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.