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Amini SK. Relative Populations of Some Tautomeric Forms of 2'-Deoxyguanosine-5-Fluorouridine Mismatch. J Phys Chem B 2018; 122:4433-4444. [PMID: 29608855 DOI: 10.1021/acs.jpcb.8b00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of the 2'-deoxyguanosine-uridine mispair as the most occurring mismatch in transcriptional studies of RNAs from DNAs is multiplied when 5-halo-substituted uridine species cause a serious increase in the probability of its occurrence. Many studies relate this higher probability to the existence of possible tautomeric and ionic forms of its constituent bases. According to these statements, relative populations of mismatches between 5-fluorouridine and both keto and enol forms of 2'-deoxyguanosine are computed by using a conformational search. In order to have a complete scan of all of the highly probable conformers in a moderate computational time, an extensive conformational search methodology is employed here, which benefits from the advantages of both the molecular dynamics simulations and quantum mechanics calculations. The population of an enolic tautomer of normal wobble orientation is about 0.057% of that of its keto tautomer, whereas the population of an enolic tautomer of reverse wobble orientation is about 0.0054% of that of its keto tautomer. Totally, the reverse wobble orientation is about six times more populated than the normal wobble orientation. Calculated populations are in good agreement with experimental populations of closely related compounds. The reliability of the applied methodology is certified, in part, by a good agreement obtained between some experimental data and corresponding Boltzmann-weighted average data of most probable conformers such as NMR parameters. The validation of this methodology is certified with high accuracy by applying it on the substituted diuridine pairs, where experimental populations are available. Not only are the calculated populations and NMR parameters of this test in very good agreement with the experimental data, but also they are free of the ambiguities mentioned by experimentalists.
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Affiliation(s)
- Saeed K Amini
- Chemistry and Chemical Engineering Research Center of Iran , Tehran , Iran
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2
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Kervio E, Claasen B, Steiner UE, Richert C. The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res 2014; 42:7409-20. [PMID: 24875480 PMCID: PMC4066754 DOI: 10.1093/nar/gku314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrich E Steiner
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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3
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Basílio Janke EM, Weisz K. A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR. Z PHYS CHEM 2013. [DOI: 10.1524/zpch.2013.0382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.
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Basílio Janke EM, Weisz K. Low-Temperature NMR Studies on the Geometry of Base Pairs Involving 5-Substituted Uracil Derivatives. J Phys Chem B 2013; 117:4853-9. [DOI: 10.1021/jp400348x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eline M. Basílio Janke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Straße 4,
D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Straße 4,
D-17487 Greifswald, Germany
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5
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Greve C, Preketes NK, Fidder H, Costard R, Koeppe B, Heisler IA, Mukamel S, Temps F, Nibbering ETJ, Elsaesser T. N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics. J Phys Chem A 2013; 117:594-606. [PMID: 23234439 DOI: 10.1021/jp310177e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.
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Affiliation(s)
- Christian Greve
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
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6
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O'Donovan DH, Kelly B, Diez-Cecilia E, Kitson M, Rozas I. A structural study of N,N′-bis-aryl-N′′-acylguanidines. NEW J CHEM 2013. [DOI: 10.1039/c3nj00285c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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7
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Liang F, Li S, Lindsay S, Zhang P. Synthesis, physicochemical properties, and hydrogen bonding of 4(5)-substituted 1-H-imidazole-2-carboxamide, a potential universal reader for DNA sequencing by recognition tunneling. Chemistry 2012; 18:5998-6007. [PMID: 22461259 PMCID: PMC3367718 DOI: 10.1002/chem.201103306] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/15/2012] [Indexed: 01/13/2023]
Abstract
We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6-10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.
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Affiliation(s)
- Feng Liang
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (USA), Fax: (+1)480-727-2378
| | - Shengqing Li
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (USA), Fax: (+1)480-727-2378
| | - Stuart Lindsay
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (USA), Fax: (+1)480-727-2378
| | - Peiming Zhang
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (USA), Fax: (+1)480-727-2378
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Janke EMB, Riechert-Krause F, Weisz K. Low-temperature NMR studies on inosine wobble base pairs. J Phys Chem B 2011; 115:8569-74. [PMID: 21644523 DOI: 10.1021/jp200840j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements at room temperature and at very low temperatures in a freonic solvent. As indicated by its significantly deshielded imino proton, the Watson-Crick-type I·C base pair forms a remarkably strong NHN hydrogen bond. For the thermodynamically less stable I·A wobble base pair, two configurations of similar population coexist at 133 K in the slow hydrogen bond exchange regime, namely a Watson-Crick(I)-Watson-Crick(A) geometry and a Watson-Crick(I)-Hoogsteen(A) geometry. I·U base pairs are stabilized by two rather weak hydrogen bonds and are significantly disfavored over inosine self-associates in a low-temperature Freon solution.
