/G(rc)| ratio is greater for the FU-G mispair than the ClU9756
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Figure 2. Molecular graph of the BrU-G and ClU-G mispair where the red points are the bond critical points. All these figures were obtained using the AIM2000 package.
Table 3. Decomposition of Total Interaction Energy of the G-C Base Pair and BrUenol-G Mispair Calculated by LMOEDA Method at M06-2X/6-31+G** Level of Theorya
a
name of the pair
electrostatic energy
exchange energy
repulsion energy
polarization energy
DFT dispersion energy
total interaction energy
G-C Br Uketo-G Br Uenol-G Br Uion-G
−43.0 −27.3 −58.2 −35.0
−25.7 −17.7 −44.5 −20.4
75.0 53.1 127.8 57.4
−20.6 −14.1 −43.9 −19.6
−16.3 −11.5 −20.0 −12.9
−30.7 −17.5 −38.6 −30.5
All the energy values are given in kilocalories per mol.
Figure 3. Hydrogen-bonding interactions of OHU-G and CH2OHU-G and CH2OLiU-G. Keto, enol, and ionized forms are represented, respectively, optimized with a M06-2X/6-31+G** level of theory. All the interaction distances are given in angstroms (gray: C; blue: N; white: H; red: O; and violet: Li).
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Table 4. Interactions Energies Were Calculated with Different Methods for the Oxy-Substituted Mispairsa name of the pair OH
Uketo-G OH Uenol-G OH Uion-G CH2OH Uketo-G CH2OH Uenol-G CH2OH Uion-G CH2OLi Uketo-G CH2OLi Uenol-G CH2OLi Uion-G a
ΔEM06‑2X/6‑31+G**
ΔGM06‑2X/6‑31+G**
ΔEMP2/aug‑cc‑pVDZ
ΔEBSSE(M06‑2X/6‑31+G**)
−17.7 −32.9 −30.9 −16.8 −26.3 −30.2 −18.2 −36.3 −46.2
−6.0 −20.2 −18.5 −4.7 −10.2 −17.9 −6.2 −23.7 −32.4
−20.1 −33.4 −32.3 −19.1 −42.9 −31.8 −20.7 −36.3 −47.8
−19.1 −43.4 −32.2 −17.9 −40.2 −31.4 −19.5 −48.3 −52.3
All the energy values are given in kilocalories per mol.
2X/6-31+G** level for CH2OLiUion-G is −32.4 kcal/mol. Note that the lithium present in CH2OLiUion can extend its stable coordination up to 4 with different ligands.69 We have also examined the four coordination of Li with water molecules considered as a solvent. The tetra-coordinated Li of CH2OLi Uionized-G mispair yields the interaction energy −65.6 kcal/mol, which is significantly higher than typical G-C base-pair of DNA (Figure S4 of the Supporting Information). The higher interaction energy of CH2OLiUionized-G mispair than G-C has also been observed in the aqueous phase as calculated with the same level of theory, which suggests that the CH2OLiUionized can induce the stability in the DNA mispair under physiological conditions (Table S5 of the Supporting Information). Importantly, the deprotonation energy calculated for CH2OLi Uionized is lowest in the studied systems and hence the formation of the ionized mispair with guanine base would be facile (Table S1 of the Supporting Information). The CH2OLiUionized-G mispair has shown much higher interaction energy among the mispair calculated because of the additional coordination of Li and oxygen [O−Li---O− C(G), 1.97 Å] (Figure 3). This additional coordination of Li altered the H-bonding arrangement in this case compared to corresponding interactions in Uionized-G mispairs in other cases (Figures 1 and 2). We have also performed gas phase single point energy calculations using MP2/aug-cc-pVDZ level of theory and observed similar trends as obtained with M06−2x/ 6-31+G** level of theory (Table 4). The topological analysis corroborates the interaction distances observed in the M06-2X/6-31+G** level optimized geometry for these oxy-substituted mispairs. The better binding ability of OHU-G mispairs than the HaloU-G mispairs has been found to be in good agreement with the |V(rc)/G(rc)| ratios obtained for respective forms (Table 5). Similar trends were also observed with CH2OHU-G and CH2OLiU-G mispairs (Table 5 and Table S3 and Figure S3 of the Supporting Information). The energy decomposition analysis (EDA) has been carried out to examine the contributions of different energies in such H-bond interactions for these oxy mispairs. The EDA analysis shows that the electrostatic energy contributes chiefly in all cases to stabilize the interaction of mispairs similar to halosubstituted uracils (Table 6).
