Uma nova visão da tripla hélice do DNA: parâmetros estruturais, espectroscópicos e eletrônicos de ligações de hidrogênio para os emparelhamentos de Watson-Crick e Hoogsteen
DOI:
https://doi.org/10.5433/1679-0375.2020v41n1p59Palavras-chave:
DNA. Tripla hélice. Ligação de hidrogênio.Resumo
Através dos cálculos B3LYP/6-31+G(d,p), as estruturas intermoleculares da dupla e tripla hélices do DNA formadas por Timina (T) Adenina (A) foram totalmente otimizadas. Com base na análise de parâmetros estruturais, modos vibracionais e intensidades de absorção no espectro de infravermelho, foram identificadas ligações de hidrogênio entre as bases purina e pirimidina. Pela transferência de carga entre os orbitais de fronteira HOMO e LUMO respectivamente do receptor e doador de prótons, a aplicação dos protocolos NBO e ChElPG proporcionaram resultados insatisfatórios. Todavia, todas as ligações de hidrogênio foram caracterizadas através de descritores QTAIM, pelos quais novos perfis intermoleculares foram obtidos tanto para a dupla (TA) quanto para a tripla (TAT) hélices do DNA.
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Referências
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SCHMIDT, G.; LEVENE, P. A. Ribonucleodepolymerase (the jones-dubos enzyme). Journal of Biological Chemistry, Bethesda, v. 126, p. 423-434, 1938. Available in: https://www.jbc.org/content/126/2/423. Access in: July, 2019.
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SINGHAL, G.; AKHTER, M. Z.; STERN, D. F.; GUPTA, S. D.; AHUJA, A.; SHARMA, U.; JAGANNATHAN, N. R.; RAJESWARI, M. R. DNA triplex-mediated inhibition of MET leads to cell death and tumor regression in hepatoma, Cancer Gene Therapy, [London], v. 18, p. 520-530, 2011. DOI: https://doi.org/10.1038/cgt.2011.21
SOFTWARE news and updates: AIM2000: a program to analiyze and visualize atoms in molecules. Journal of Computational Chemistry, New York, v. 22, p. 545-559, 2001. DOI: https://doi.org/10.1002/1096-987X(20010415)22:5<545::AID-JCC1027>3.0.CO;2-Y
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AVIÑÓ, A., FRIEDEN, M.; MORALES, J. C.; DE LA TORRE, B. G.; GARCÍA, R. G.; AZORÍN, F.; GELPÍ, J. L.; OROZCO, M.; GONZÁLEZ, C.; ERITJA, R. Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines. Nucleic Acids Research, v. 30, p. 2609–2619, 2002. DOI: https://doi.org/10.1093/nar/gkf374
BACHURIN, S. S.; KLETSKII, M. E.; BUROV, O. N.; KURBATOV, S. V. , Non-canonical DNA structures: comparative quantum mechanical study. Biophysical Chemistry, v. 235, p. 19-28, 2018. DOI: https://doi.org/10.1016/j.bpc.2018.02.003
BADER, R. F.W. A quantum theory of molecular structure and its applications. Chemical Reviews, v. 91, p. 893-928, 1991. DOI: https://doi.org/10.1021/cr00005a013
BUENO M. A.; OLIVEIRA, B. G. A influência da ligação de hidrogênio em reações químicas: reação de Prileschajew. Química Nova, São Paulo, v. 38, p. 1-7, 2014. DOI: https://doi.org/10.5935/0100-4042.20140296
CHARGAFF, E., Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia, v. 6, p. 201-209, 1950. DOI: https://doi.org/10.1007/BF02173653
COULSON, C. A.; DANIELSON, U. Ionic and covalent contributions to the hydrogen bond. Arkiv för Fysik, Estocolmo, v. 8, p. 246-244, 1954.
