Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine.
density functional calculations
hydrogen bonds
interaction energies
nucleobases
substituent effects
Journal
Chembiochem : a European journal of chemical biology
ISSN: 1439-7633
Titre abrégé: Chembiochem
Pays: Germany
ID NLM: 100937360
Informations de publication
Date de publication:
02 09 2019
02 09 2019
Historique:
received:
13
04
2019
pubmed:
16
4
2019
medline:
9
9
2020
entrez:
16
4
2019
Statut:
ppublish
Résumé
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
Identifiants
pubmed: 30983115
doi: 10.1002/cbic.201900245
doi:
Substances chimiques
isocytosine
108-53-2
Cytosine
8J337D1HZY
Azaguanine
Q150359I72
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2262-2270Informations de copyright
© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Références
A. Czerwoniec, S. Dunin-Horkawicz, E. Purta, K. H. Kaminska, J. M. Kasprzak, J. M. Bujnicki, H. Grosjean, K. Rother, Nucleic Acids Res. 2009, 37, D118-D121.
G. Egger, G. N. Liang, A. Aparicio, P. A. Jones, Nature 2004, 429, 457-463;
P. A. Jones, D. Takai, Science 2001, 293, 1068-1070;
B. E. Bernstein, A. Meissner, E. S. Lander, Cell 2007, 128, 669-681.
D. H. Appella, Curr. Opin. Chem. Biol. 2009, 13, 687-696;
J. S. Choi, A. Dasari, P. Hu, S. J. Benkovic, A. J. Berdis, Nucleic Acids Res. 2016, 44, 1022-1035;
I. Lee, A. J. Berdis, Biochim. Biophys. Acta, Proteins Proteom. 2010, 1804, 1064-1080;
W. Xu, K. M. Chan, E. T. Kool, Nat. Chem. 2017, 9, 1043-1055;
M. Terrazas, E. T. Kool, Nucleic Acids Res. 2009, 37, 346-353;
H. Peacock, R. V. Fucini, P. Jayalath, J. M. Ibarra-Soza, H. J. Haringsma, W. M. Flanagan, A. Willingham, P. A. Beal, J. Am. Chem. Soc. 2011, 133, 9200-9203.
A. Avino, C. Fabrega, M. Tintore, R. Eritja, Curr. Pharm. Des. 2012, 18, 2036-2047;
J. Gros, F. Rosu, S. Amrane, A. De Cian, V. Gabelica, L. Lacroix, J. L. Mergny, Nucleic Acids Res. 2007, 35, 3064-3075;
C. J. Lech, J. K. Cheow Lim, J. M. Wen Lim, S. Amrane, B. Heddi, A. T. Phan, Biophys. J. 2011, 101, 1987-1998;
J. Sagi, J. Biomol. Struct. Dyn. 2014, 32, 477-511.
G. Haaima, H. F. Hansen, L. Christensen, O. Dahl, P. E. Nielsen, Nucleic Acids Res. 1997, 25, 4639-4643;
Z. Li, C. J. Lech, A. T. Phan, Nucleic Acids Res. 2014, 42, 4068-4079;
A. Paul, P. Sengupta, Y. Krishnan, S. Ladame, Chem. Eur. J. 2008, 14, 8682-8689;
C. G. Peng, M. J. Damha, Nucleic Acids Res. 2007, 35, 4977-4988.
A. R. Hernández, L. W. Peterson, E. T. Kool, ACS Chem. Biol. 2012, 7, 1454-1461;
J. M. Layzer, A. P. McCaffrey, A. K. Tanner, Z. Huang, M. A. Kay, B. A. Sullenger, RNA 2004, 10, 766-771.
M. Grammel, H. C. Hang, Nat. Chem. Biol. 2013, 9, 475-484.
J. M. Ibarra-Soza, A. A. Morris, P. Jayalath, H. Peacock, W. E. Conrad, M. B. Donald, M. J. Kurth, P. A. Beal, Org. Biomol. Chem. 2012, 10, 6491-6497.
M. M. Georgiadis, I. Singh, W. F. Kellett, S. Hoshika, S. A. Benner, N. G. J. Richards, J. Am. Chem. Soc. 2015, 137, 6947-6955.
K. Dhami, D. A. Malyshev, P. Ordoukhanian, T. Kubelka, M. Hocek, F. E. Romesberg, Nucleic Acids Res. 2014, 42, 10235-10244;
L. Li, M. Degardin, T. Lavergne, D. A. Malyshev, K. Dhami, P. Ordoukhanian, F. E. Romesberg, J. Am. Chem. Soc. 2014, 136, 826-829.
