Abstract
Base pairs involving protonated nucleobases play important roles in the DNA republication. Xanthine is an oxidative product of guanine. In this work, we employ density functional theory to investigate the protonation properties of xanthine (X), adenine (A), cytosine (C), guanine (G), and thymine (T). With regard to the proton affinity, we study the protonated base pairs between X and A, C, G, T. The quantum theory of atoms in molecule and the natural bond orbital analysis are employed to elucidate the interaction characteristics. The interaction energy and structural parameters show the relative stability of the protonated base pairs: X:AH+ > X:CH+ > X:GH+ > XH+:T. The occurrence of X(syn):AH+(anti) structure may lead to a G:C → T:A transition.
Similar content being viewed by others
REFERENCES
J. C. Gong and S. J. Sturla. J. Am. Chem. Soc., 2007, 129, 4882.
V. Thiviyanathan, A. Somasunderam, D. E. Volk, T. K. Hazra, S. Mitra, and D. G. Gorenstein. Biochem. Biophys. Res. Commun., 2008, 366(3), 752.
D. Bhattacharyya, S. C. Koripella, A. Mitra, V. B. Rajendran, and B. Sinha. J. Biosci., 2007, 32, 809.
Z. Qiu, Y. Xia, H. Wang, and K. Diao. J. Struct. Chem., 2011, 52(3), 462.
K. Gehring, J. L. Leroy, and M. Guéron. Nature, 1993, 363, 561.
X. H. Zhang, M. Li, Y. T. Wang, and Z. C. Ouyang. Chin. Phys. B, 2014, 23(2), 020702.
J. J. Dannenberg and M. Tomasz. J. Am. Chem. Soc., 2000, 122(9), 2062.
M. Noguera, M. Sodupe, and J. Bertrán. Theor. Chem. Acc., 2007, 118, 113.
J. Bertran, M. Noguera, and M. Sodupe. Afinidad, 2002, 59, 470.
H. Y. Wang, J. D. Zhang, and H. F. Schaefer. Chem. Phys. Chem., 2010, 11, 622.
B. Yang and M. T. Rodgers. J. Am. Soc. Mass. Spectrom., 2015, 26, 1394.
R. Eritja, D. M. Horowitz, P. A. Walker, J. P. Ziehler-Martin, M. S. Boosalis, M. F. Goodman, K. Itakura, and B. E. Kaplan. Nucleic Acids Res., 1986, 14, 8135.
V. Vongchampa, M. Dong, L. Gingipalli, and P. Dedon. Nucleic Acids Res., 2003, 31, 1045.
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox. Gaussian 09. Gaussian: Wallingford CT, 2009.
P. Hobza and R. Zahradnik. Intermolecular Complexes. Elsevier: Amsterdam, 1988.
F. B. van Duijneveldt, J. G. C. M. van Duijneveldt-van de Rijdt, and J. H. van Lenthe. Chem. Rev., 1994, 94, 1873.
S. Grimme, J. Antony, S. Ehrlich, and H. Krieg. DFT-D3 – A Dispersion Correction for DFT-Functions. http://toc.uni-muenster.de/DFTD3.
I. Alkorta, I. Rozas, and J. Elguero. Struct. Chem., 1998, 9, 243.
R. F. W. Bader. Chem. Rev., 1991, 91, 893.
F. Greco, A. Liguori, G. Sindona, and N. Ucella. J. Am. Chem. Soc., 1990, 112, 9092.
D. Armentano, G. De Munno, L. Di Donna, G. Sindona, and G. Giorgi. J. Am. Soc. Mass. Spectrom., 2004, 15, 268.
J. M. Rosenberg, N. C. Seeman, R. O. Day, and A. Rich. J. Mol. Bio., 1976, 104(1), 145.
Funding
This work was supported by the grant from the National Natural Science Foundation of China (21520102007), the Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation Open Found (JXMS202023), and the Doctor Foundation of the East China University of Technology (DHBK2019269).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
The authors declare that they have no conflict of interests.
Rights and permissions
About this article
Cite this article
Qiu, Z.M., Zhang, X.P. THE RELATIVE STABILITY OF PROTONATED BASE PAIRS BETWEEN XANTHINE AND DNA BASES. J Struct Chem 62, 29–36 (2021). https://doi.org/10.1134/S0022476621010042
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0022476621010042