Introduction
The genetic information of the cell is stored in nucleic acids. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids play a main role in vary biological events concerned with the utilization of genetic information. Each nucleic acid contains four of five possible nitrogen-containing bases: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). All nucleic acids contain the bases A, C, and G; T, however, is found only in DNA, while U is found in RNA. Adenine and guanine have a fused-ring skeletal structure derived of purine, hence they are called purine bases. Similarly, the simple-ring structure of cytosine, uracil, and thymine is derived of pyrimidine, so those three bases are called the pyrimidine bases. Watson and Crick in 1953 proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix [11. Watson, J. D., Crick, F. H. C. Nature (London) .1953 ,171, 737-738.]. Base-pairing takes place between a purine and pyrimidine. This allows an ‘A’ to pair with a ‘T’ through two hydrogen bonds and a ‘G’ with a ‘C’ through three hydrogen bonds. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs.
The incorporation of non-Watson-Crick base pairs in duplex DNA is one of the errors affecting DNA replication [22. Kornberg, A., Baker, T. A. DNA replication. Freeman, New York. 1992 .-33. Drake, J. H. The molecular basis of mutation. Holden-Day, San Francisco.1970 .44. Tamm, C., Stazewski, P.Angew Chem Int Ed Engl, 1990 , 29, 36–57.]. Such pairings are referred to as mismatches or mispairs, such as guanine pairing with adenine. Mismatch base pairing occurs in both prokaryote and eukaryote cells during genetic recombination and/or replication and as a consequence of biosynthetic errors during nucleic acid synthesis. Mispairs have been encountered in several biological processes [55. Brown, T., Hunter, W. N. Biopolymers ,1997 , 44, 91–103.]. The effect of mismatches on DNA structure and stability studied in several papers [66. Roongta, V. A., Jones, C. R., Gorenstein, D. G. Biochemistry ,1990 , 29, 5245-5258.-77. Urakawa, H., Noble, P. A., El Fantroussi, S., Kelly, J. J., Stahl, D. A. Appl. Environ. Microbiol . 2002 , 68, 235-244.88. Yang, M., McGovem, M. E., Thompson, M. Anal. Chim. Acta , 1997 , 346, 259-275.]. The conformation and stability of base-pair mismatches in DNA duplexes are investigated by physical methods such as nuclear magnetic resonance spectroscopy [99. Patel, D. J., Shapiro, L., Hare, D., In Nucleic Acids and Molecular Biology (Eckstein, F., Lilley. D. M., eds). Springer-Verlap. Berlin, Heidelberg, New York,1987 , vol. 1, pp. 70-84.], X-ray crystallography [1010. Kennard, In Nucleic Acids and Molecular biology (Eckstein, F., Lilley, D. M., eds). Springer-Verlag. Berlin, Heidelberg, New York. 1987 , vol. 1. pp. 25-52.] and ultraviolet light melting studies [1111. Martin, F. H., Castro, M. M., Aboul-Ela, F., Tinoko, I. Jr., Nucl. Acids Res .1985, 13, 8927-8938.].
Adenine – Guanine mismatches are possible in DNA [1212. Hunter, W.N., Brown, T. In: Neidle S (ed) Oxford handbook of nucleic acid structure. Oxford University Press, Oxford, 1999 , pp 313–330.] and RNA structures [1313. Leontis, N. B., Stombaugh, J., Westhof, E. Nucleic Acids Res , 2002 , 30, 3497–3531.]. It is known that the A-G mismatch is conformationally variable. A-G mismatch can come in different forms, involving the dominant or a rare adenine tautomer of A or a protonated adenine [1414. Lippert, B., Gupta, D. Dalton Trans.2009 , 4619–4634.]. The two most common DNA mispairs containing neutral bases are Aanti-Ganti[1515. Privé, G. G., Heinemann, U., Chandrasegaran, S., Kan, L-S., Kopka, M. L., Dickerson, R. E. Science . 1987 , 238, 498–504.] and Asyn-Ganti[1616. Brown, T., Hunter, W. N., Kneale, G., Kennard, O.Proc Natl Acad Sci USA , 1986 , 83, 2402–8406.]. Ultraviolet light melting studies [1717. Brown, T., Leonard. G. A., Booth, E. D., Chambers, J. J. Mol. Biol. 1989 , 207, 455-467.] and nuclear magnetic resonance spectroscopy [1818. Gao, X., Patel, D. J. J. Amer. Chem. Soc.1988 , 110, 5178-5182.] have been applied to probe the variability in the stability and conformation of the A-G mismatch as a function of pH. Both the Aanti-Ganti and Asyn-Ganti mismatches exist at neutral pH depending on the base stacking environment.
