Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases

Paragi, Gábor; Szájli, Emília; Bogár, Ferenc; Kovács, Lajos; Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

doi:10.1039/b803593h

Cited by 13 publications

(5 citation statements)

References 34 publications

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“…In systems with a clear σ/π or A′/A′′ separation (such as our planar ribbon and tetrameric structures), the symmetry partitioning in our approach proved to be the most informative, as has been shown …”

Section: Computational Detailsmentioning

confidence: 64%

Cooperativity in the Self‐Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces

Paragi

Guerra

2017

Chemistry A European J

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The guanine nucleobase can self-assemble into tetrameric or ribbon structures on surfaces or in solution. The origin for the occurrence of different aggregation patterns has not yet been investigated. Herein, a quantum chemical study on the different self-assembled structures of guanine and xanthine by using dispersion-corrected DFT is presented. Theoretical investigations can be used to explain, from an electronic point of view, the differences between the experimental findings. With quantitative Kohn-Sham molecular orbital theory and the accompanying energy decomposition analysis, the hydrogen-bonding mechanism within the guanine ribbons can be disclosed and the preferred self-assembled structures under different experimental conditions can be explained. An important role of the σ-electronic system in the guanine self-assembled structures is revealed as the main factor for the switch between different arrangements on surfaces and in crystals.

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Section: Computational Detailsmentioning

confidence: 64%

Cooperativity in the Self‐Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces

Paragi

Guerra

2017

Chemistry A European J

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“…Selectively, A forms WC base pairing with U and G forms WC base pairing with C. Several theoretical and experimental studies have been reported in the literature on natural, as well as modified, base pairs of the nucleosides (or nucleobases) in order to explore their structural stability, electrical conductivity, optical and magnetic properties. 8,9 These include various metal-modified WC base pairs [10][11][12][13][14][15] and artificial base pairs, [16][17][18][19][20][21][22][23] analogues of natural nucleosides. These motivate chemists to explore new analogues of nucleosides.…”

Section: Introductionmentioning

confidence: 99%

Structural, electronic and photophysical properties of analogous RNA nucleosides: a theoretical study

Samanta

Pati

2013

New J. Chem.

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We use first-principles density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to investigate the structural, energetic and bonding aspects, and optical properties of two analogues of RNA nucleosides. The results are compared against the findings obtained for the natural and both modified nucleosides, as well as available experimental data. We find that the modified nucleosides form the hydrogen bonded (H-bonded) Watson-Crick (WC) base pairing with a similar H-bonding energy to that obtained for the natural nucleosides. These modified nucleosides can also form WC base pairing with their natural complementary nucleosides. We also focus on the optical absorption properties of these modified nucleosides and their WC H-bonded base pairs in gas phase as well as in implicit water solvent. Our simulated results show that the low energy peaks in the absorption spectra mainly arise because of the p-p* electronic transition for both the modified nucleosides. The calculated absorption and emission spectra in the presence of solvent follow the same trend as that found experimentally. Our results demonstrate that the modified nucleosides show significantly different electronic and optical properties, although the basic structural and bonding aspects remain the same. They also give microscopic details of the experimentally observed photophysical properties of the modified nucleosides.

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“…6-Aminouracil derivatives are of particular interest in molecular biology and in pharmacology. Their fields of application include artificial nucleobases (Paragi et al, 2008), starting materials for fused uracils (Ribeiro da Silva et al, 2011), heterocyclic compounds (Mü ller, 1991) and pharmaceutical uses, e.g. diuretic and smooth muscle relaxant agents (Mustafa et al, 1989), anticancer agents (Bernier et al, 1985), and semiproducts in drugs for use in asthma (Kjellin & Persson, 1980), allergy and depression therapy (Chmiel-Szukiewicz, 2006).…”

Section: Introductionmentioning

confidence: 99%

Three new pseudopolymorphs of 6-aminouracil

Gerhardt

Bolte

2013

Acta Crystallogr C

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Since 6-aminouracil derivatives show diversified use in various fields of application, we crystallized 6-aminouracil to examine its preferred hydrogen-bonding frameworks. 6-Aminouracil shows two rigid hydrogen-bonding sites, viz. one acceptor-donor-acceptor (ADA) site and one donor-donor-acceptor (DDA) site. During various crystallization attempts, we obtained three structures, namely two dimethylacetamide monosolvates, C4H5N3O2·C4H9NO, and a 1-methylpyrrolidin-2-one monosolvate, C4H5N3O2·C5H9NO. In all three structures, R2(1)(6) N-H...O hydrogen-bonding patterns link the molecules to their respective solvent molecules. The formation of R2(2)(8) N-H...O hydrogen-bond motifs between 6-aminouracil molecules can only be found in two-dimensional frameworks, whereas R3(3)(14) N-H...O patterns are present when zigzag chzins of 6-aminouracil molecules are formed.

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Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases

Cited by 13 publications

References 34 publications

Cooperativity in the Self‐Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces

Cooperativity in the Self‐Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces

Structural, electronic and photophysical properties of analogous RNA nucleosides: a theoretical study

Three new pseudopolymorphs of 6-aminouracil

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