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9
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Xiao Z, Weisz K. Base-base recognition of nonionic dinucleotide analogues in an apolar environment studied by low-temperature NMR spectroscopy. J Am Chem Soc 2010; 132:3862-9. [PMID: 20180555 DOI: 10.1021/ja910220s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Two self-complementary dinucleotide analogues T(Si)A and A(Si)T with a nonionic diisopropylsilyl-modified backbone were synthesized, and their association in a nonaqueous aprotic environment was studied by NMR spectroscopy. Using a CDClF(2)/CDF(3) solvent mixture, measurements at temperatures as low as 113 K allowed the observation and structural characterization of individual complexes in the slow exchange regime. The A(Si)T analogue associates to exclusively form a dinucleotide antiparallel duplex with regular Watson-Crick base pairing, but both A and T nucleosides exhibit a predominant C3'-endo sugar pucker reminiscent of an A-type conformation. In contrast to A(Si)T, the T(Si)A dinucleotide is found to exhibit significant variability and flexibility. Thus, different secondary structures with weaker hydrogen bonds for all T(Si)A structures are observed at low temperatures. Although a B-like Watson-Crick antiparallel dinucleotide duplex with a preferred C2'-endo sugar pucker largely predominates at temperatures above 153 K, two additional species, namely a dinucleotide Hoogsteen duplex with a syn glycosidic torsion angle of the adenosine nucleoside and a presumably intramolecularly folded structure, are increasingly populated upon further cooling. By adding typical DNA intercalators like anthracene or benz[c]acridine derivatives to the A(Si)T dinucleotide duplex in the aprotic solvent environment, no binding of the polycyclic aromatic molecules can be detected even at lower temperatures. Obviously, van der Waals and stacking interactions are insufficient to compensate for the other unfavorable contributions to the overall free energy of binding, and only in the presence of additional hydrophobic effects in an aqueous environment does binding occur.
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Affiliation(s)
- Zhou Xiao
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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10
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Schlund S, Basílio Janke EM, Weisz K, Engels B. Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason? J Comput Chem 2010; 31:665-70. [PMID: 19557765 DOI: 10.1002/jcc.21354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by approximately 10 kJ mol(-1), whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double zeta basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria.
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Affiliation(s)
- Sebastian Schlund
- Institute for Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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11
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Abstract
Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3'-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3'-terminal 2'-anthraquinoylamido-2'-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5'-terminus of the target strand through a combination of pi-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3'-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a DeltaT(m) in the UV melting point of up to +18.2 degrees C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3'-terminus gives DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.
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Affiliation(s)
- Amritraj Patra
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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12
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Janke EMB, Schlund S, Paasche A, Engels B, Dede R, Hussain I, Langer P, Rettig M, Weisz K. Tautomeric equilibria of 3-formylacetylacetone: low-temperature NMR spectroscopy and ab initio calculations. J Org Chem 2009; 74:4878-81. [PMID: 19485345 DOI: 10.1021/jo9004475] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Keto-enol tautomerization of 3-formylacetylacetone has been studied by NMR spectroscopy, ab initio, and DFT calculations in the gas phase and continuum solvation. By employing very low temperatures in a freonic solvent, tautomeric and conformational equilibria in the slow exchange regime were analyzed in detail. The beta-tricarbonyl compound always adopts a structure with an enolized keto group irrespective of an increasing dielectric constant of the solvent when lowering the temperature of the Freon mixture. This experimentally observed tautomeric distribution of 3-formylacetylacetone is correctly reproduced by continuum solvated DFT calculations.