DAHM, R. Friedrich Miescher and the discovery of DNA. Developmental Biology, v. 278, p. 274-288, 2005. DOI: https://doi.org/10.1016/j.ydbio.2004.11.028
DELGADO, J. L.; VANCE, N. R.; KERNS, R. J. Crystal structure of DNA dodecamer D(CGCGAATTCGCG). Protein Data Bank, DOI: https://doi.org/10.2210/pdb6CQ3/pdb
DESIRAJU, G. R. A Bond by Any Other Name. Angewandte Chemie International Edition, v. 50, p. 52-59, 2011. DOI: https://doi.org/10.1002/anie.201002960
FELSENFELD, G.; RICH, A. Studies on the formation of two- and three-stranded polyribonucleotides. Biochimica et Biophysica Acta, v. 26, p. 457-468, 1957. DOI: https://doi.org/10.1016/0006-3002(57)90091-4
FRANKLIN, R. E.; GOSLING, R. G. The structure of sodium thymonucleate fibres. I. The influence of water content. Acta Crystallographica, v. 673, p. 678-677, 1953. DOI: https://doi.org/10.1107/S0365110X53001939
FRISCH, M. J.; TRUCKS, G. W.; SCHLEGEL, H. B.; SCUSERIA, G. E.; ROBB, M. A.; CHEESEMAN, J. R.; MONTGOMERY JR., J. A.; VREVEN, T.; KUDIN, K. N.; BURANT, J. C.; MILLAM, J. M.; IYENGAR, S. S.; TOMASI, J.; BARONE, V.; MENNUCCI, B.; COSSI, M.; SCALMANI, G.; REGA, N.; PETERSSON, G. A.; 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, J. E.; HRATCHIAN, H. P.; CROSS, J. B.; ADAMO, C.; JARAMILLO, J.; GOMPERTS, R.; STRATMANN, R. E.; YAZYEV, O.; AUSTIN, A. J.; CAMMI, R.; POMELLI, C.; OCHTERSKI, J. W.; AYALA, P. Y.; MOROKUMA, K.; VOTH, G. A.; SALVADOR, P.; DANNENBERG, J. J.; ZAKRZEWSKI, V. G.; DAPPRICH, S.; DANIELS, A. D.; STRAIN, M. C.; FARKAS, O.; MALICK, D. K.; RABUCK, A. D.; RAGHAVACHARI, K.; FORESMAN, J. B.; ORTIZ, J. V.; CUI, Q.; BABOUL, A. G.; CLIFFORD, S.; CIOSLOWSKI, J.; STEFANOV, B. B.; LIU, G.; LIASHENKO, A.; PISKORZ, P.; KOMAROMI, I.; MARTIN, R. L.; FOX, D. J.; KEITH, T.; AL-LAHAM, M. A.; PENG, C. Y.; NANAYAKKARA, A.; CHALLACOMBE, M.; GILL, P. M. W.; JOHNSON, B.; CHEN, W.; WONG, M. W.; GONZALEZ, C.; POPLE, J. A. Gaussian 03, Revision C. 01, Gaussian, Inc. Wallingford: CT, 2004.
GODBEER, A. D.; AL-KHALILI, J. S.; STEVENSON, P. D. Modelling proton tunnelling in the adenine–thymine base pair. Physical Chemistry Chemical Physics, v. 17, p. 13034-13044, 2015. DOI: https://doi.org/10.1039/c5cp00472a
GOÑI, J. R.; DE LA CRUZ, X.; OROZCO, M. Triplexforming oligonucleotide target sequences in the human genome. Nuclear Acids Research, v. 32, p. 354-360, 2004. DOI: https://doi.org/10.1093/nar/gkh188
GOTFREDSEN, C. H.; SCHULTZE, P.; FEIGON, J. Intramolecular DNA triplex with RNA third strand, NMR, 10 structures. Protein Data Bank, DOI: https://doi.org/10.2210/pdb1r3x/pdb
GRABOWSKI, S. J. What is the covalency of hydrogen bonding?. Chemical Reviews, v. 111, p. 2597-2625, 2011. DOI: https://doi.org/10.1021/cr800346f
HOOGSTEEN, K. The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine¸ Acta Crystallograpica, v. 12, p. 822-823, 1959. DOI: https://doi.org/10.1107/S0365110X59002389
KOOL, E. T. Hydrogen bonding, base stacking, and stericeffects in DNA replication. Annual Review of Biophysics and Biomolecular Structure, Palo Alto, v.30, p. 1-22, 2001. DOI: https://doi.org/10.1146/annurev.biophys.30.1.1
LEWIS, G. N. The atom and the molecule. Journal of the American Chemical Society, v. 38, p. 762-785, 1916. DOI: https://doi.org/10.1021/ja02261a002
LUO, J.; LIU, Y.; YANG, S. J. Role of base arrangements and intermolecular hydrogen bonding in charge-transfer states of thymine-adenine dinucleotide in aqueous solution. Journal of Photochemistry and Photobiology A: Chemistry, v. 337, p. 1-5, 2017.
DOI: https://doi.org/10.1016/j.jphotochem.2017.01.001
MAO, J. X. Atomic charges in molecules: a classical concept in modern com-putational chemistry, PostDoc Journal: Reviews, [S. l.], v. 2, p. 15-18, 2014.
MORGAN, A. R., WELLS, R. D.: Specificity of the threestranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. Journal of Molecular Biology, v. 37, p. 63-80, 1968. DOI: https://doi.org/10.1016/0022-2836(68)90073-9
MURPHY, L. R.; MEEK, T. L.; ALLRED, A. L.; ALLEN, L. C. Evaluation and test of Pauling’s electronegativity scale, Journal of Physical Chemistry A, v. 104, p. 5867–5871, 2000.