effective interaction with the guanine base of DNA (Figure 3). The M06-2X/6-31+G** level of theory calculated results show that the OHUketo-G and OHUenol-G mispairs interact more strongly than the halo-substituted uracils with guanine (Tables 1 and 4). The OHUionized form, however, is not significantly better in terms of its interaction with G compared to the corresponding halo-uracils (Table 1). In this case, an additional acidic proton is available in the 5-position. The pKa values observed for this acidic proton is lower than the N3−H proton.63 Therefore, it appears that the effective interaction of the OHUionized-G mispair can be achieved at a higher pH condition. The deprotonation energies calculated with the M06-2X/6-31+G** level of theory, however, revealed that the role of solvation is important in this case. The N−H deprotonation is relatively lower in energy compared to the OH deprotonation in 5-hydroxy uracil. The implicit solvation model (SMD) and the involvement of explicit water molecule, however, showed that the deprotonation energy gap is reduced for the abstraction of N−H and O−H protons from 5-hydroxy uracil (Table S4 of the Supporting Information). These results presumably suggest that more solvent molecules may be needed for direct comparison with the observed pka values in this case. We have further extended the model study of mispair interactions with the −CH2OH group as a substituent at the 5position of uracil. The −CH2OH group can help to form more stable 6-membered rings by intramolecular hydrogen bonding (Figure 3).64−66 The M06-2X/6-31+G** level of theory calculated results show that the mispair interactions of CH2OH U with G is energetically lower than the OHU (Table 4). The intramolecular hydrogen bonding is weaker due to the presence of the electron-releasing methylene group of −CH2OH and the nonplanarity of the 6-membered ring formed in this case. The geometrical constraints avoid the 6membered ring to achieve planarity for CH2OHU with G (Figure 3).67 We have exploited the structural advantage of CH2OH using the electropositive lithium (Li) in place of the OH hydrogen atom. The electropositive lithium (Li) can make the mispair interactions even stronger by additional coordination with neighboring functional groups (Figure 3). We have considered lithium because it is highly electropositive in nature, multicoordination property and lithium salts have been extensively and successfully used for the treatment of manic depression and other neurological and psychiatric disorders.68 The calculated results suggest that the CH2OLiU-G mispair interactions enhanced significantly for CH2OLiUenol-G and CH2OLiUionized-G mispairs (Table 4). The calculated free energy with the M06-
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CONCLUSIONS In this work, we have reported the mutagenic property of substituted uracils with the DNA base. The halo-substituted uracils have been examined computationally with guanine of DNA base pairs. The halouracils, in particular BrU, have been extensively studied by experimentalists; however, their toxicity 9758
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Table 5. Topological Analysis of Noncovalent HydrogenBonding Interactions Calculated by the M06-2X/6-31+G** Level of Theory Obtained Wave Function pair OH
Uketo-G
OH
Uenol-G
OH
Uion-G
CH2OH
Uion-G
CH2OLi
Uion-G
bonds O---H−N N−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O−H---O O---H−N N---H−N O−H---O(CH2OH--O) N---H−N O---H−N O−Li---O−C(G) O−Li---O−C(U)
Rho[ρ(rc)]
∇2(rc)
|V(rc)/ G(rc)|
0.03610 0.03647 0.02390 0.04796 0.09846 0.03572 0.03173 0.02872 0.03362 0.03275 0.02591
0.119 0.115 0.073 0.111 0.078 0.109 0.079 0.098 0.102 0.081 0.080
0.978 0.984 1.014 1.121 1.721 1.010 1.035 1.020 1.011 1.039 1.051
0.03267 0.06758 0.02613 0.02824
0.082 0.159 0.175 0.202
1.042 1.223 0.780 0.776
Article
ASSOCIATED CONTENT
S Supporting Information *
Experiemental pKa values and deprotonation energies and free energies, AIM analyzed data, molecular graph generated by AIM2000 package, EDA energies, M06-2X/6-31+G** level of theory optimized Cartesian coordinates of all these mispairs, and NBO charge analysis. This material is available free of charge via the Internet at http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
*E-mail: [email protected]. Tel: +91-278-2567760, ext 6770. Fax: (+91)-278-2567562. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS CSMCRI communication no: 089/2014. K.J. is thankful to UGC, New Delhi, India, for awarding a junior research fellowship. K.J. acknowledges AcSIR for his Ph.D. enrolment. B.G. thanks MSM, SIP (CSIR, New Delhi), and BRNS, Mumbai, for financial support. We thank the reviewer’s for their valuable comments/suggestions that have helped us to improve the paper.