Y. Aubert, L. Perrouault, C. Helene, C. Giovannangeli, U. Asseline, Bioorg. Med. Chem. 2001, 9, 1617-1624;
N. Ramzaeva, F. Seela, Helv. Chim. Acta 1996, 79, 1549-1558;
F. Seela, M. Zulauf, Chem. Eur. J. 1998, 4, 1781-1790;
W. Q. Lin, K. Y. Xu, F. Seela, Nucleosides Nucleotides Nucleic Acids 2005, 24, 869-873;
F. Seela, G. Becher, M. Zulauf, Nucleosides Nucleotides 1999, 18, 1399-1400;
F. Seela, N. Ramzaeva, M. Zulauf, Nucleosides Nucleotides 1997, 16, 963-966;
F. Seela, R. Kroschel, Nucleic Acids Res. 2003, 31, 7150-7158;
F. Seela, X. Peng, H. Li, J. Am. Chem. Soc. 2005, 127, 7739-7751;
F. Seela, C. F. Wei, Z. Kazimierczuk, Helv. Chim. Acta 1995, 78, 1843-1854.
K. J. Phelps, J. M. Ibarra-Soza, K. Tran, A. J. Fisher, P. A. Beal, ACS Chem. Biol. 2014, 9, 1780-1787.
K. Phelps, A. Morris, P. A. Beal, ACS Chem. Biol. 2012, 7, 100-109.
M. Chawla, R. Credendino, R. Oliva, L. Cavallo, J. Phys. Chem. B 2015, 119, 12982-12989.
F. Seela, G. Becher, Synthesis 1998, 207-214;
F. Seela, H. Driller, Helv. Chim. Acta 1988, 71, 1191-1198;
F. Seela, G. Becher, H. Rosemeyer, H. Reuter, G. Kastner, I. A. Mikhailopulo, Helv. Chim. Acta 1999, 82, 105-124;
F. Seela, H. Driller, Helv. Chim. Acta 1988, 71, 757-761.
F. Seela, G. Becher, Helv. Chim. Acta 1999, 82, 1640-1655.
S. A. Ingale, S. S. Pujari, V. R. Sirivolu, P. Ding, H. Xiong, H. Mei, F. Seela, J. Org. Chem. 2012, 77, 188-199.
H. Xiong, P. Leonard, F. Seela, Bioconjugate Chem. 2012, 23, 856-870.
F. A. Rogers, J. A. Lloyd, M. K. Tiwari, Artif. DNA PNA XNA 2014, 5, e27792.
M. Forconi, T. Benz-Moy, K. R. Gleitsman, E. Ruben, C. Metz, D. Herschlag, RNA 2012, 18, 1222-1229.
M. Chawla, S. Abdel-Azeim, R. Oliva, L. Cavallo, Nucleic Acids Res. 2014, 42, 714-726;
M. Chawla, R. Oliva, J. M. Bujnicki, L. Cavallo, Nucleic Acids Res. 2015, 43, 6714-6729;
M. Chawla, A. Poater, P. Besalu-Sala, K. Kalra, R. Oliva, L. Cavallo, Phys. Chem. Chem. Phys. 2018, 20, 7676-7685;
M. Chawla, A. Poater, R. Oliva, L. Cavallo, Phys. Chem. Chem. Phys. 2016, 18, 18045-18053;
M. Chawla, I. Autiero, R. Oliva, L. Cavallo, Phys. Chem. Chem. Phys. 2018, 20, 3699-3709;
M. Chawla, R. Credendino, E. Chermak, R. Oliva, L. Cavallo, J. Phys. Chem. B 2016, 120, 2216-2224;
J. Sponer, P. Jurecka, P. Hobza, J. Am. Chem. Soc. 2004, 126, 10142-10151;
G. Paragi, E. Szajli, F. Bogar, L. Kovacs, C. F. Guerra, F. M. Bickelhaupt, New J. Chem. 2008, 32, 1981-1987.
A. A. Sawant, P. P. Mukherjee, R. K. Jangid, S. Galande, S. G. Srivatsan, Org. Biomol. Chem. 2016, 14, 5832-5842;
S. R. Suter, A. Ball-Jones, M. M. Mumbleau, R. Valenzuela, J. Ibarra-Soza, H. Owens, A. J. Fisher, P. A. Beal, Org. Biomol. Chem. 2017, 15, 10029-10036;
E. Paredes, S. R. Das, ChemBioChem 2011, 12, 125-131;
F. Seela, H. Xiong, P. Leonard, S. Budow, Org. Biomol. Chem. 2009, 7, 1374-1387.
C. Hansch, A. Leo, R. W. Taft, Chem. Rev. 1991, 91, 165-195.
A. K. Shchyolkina, O. F. Borisova, M. A. Livshits, T. M. Jovin, Mol. Biol. 2003, 37, 223-231;
X. L. Yang, H. Sugiyama, S. Ikeda, I. Saito, A. H. J. Wang, Biophys. J. 1998, 75, 1163-1171.
R. Oliva, L. Cavallo, A. Tramontano, Nucleic Acids Res. 2006, 34, 865-879;
R. Oliva, A. Tramontano, L. Cavallo, RNA 2007, 13, 1427-1436;
K. Rippe, N. B. Ramsing, R. Klement, T. M. Jovin, J. Biomol. Struct. Dyn. 1990, 7, 1199-1209.
H. Kruse, P. Banas, J. Sponer, J. Chem. Theory Comput. 2019, 15, 95-115;
H. Kruse, A. Mladek, K. Gkionis, A. Hansen, S. Grimme, J. Sponer, J. Chem. Theory Comput. 2015, 11, 4972-4991;
J. E. Sponer, K. Reblova, A. Mokdad, V. Sychrovsky, J. Leszczynski, J. Sponer, J. Phys. Chem. B 2007, 111, 9153-9164.
H. Kruse, J. Sponer, Int. J. Quantum Chem. 2018, 118, e25624.
M. Chawla, E. Chermak, Q. Y. Zhang, J. M. Bujnicki, R. Oliva, L. Cavallo, Nucleic Acids Res. 2017, 45, 11019-11032.
R. Strack, Nat. Methods 2015, 12, 284.
T. J. Walter, C. Richert, Nucleic Acids Res. 2018, 46, 8069-8078;
W. Kusser, J. Biotechnol. 2000, 74, 27-38.
D. R. Corey, J. Clin. Invest. 2007, 117, 3615-3622;
J. C. Burnett, J. J. Rossi, Chem. Biol. 2012, 19, 60-71;
J. Chung, D. L. DiGiusto, J. J. Rossi, Expert Opin. Biol. Ther. 2013, 13, 437-445.