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Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines

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Abstract

Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.

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References

  1. Sessler JL, Jayawickramarajah J. Functionalized base-pairs: Versatile scaffolds for self-assembly. Chem Commun, 2005, 15: 1939–1949

    Article  Google Scholar 

  2. Jeffrey GA, Saenger W. Hydrogen Bonding in Biological Structures. Berlin: Springer, 1991

    Google Scholar 

  3. Kelly REA, Kantorovich LN. Homopairing possibilities of the DNA base thymine and the RNA base uracil: An ab initio density functional theory study. J Phys Chem B, 2006, 110: 2249–2255

    Article  CAS  Google Scholar 

  4. Kelly REA, Kantorovich LN. Planar heteropairing possibilities of the DNA and RNA bases: An ab initio density functional theory study. J Phys Chem C, 2007, 111: 3883–3892

    Article  CAS  Google Scholar 

  5. Sivakova S, Rowan SJ. Nucleobases as supramolecular motifs. Chem Soc Rev, 2005, 34: 9–21

    Article  CAS  Google Scholar 

  6. Mamdouh W, Dong M, Xu S, Rauls E, Besenbacher F. Supramolecular nanopatterns self-assembled by adenine-thymine quartets at the liquid/solid interface. J Am Chem Soc, 2006, 128: 13305–13311

    Article  CAS  Google Scholar 

  7. Sreenivasachary N, Lehn J-M. Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation. Proc Natl Acad Sic USA, 2005, 102: 5938–5943

    Article  CAS  Google Scholar 

  8. Shi X, Mullaugh KM, Fettinger JC, Jiang Y, Hofstadler SA, Davis JT. Lipophilic G-quadruplexes are self-assembled ion pair receptors, and the bound anion modulates the kinetic stability of these complexes. J Am Chem Soc, 2003, 125: 10830–10841

    Article  CAS  Google Scholar 

  9. Kawai T, Tanaka H, Nakagawa T. Low dimensional self-organization of DNA-base molecules on Cu (111) surfaces. Surf Sci, 1997, 386: 124–136

    Article  CAS  Google Scholar 

  10. Tao NJ, Shi Z. Kinetics of oxidation of guanine monolayers at the graphite-water interface studied by AFM/STM. J Phys Chem, 1994, 98: 7422–7426

    Article  CAS  Google Scholar 

  11. Davis JT, Spada GP. Supramolecular architectures generated by self-assembly of guanosine derivatives. Chem Soc Rev, 2007, 36: 296–313

    Article  CAS  Google Scholar 

  12. Luhrs C. Polyomino-safe DNA self-assembly via block replacement. Nat Comput, 2010, 9: 97–109

    Article  CAS  Google Scholar 

  13. Wong A, Ida R, Spindler L, Wu G. Disodium Guanosine 5′-monophosphate self-associates into nanoscale cylinders at PH 8: A combined diffusion NMR spectroscopy and dynamic light scattering study. J Am Chem Soc, 2005, 127: 6990–6998

    Article  CAS  Google Scholar 

  14. Otero R, Schock M, Molina LM. Guanine quartet networks stabilized by cooperative hydrogen bonds. Angew Chem Int Ed, 2005, 44: 2270–2275

    Article  CAS  Google Scholar 

  15. Tanaka H, Nakagawa T, Kawai T. Two-dimensional self-assembly of DNA base molecules on Cu(111) surfaces. Surf Sci, 1996, 364: L575–L579

    Article  CAS  Google Scholar 

  16. Nakagawa T, Tanaka H, Kawai T. Two-dimensional self-assembly of uracil molecules on Cu(111) surfaces: A low-temperature STM study. Surf Sci, 1997, 370: L144–L148

    Article  CAS  Google Scholar 

  17. Boys SF, Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys, 1970, 19: 553–566

    Article  CAS  Google Scholar 

  18. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr., T. V, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA: Gaussian 03. Revision B. 02. Pittsburgh (PA): Gaussian, Inc. 2003

    Google Scholar 

  19. Biegler-Konig F, Schonbohm J, Bayles D. Software news and updates AIM2000-A program to analyze and visualize atoms in molecules. J Comput Chem, 2001, 22: 545–559

    Article  Google Scholar 

  20. Kratochvil M, Engkvist O, Sponer J, Jungwirth P, Hobza P. Uracil dimer: Potential energy and free energy surfaces. Ab initio beyond Hartree-Fock and empirical potential studies. J Phys Chem A, 1998, 102: 6921–6926

    Article  CAS  Google Scholar 

  21. Frey JA, Muller A, Losada M, Leutwyler S. Isomers of the uracil dimer: An ab initio benchmark study. J Phys Chem B, 2007, 111: 3534–3542

    Article  CAS  Google Scholar 

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  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China

    Yang Li & ChangSheng Wang

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  1. Yang Li
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  2. ChangSheng Wang
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Correspondence to ChangSheng Wang.

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Li, Y., Wang, C. Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines. Sci. China Chem. 54, 1759–1769 (2011). https://doi.org/10.1007/s11426-011-4411-y

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  • DOI: https://doi.org/10.1007/s11426-011-4411-y

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