A new vision of the DNA triple-helix: structural, spectroscopic and electronic parameters for hydrogen bonding for Watson-Crick and Hoogsteen pairing
DOI:
https://doi.org/10.5433/1679-0375.2020v41n1p59Keywords:
DNA. Triple-helix. Hydrogen bond.Abstract
Through the B3LYP/6-31+G(d,p) calculations, the intermolecular structures of double and triple DNA helix formed by Thymine (T) Adenine (A) were fully optimized. Based on analysis of structural parameters, vibrational modes and infrared absorption intensities, specific hydrogen bonds on the scaffolds of the purine and pyrimidine were identified. On behalf of charge transfer criterion between the HOMO and LUMO frontier orbitals of the proton receptor and donor respectively, the application of the NBO and ChElPG protocols have provided unsatisfactory results. Meanwhile, all hydrogen bonds were characterized through the QTAIM descriptors, by which new intermolecular profiles have been pointed out to both of double (TA) and (TAT) triple-DNA helix.Downloads
Download data is not yet available.
References
ARUNAN, E.; DESIRAJU, G. R.; KLEIN, R. A.; SADLEJ, J.; SCHEINER, S.; ALKORTA, I.; CLARY, D. C.; CRABTREE, R. H.; DANNENBERG, J. J.; HOBZA, P.; KJAERGAARD, H. G.; LEGON, A. C.; MENNUCCI, B.; NESBITT, D. J., Definition of the hydrogen bond (IUPAC Recommendations 2011)*. Pure nd Applied Chemistry, v. 83, p. 1637-1641, 2011. DOI: https://doi.org/10.1351/PAC-REC-10-01-02
AVERY, O. T.; MACLEOD, C. M.; MCCARTY, M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine, v. 79, p. 137-158, 1944. DOI: https://doi.org/10.1084/jem.79.2.137
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
TRAVERS, A.; MUSKHELISHVILI, G. DNA structure and function. FEBS Journal, Oxford, v. 282, p. 2279-2295, 2015. DOI: https://doi.org/10.1111/febs.13307
WATSON, J. D.; CRICK, F. H. C. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, Nature, v. 171, p. 737-738, 1953. DOI: https://doi.org/10.1038/171737a0
WIBERG, K. K.; RABLEN, P. R. Atomic Charges. Journal of Organic Chemistry, v. 83, p. 15463–15469, 2018. DOI: https://doi.org/10.1021/acs.joc.8b02740
AVERY, O. T.; MACLEOD, C. M.; MCCARTY, M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine, v. 79, p. 137-158, 1944. DOI: https://doi.org/10.1084/jem.79.2.137
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
TRAVERS, A.; MUSKHELISHVILI, G. DNA structure and function. FEBS Journal, Oxford, v. 282, p. 2279-2295, 2015. DOI: https://doi.org/10.1111/febs.13307
WATSON, J. D.; CRICK, F. H. C. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, Nature, v. 171, p. 737-738, 1953. DOI: https://doi.org/10.1038/171737a0
WIBERG, K. K.; RABLEN, P. R. Atomic Charges. Journal of Organic Chemistry, v. 83, p. 15463–15469, 2018. DOI: https://doi.org/10.1021/acs.joc.8b02740
Downloads
Published
2020-06-20
How to Cite
Rego, D., & Oliveira, B. (2020). A new vision of the DNA triple-helix: structural, spectroscopic and electronic parameters for hydrogen bonding for Watson-Crick and Hoogsteen pairing. Semina: Ciências Exatas E Tecnológicas, 41(1), 59–70. https://doi.org/10.5433/1679-0375.2020v41n1p59
Issue
Section
Original Article
License
The Copyright Declaration for articles published in this journal is the author’s right. Since manuscripts are published in an open access Journal, they are free to use, with their own attributions, in educational and non-commercial applications. The Journal has the right to make, in the original document, changes regarding linguistic norms, orthography, and grammar, with the purpose of ensuring the standard norms of the language and the credibility of the Journal. It will, however, respect the writing style of the authors. When necessary, conceptual changes, corrections, or suggestions will be forwarded to the authors. In such cases, the manuscript shall be subjected to a new evaluation after revision. Responsibility for the opinions expressed in the manuscripts lies entirely with the authors.
This journal is licensed with a license Creative Commons Attribution-NonCommercial 4.0 International.