NIKOLOVA, E. N.; KIM, E.; WISE, A. A.; O’BRIEN, P. J.; ANDRICIOAEI, I.; AL-HASHIMI, H. M., Transient Hoogsteen base pairs in canonical duplex DNA. Nature, London, v. 470, p. 498-502, 2011. DOI: https://doi.org/10.1038/nature09775
NOSENKO, Y.; KUNITSKY, M.; STARK, T.; GÖ-BEL, M.; TARAKESHWAR, P.; BRUTSCHY, B., Vibrational signatures of Watson-Crick base pairing in adenine-thymine mimics. Physical Chemistry Chemical Physics, Cambridge, v. 15, p. 11520-11530, 2013. DOI: https://doi.org/10.1039/C3CP50337B
OLIVEIRA, B. G. Structure, energy, vibrational spectrum, and Bader‘s analysis of of π•••H hydrogen bonds and H-δ•••H+δ dihydrogen bonds. Physical Chemistry Chemical Physics, Cambridge, v. 15, p. 37-79, 2013. DOI: https://doi.org/10.1039/C2CP41749A
OLIVEIRA, B. G.; ARAÚJO, R. C. M. U.; CARVALHO, A. B.; RAMOS, M. N. A., A chemometrical study of intermolecular properties of hydrogen-bonded complexes formed by C2H4O⋅⋅⋅HX and C2H5N⋅⋅⋅HX with X = F, CN, NC, and CCH. Journal of Molecular Modeling, Berlin, v. 15, p. 421-432, 2009. DOI: https://doi.org/10.1007/s00894-008-0422-9
PAULING, L.; COREY, R. B. Compound helical configurations of polypeptide chains: structure of proteins of the a-keratin type. Nature, v. 39, p. 1481-1486, 1952.
PENG, B.; MCNEW, S. R.; LI, Q. -S.; XIE, Y.; SCHAEFER III, H. F., Remarkable hydrogen bonding in the radical anions of guanine–cytosine and adenine–thymine. Chemical Physics Letters, Amsterdam, v. 523, p. 120-123, 2012. DOI: https://doi.org/10.1016/j.cplett.2011.12.003
RICH, A.; DAVIES, D. R.; CRICK, F. H.; WATSON, J. D., The molecular structure of polyadenylic acid. Journal of Molecular Biology, London, v. 3, p. 71-86, 1961. DOI: https://doi.org/10.1016/s0022-2836(61)80009-0
RICHARDSON, N. A.; WESOLOWSKI, S. S.; SCHAEFER III, H. F. The adenine-thymine base pair radical anion: Adding an electron results in a major structural change. Journal of Physical Chemistry B, Washington, v. 107, p. 848-853, 2003. DOI: https://doi.org/10.1021/jp022111l
ROWLAND, R. S.; TAYLOR, R. Intermolecular Nonbonded contact distances in organic crystal structures: comparison with distances expected from van der Waals radii. Journal of Physical Chemistry, Easton, v. 100, p. 7384-7391, 1996. DOI: https://doi.org/10.1021/jp953141+
SANTOS, I. T. O.; REGO, D. G.; OLIVEIRA, B. G. A regra de Bent contextualiza a força da ligação de hidrogênio em cluster trimoleculares. Química Nova, São Paulo, v. 37, p. 624-630, 2014. DOI: https://doi.org/10.5935/0100-4042.20140107
SCHMIDT, G.; LEVENE, P. A. Ribonucleodepolymerase (the jones-dubos enzyme). Journal of Biological Chemistry, Bethesda, v. 126, p. 423-434, 1938. Available in: https://www.jbc.org/content/126/2/423. Access in: July, 2019.
SCHUSTER, G. B. Long-range charge transfer in DNA II, [London], Springer, 2004.
SHERRILL, C. D. Distinguishing basis set superposition error (BSSE) from basis set incompleteness error (BSIE)., 2017. Available in: http://vergil.chemistry.gatech.edu/notes/bsse-vs-bsie.pdf. Access in: July, 2019.
SINGHAL, G.; AKHTER, M. Z.; STERN, D. F.; GUPTA, S. D.; AHUJA, A.; SHARMA, U.; JAGANNATHAN, N. R.; RAJESWARI, M. R. DNA triplex-mediated inhibition of MET leads to cell death and tumor regression in hepatoma, Cancer Gene Therapy, [London], v. 18, p. 520-530, 2011. DOI: https://doi.org/10.1038/cgt.2011.21
SOFTWARE news and updates: AIM2000: a program to analiyze and visualize atoms in molecules. Journal of Computational Chemistry, New York, v. 22, p. 545-559, 2001. DOI: https://doi.org/10.1002/1096-987X(20010415)22:5<545::AID-JCC1027>3.0.CO;2-Y
SZATYŁOWICZ, H.; SADLEJ-SOSNOWSKA, N. Characterizing the strength of individual hydrogen bonds in DNA base pairs. Journal of Chemical Information and Modeling, Washington, v. 50, p. 2151-2161, 2010. DOI: https://doi.org/10.1021/ci100288h
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2020-06-20
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Rego, D., & Oliveira, B. (2020). Uma nova visão da tripla hélice do DNA: parâmetros estruturais, espectroscópicos e eletrônicos de ligações de hidrogênio para os emparelhamentos de Watson-Crick e Hoogsteen. Semina: Ciências Exatas E Tecnológicas, 41(1), 59–70. https://doi.org/10.5433/1679-0375.2020v41n1p59
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