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or size factor limits them to be good mutagenic agents. We have examined the interaction energies of halouracil-guanine mispairs and compared with the guanine-cytosine DNA base pairs. The easily accessible Uionized forms of substituted uracil with G are energetically slightly better than the G-C basepair. The remarkable stability of U with hydroxyl substituents has been achieved in the studied mispairs. CH2OLiUionized-G mispair has shown the highest stability (−52.3 kcal/mol) among the mispairs studied here. The advantage of multicoordination of electropositive lithium and the contribution of higher electrostatic interaction energy augments the stability of this mispair. Lithium is not expected to bioaccumulate, and it does not show higher toxicity in the human body. The DFT calculated results have been further corroborated by AIM and EDA analyses. The electrostatic interactions contribute mainly toward the hydrogen-bonding interactions in such mispairs. The stability of mispair is considered to be one of the important criteria in mutagenesis, and these results would encourage the researchers to design similar unnatural bases to achieve the mutagenetic process. We are further pursuing the mutagenic study with other DNA basepairs and will report in the future.
REFERENCES
(1) James, C. D.; Jianmin, G.; Haibo, L.; Nidhi, S.; John, E. M.; Eric, K. T. Efficient Replication Bypass of Size-Expanded DNA Base Pairs in Bacterial Cells. Angew. Chem., Int. Ed. 2009, 48, 4524−4527. (2) Mogens, R.; Rudolf, T. Chromosome Banding by in Vitro Exposure to dA-dT Probes and BUdR. Relationships Between DNA Base Clusters, Replication Pattern, And Banding. Hereditas (Lund, Sweden) 1983, 99, 245−250. (3) Bode, J.; Goetze, S.; Heng, H.; Krawetz, S. A.; Benham, C. From DNA Structure to Gene Expression: Mediators of Nuclear Compartmentalization and Dynamics. Chromosome Res. 2003, 11, 435−445. (4) Manalo, M. N.; Perez, L. M.; LiWang, A. Hydrogen-Bonding and π-π Base-Stacking Interactions are Coupled in DNA, As Suggested by Calculated and Experimental Trans-Hbond Deuterium Isotope Shifts. J. Am. Chem. Soc. 2007, 129, 11298−11299. (5) Bick, M. D.; Davidson, R. L. Total Substitution of Bromodeoxyuridine for Thymidine in the DNA of a Bromodeoxyuridine-Dependent Cell Line. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 2082−2086. (6) Brown, T.; Kneale, G.; Hunter, W. N.; Kennard, O. Structural Characterisation of the Bromouracil, Guanine Base Pair Mismatch in a Z-DNA Fragment. Nucleic Acids Res. 1986, 14, 1801−1809.
Table 6. Decomposition of Total Interaction Energy of the Oxy-Substituted Mispairs Calculated by LMOEDA Method at M062X/6-31+G** Level of Theorya Name of the Pair OH
Uketo-G OH Uenol-G OH Uion-G CH2OH Uketo-G CH2OH Uenol-G CH2OH Uion-G CH2OLi Uketo-G CH2OLi Uenol-G CH2OLi Uion-G a
Electrostatic Energy
Exchange Energy
Repulsion Energy
Polarization Energy
DFT Dispersion Energy
Total Interactions Energy
−29.4 −63.8 −37.1 −27.4 −60.3 −36.1 −29.6 −68.8 −71.2
−18.8 −48.9 −21.4 −17.4 −45.4 −20.9 −18.5 −51.2 −40.9
56.0 140.1 59.9 52.0 130.2 58.6 55.3 146.1 116.5
−15.1 −49.9 −20.7 −13.8 −44.5 −20.2 −14.9 −53.1 −36.6
−11.8 −20.8 −12.9 −11.3 −20.2 −12.8 −11.8 −21.3 −20.1
−19.1 −43.4 −32.2 −17.9 −40.2 −31.4 −19.5 −48.3 −52.3
All the energy values are given in kilocalories per mol. 9759
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