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Affiliation(s)
- Eline M. Basílio Janke
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Sebastian Schlund
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Alexander Paasche
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Bernd Engels
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Rüdiger Dede
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Ibrar Hussain
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Peter Langer
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Michael Rettig
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
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Ritter A, Bernet B, Vasella A. Oligonucleotide Analogues with Integrated Bases and Backbone. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Janke EMB, Weisz K. Switching Binding Sites: Low-Temperature NMR Studies on Adenosine−Aspartic Acid Interactions. J Phys Chem A 2007; 111:12136-40. [DOI: 10.1021/jp076429v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eline M. Basílio Janke
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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15
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. J Phys Chem B 2007; 111:9655-63. [PMID: 17655217 DOI: 10.1021/jp073203j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive conformational analysis of isolated 2'-beta-deoxy-thymidine (T), canonical DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. At 298.15 K, all 92 conformers of isolated dT are within a 7.49 kcal/mol Gibbs energy range. Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases: syn/anti = 38.0%:62.0% and S/N = 59.5%:40.5%. The whole conformational parameters (P, chi, gamma, delta, beta, epsilon, nu max) were analyzed as well as the energies of the OH...O intramolecular H-bonds on the basis of nu(OH) stretching vibrations. Convolution of calculated IR spectra of all of the T conformers appears consistent with its low-temperature matrix spectrum (Ivanov et al. Low Temp. Phys. 2003, 29, 809). The maximal discrepancy in frequencies between calculated and experimental spectra is less than 1%. A conclusion was made that for reliable reconstruction of the isolated nucleoside IR spectrum the quasi whole set of conformers should be taken into consideration. In essence, this result opens up a possibility to reconstruct IR spectra of isolated nucleosides at physiological temperatures with rather satisfactory probability.
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Affiliation(s)
- Yevgen P Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143 Kyiv, Ukraine
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Schlund S, Mladenovic M, Basílio Janke EM, Engels B, Weisz K. Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes. J Am Chem Soc 2005; 127:16151-8. [PMID: 16287303 DOI: 10.1021/ja0531430] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.
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Affiliation(s)
- Sebastian Schlund
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97070 Würzburg, Germany
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Hupp T, Sturm C, Basílio Janke EM, Cabre MP, Weisz K, Engels B. A Combined Computational and Experimental Study of the Hydrogen-Bonded Dimers of Xanthine and Hypoxanthine. J Phys Chem A 2005; 109:1703-12. [PMID: 16833495 DOI: 10.1021/jp0460588] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In addition to uracil, the noncanonical nucleobases xanthine and hypoxanthine are important lesions that are formed from the canonical bases when a cell is under oxidative stress. It is known that they lead to point mutations; however, more detailed information about their ability to form hydrogen-bonded complexes is not available. In the present paper such information is obtained by a combined experimental and theoretical approach. Accurate association constants of xanthosine and inosine dimers are determined by concentration dependent 1H NMR experiments, and a structural characterization of individual complexes formed in solution is performed through measurements under slow exchange conditions at very low temperatures. An interpretation of the experimental data concerning complex geometries becomes possible through a comparison of measured and computed NMR chemical shifts. Further qualitative insights into the hydrogen bonding abilities of xanthine and hypoxanthine are obtained by a theoretical characterization of all possible pairing modes of xanthine and hypoxanthine dimers and by a comparison with simplified model systems. The influence of a polar medium on the bonding properties is also estimated and the importance of the various effects is discussed. Our analysis shows to what extent secondary electronic and electrostatic effects influence the hydrogen bonding properties of xanthine and hypoxanthine in the gas phase and in polar solvents.
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Affiliation(s)
- Thomas Hupp
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97070 Würzburg
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Barthelemy P, Prata CAH, Filocamo SF, Immoos CE, Maynor BW, Hashmi SAN, Lee SJ, Grinstaff MW. Supramolecular assemblies of DNA with neutral nucleoside amphiphiles. Chem Commun (Camb) 2005:1261-3. [PMID: 15742045 DOI: 10.1039/b412670j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A neutral uridine-based amphiphile is described which condenses plasmid DNA. AFM studies show that the three distinct structural components of the amphiphile (i.e, nucleobase, alkyl chains, and poly(ethylene glycol)) are required for the formation of DNA-amphiphile supramolecular assemblies on a mica surface.