Interactions between nucleic acids and metal cations has attracted considerable attention duo to the biological role that these ions play in determining the structure and function of fundamental blocks of living organisms [1919. Egli, M. Chem. Biol.2002 , 9, 277–286.-2020. Anastassopoulou, J. J. Mol. Struct. 2003 , 651–653, 19–26.2121. Dugid, J., Bloomfield, V. A., Benevides, J., Thomas, G. J., Biophys. J.1993 , 65 , 1916–1928.2222. Krasovska, M. V., Sefcikova, J., Reblova, K., Schneider, B., Walter, N. G., Sponer, J.Biophys J . 2006 , 91, 626-638.]. To better understand mechanisms of metal–nucleic acid interactions occurring in vivo, numerous in vitro studies of model reactions and structures of metal–nucleic acid complexes have been carried out [2323. Hud, N. V., Polak, M. Curr. Opin. Struct. Biol. , 2001 , 11, 293-301.-2424. Sigel, H., Song, B. Met. Ions Biol. Syst. , 1996 , 32, 135-205.2525. Martin, R. B.Acc. Chem. Res. 1985 , 18, 32-38.].
Also, interactions between bases or base pairs and metal cations are investigated by Quantum Mechanical Calculations [2626. Colson, A.O., Besler, B., Close, D. M., Sevilla, M. D. J. Phys. Chem.1992 , 96, 661-668.-2727. Valdespino-Saenz, J., Martinez, A. J. Mol. Struct. (THEOCHEM) , 2010 , 939, 34-43.2828. Burda, J. V., Sÿponer, J., Hobza, P. J. Phys. Chem. 1996 , 100, 7250-7255.]. The most important conclusion from initial calculations, were carried out in the 1980s, show that the polarization effects of base pairing increases due to the metal coordination [2929. Basch, H., Krauss, M., Stevens, W. J. J. Am. Chem. Soc . 1985 ,107, 7267-7271.-3030. Lipinski, J. J. Mol. Struct. (THEOCHEM) , 1989 , 201, 87-98.3131. Del Bene, J. J. Mol. Struct (THEOCHEM) , 1985 , 124, 201-212.]. In several study, Syponer et al., investigated the interactions between mono- and divalent metal cations and nucleobases, as well as the Watson-Crick and reverse Hoogsteen base pairs [3232. Sÿponer, J., Burda, J. V., Mejzlik, P., Leszczynski, J., Hobza, P. J. Biomol. Struct. Dyn. 1997 , 14, 613-628.,3333. Burda, J. V., Sÿponer, J., Leszczynski, J., Hobza, P. J. Phys. Chem. B. 1997 , 101, 9670-9677.,28]. The results demonstrated that every cation has a rather unique interaction with the DNA bases and base pairs. The binding energies and geometries are determined by the charges, atomic radii, electronic structure of the cation and relativistic effects. Also, the effect of interactions of mono and bivalent metal cations with A-T and G-C base pairs have been studied by Ebrahimi et al., [3434. Delarami, H., Ebrahimi, A., Habibi Khorassani, S. M., Abedini S., Mostafavi, N.Phys. Chem. Res., 2013 , 1, 81-89.]. They are shown that the total binding energies in G-C derivatives significantly are increased in the presence of more positive cations, while the changes of binding energies in the A-T derivatives are not in agreement with the charges of cations. In another study, interaction between the G-C base pair and hydrated Mg2+,Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+ metal cations investigated [3535. Sÿponer, J., Burda, J. V., Sabat, M., Leszczynski, J., Hobza, P. J. Phys. Chem. A. 1998 , 102, 5951-5957.]. The results indicate that the strength of the G-C base pair is enhanced due to the coordination of the hydrated cation.
In pervious our work, we theoretically demonstrate the influence of binding of Cu+ ion to N3- and N7-positions of hypoxanthine on the energetic, geometrical and topological properties of hypoxanthine–guanine, hypoxanthine–adenine, hypoxanthine–cytosine, hypoxanthine–thymine and hypoxanthine–hypoxanthine mismatches [3636. Masoodi, H. R., Bagheri, S., Ghaderi, Z., Journal of Biomolecular Structure and Dynamics , 2018 , 37,1923-1934.]. In this work, we have investigated the effect of Li+, Na+ and K+ cations on the properties of hydrogen bonds in the preferred tautomeric forms Aanti-Ganti and Asyn-Ganti mismatches. Also, we have compared geometry parameters and energy data in the Aanti-Ganti and Asyn-Ganti mispairs in the presence of various cations.