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Basílio Janke EM, Limbach HH, Weisz K. Binding of an Acetic Acid Ligand to Adenosine: A Low-Temperature NMR Study. J Am Chem Soc 2004; 126:2135-41. [PMID: 14971948 DOI: 10.1021/ja038630z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of an acetic acid (HAc) ligand to adenosine (A) was studied by (1)H NMR spectroscopic techniques. Using a low-melting deuterated Freon mixture as solvent, liquid-state measurements could be performed in the slow exchange regime and allowed a detailed characterization of the formed associates. Thus, at 128 K, trimolecular complexes A.HAc(2) and A(2).HAc with both Watson-Crick and Hoogsteen sites of the central adenine base occupied coexist in various amounts depending on the adenosine:acetic acid molar ratio. Whereas the carboxylic acid OH proton is located closer to the acid for all hydrogen bonds formed, a more deshielded proton at the Watson-Crick site is evidence for a stronger hydrogen bond as compared to the Hoogsteen interaction. For the binding of acetic acid to an adenosine-thymidine base pair in either a Watson-Crick or a Hoogsteen configuration, hydrogen bonds to the available adenine binding site are strengthened as compared to the corresponding hydrogen bonds in the A.HAc(2) complex.
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Affiliation(s)
- Eline M Basílio Janke
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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Schmidt KS, Reedijk J, Weisz K, Basilio Janke EM, Sponer JE, Sponer J, Lippert B. Loss of Hoogsteen pairing ability upon N1 adenine platinum binding. Inorg Chem 2002; 41:2855-63. [PMID: 12033892 DOI: 10.1021/ic0109602] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroform- and Freon-soluble mixed thymine, adenine complexes trans-[Pt(MeNH(2))(2)(ChmT-N3)(ChmA-N1)]NO(3) (2) and trans-[Pt(MeNH(2))(2)(ChmT-N3)(TBDMS-ado-N1)]BF(4) (3) (ChmT = anion of 1-cyclohexylmethylthymine ChmTH, ChmA = 9-cyclohexylmethyladenine, TBDMS-ado = 2',3',5'-tri-tert-butyldimethylsilyladenosine) have been prepared and characterized to study their propensity to undergo Hoogsteen and/or reversed Hoogsteen pairing in solution with free ChmTH and free 3',5'-diacetyl-2'-deoxyuridine, respectively. No Hoogsteen or reversed Hoogsteen pairing between 2 and ChmT takes place in CDCl(3). In Freon, partial H bonding between N1 platinated TBDMS-ado and 3',5'-diacetyl-2'-deoxyuridine as well as its [3-(15)N] labeled analogue is unambiguously observed only below 150 K. Comparison of (1)J ((15)N-(1)H) coupling constants of 3',5'-diacetyl-2'-deoxyuridine involved in Hoogsteen pairing with free and N1 platinated adenine suggests that the interaction is inherently weaker in the case of platinated adenine. To better understand the complete absence of hydrogen bonding between the ChmA ligand in 2 and free ChmTH, ab initio calculations (gas phase, 0 K) have been carried out for Hoogsteen pairs involving adenine (A) and thymine (T), as well as simplified analogues of 2 and T, both in the presence and absence of counteranions. The data strongly suggest that reduction of the effective positive charge of the heavy metal ion Pt(2+) by counterions diminishes interaction energies. With regard to mixtures of 2 and ChmTH in chloroform, this implies that ion pair formation between the cation of 2 and NO(3)(-) may be responsible for the lack of any measurable Hoogsteen pairing in this solvent.
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Dunger A, Limbach HH, Weisz K. Geometry and Strength of Hydrogen Bonds in Complexes of 2‘-Deoxyadenosine with 2‘-Deoxyuridine. J Am Chem Soc 2000. [DOI: 10.1021/ja000718e] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anita Dunger
- Contribution from the Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Hans-Heinrich Limbach
- Contribution from the Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Klaus Weisz
- Contribution from the Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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Steinbeck C, Richert C. The Role of Ionic Backbones in RNA Structure: An Unusually Stable Non-Watson−Crick Duplex of a Nonionic Analog in an Apolar Medium. J Am Chem Soc 1998. [DOI: 10.1021/ja9817951] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christoph Steinbeck
- Contribution from the Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155
| | - Clemens Richert
- Contribution from the Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155
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Chandra AK, Nguyen MT, Zeegers-Huyskens T. Theoretical Study of the Interaction between Thymine and Water. Protonation and Deprotonation Enthalpies and Comparison with Uracil. J Phys Chem A 1998. [DOI: 10.1021/jp981259v] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Asit K. Chandra
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
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