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Leitão MIPS, Orsini G, Murtinheira F, Gomes CSB, Herrera F, Petronilho A. Synthesis, Base Pairing Properties, and Biological Activity Studies of Platinum(II) Complexes Based on Uracil Nucleosides. Inorg Chem 2023; 62:16412-16425. [PMID: 37768109 DOI: 10.1021/acs.inorgchem.3c02071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The synthesis and base pairing properties of platinum complexes based on uridine and deoxyuridine nucleosides and preliminary studies of their antiproliferative activity are described. Platinum(II) uridine and deoxyuridine complexes were synthesized by C-I oxidative addition to Pt(0)(PPh3)4. First, the synthesis was performed with protected nucleosides to generate complexes 1 and 2, which were deprotected under basic conditions, affording complexes 3 and 4 in good yields. The synthesis with the unprotected nucleosides was also performed and provided complexes 3 and 4 effectively. Base pairing interactions were measured for complex 1, either for self-base pairing or for the Watson-Crick base pair. Complex 1 undergoes self-base pairing in CDCl3, and this aggregation was found not to be dependent on metalation. Contrastingly, for the Watson-Crick base pair with adenine, base pairing was also observed, but metalation was found to affect hydrogen bonding considerably. Complexes 3 and 4 and the corresponding ligand precursors were evaluated for their antiproliferative activity against human glioblastoma cell line U-251. The compounds showed IC50 values of 3.30 (3) and 1.84 (4) μM but are also toxic for nontumorous cell lines.
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Affiliation(s)
- Maria Inês P S Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
| | - Giulia Orsini
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
| | - Fernanda Murtinheira
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Dep. Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Clara S B Gomes
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO and i4HB - Applied Molecular Biosciences Unit and Institute for Health and Bioeconomy, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Federico Herrera
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Dep. Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Ana Petronilho
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
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Buyens DMS, Pilcher LA, Cukrowski I. Coordination Sites for Sodium and Potassium Ions in Nucleophilic Adeninate Contact ion-Pairs: A Molecular-Wide and Electron Density-Based (MOWED) Perspective. Molecules 2022; 27:6111. [PMID: 36144844 PMCID: PMC9505275 DOI: 10.3390/molecules27186111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The adeninate anion (Ade-) is a useful nucleophile used in the synthesis of many prodrugs (including those for HIV AIDS treatment). It exists as a contact ion-pair (CIP) with Na+ and K+ (M+) but the site of coordination is not obvious from spectroscopic data. Herein, a molecular-wide and electron density-based (MOWED) computational approach implemented in the implicit solvation model showed a strong preference for bidentate ion coordination at the N3 and N9 atoms. The N3N9-CIP has (i) the strongest inter-ionic interaction, by -30 kcal mol-1, with a significant (10-15%) covalent contribution, (ii) the most stabilized bonding framework for Ade-, and (iii) displays the largest ion-induced polarization of Ade-, rendering the N3 and N9 the most negative and, hence, most nucleophilic atoms. Alkylation of the adeninate anion at these two positions can therefore be readily explained when the metal coordinated complex is considered as the nucleophile. The addition of explicit DMSO solvent molecules did not change the trend in most nucleophilic N-atoms of Ade- for the in-plane M-Ade complexes in M-Ade-(DMSO)4 molecular systems. MOWED-based studies of the strength and nature of interactions between DMSO solvent molecules and counter ions and Ade- revealed an interesting and unexpected chemistry of intermolecular chemical bonding.
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Affiliation(s)
| | | | - Ignacy Cukrowski
- Department of Chemistry, University of Pretoria, Pretoria 0002, South Africa
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Buyens DMS, Pilcher LA, Roduner E. Towards a Molecular Understanding of Cation-Anion Interactions and Self-aggregation of Adeninate Salts in DMSO by NMR and UV Spectroscopy and Crystallography. Chemphyschem 2021; 22:2025-2033. [PMID: 34153151 PMCID: PMC8518609 DOI: 10.1002/cphc.202100098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Indexed: 11/20/2022]
Abstract
Rare anionic forms of nucleic acids play a significant biological role and lead to spontaneous mutations and replication and translational errors. There is a lack of information surrounding the stability and reactivity of these forms. Ion pairs of mono‐sodium and ‐potassium salts of adenine exist in DMSO solution with possible cation coordination sites at the N1, N7 and N9 atoms of the purine ring. At increasing concentrations π‐π stacked dimers are the predominant species of aggregates followed by higher order aggregation governed by coordination to metal cations in which the type of counter ion present has a central role in the aggregate formation.
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Affiliation(s)
- Dominique M S Buyens
- Department of Chemistry, University of Pretoria, Pretoria, 0002, Republic of South Africa
| | - Lynne A Pilcher
- Department of Chemistry, University of Pretoria, Pretoria, 0002, Republic of South Africa
| | - Emil Roduner
- Institute of Physical Chemistry, University of Stuttgart, 70569, Stuttgart, Germany.,Department of Chemistry, University of Pretoria, Pretoria, 0002, Republic of South Africa
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Ma C, Cheng CCW, Chan CTL, Chan RCT, Kwok WM. Remarkable effects of solvent and substitution on the photo-dynamics of cytosine: a femtosecond broadband time-resolved fluorescence and transient absorption study. Phys Chem Chem Phys 2016; 17:19045-57. [PMID: 26126728 DOI: 10.1039/c5cp02624e] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytosine (Cyt) among all the nucleic acid bases features the most complex and least understood nonradiative deactivation, a process that is crucially important for its photostability. Herein, the excited state dynamics of Cyt and a series of its N1- and C5-derivatives, including the full set of Cyt nucleosides and nucleotides in DNA and RNA and the nucleosides of 5-methyl cytosine, 5-methylcytidine and 2'-deoxy-5-methylcytidine, have been investigated in water and in methanol employing femtosecond broadband time-resolved fluorescence coupled with fs transient absorption spectroscopy. The results reveal remarkable state-specific effects of the substitution and solvent in tuning distinctively the timescales and pathways of the nonradiative decays. For Cyt and the N1-derivatives, the nonradiative deactivations occur in a common two-state process through three channels, two from the light-absorbing ππ* state with respectively the sub-picosecond (∼0.2 ps) and the picosecond (∼1.5 ps) time constant, and the third is due to an optically dark nπ* state with the lifetime ranging from several to hundreds of picoseconds depending on solvents and substitutions. Compared to Cyt, the presence of the ribose or deoxyribose moiety at the N1 position of N1-derivatives facilitates the formation of the nπ* at the sub-picosecond timescale and at the same time increases its lifetime by ∼4-6 times in both water and methanol. In sharp contrast, the existence of the methyl group at the C5 position of the C5-derivatives eliminates completely the sub-picosecond ππ* channel and the channel due to the nπ*, but on the other hand slows down the decay of the ππ* state which after relaxation exhibits a single time constant of ∼4.1 to ∼7.6 ps depending on solvents. Varying the solvent from water to methanol accelerates only slightly the decay of the ππ* state in all the compounds; while for Cyt and its N1-derivatives, this change of solvent also retards strongly the nπ* channel, prolongs its lifetime from such as ∼7.7 ps in water to ∼52 ps in methanol for Cyt and from ∼30 ps in water to ∼186 ps in methanol for deoxycytidine. The spectral signatures we obtained for the ππ* and the nπ* states allow unambiguous evidence for clarifying uncertainties in the excited states of Cyt and the derivatives. The results provide a unifying experimental characterization at an improved level of detail about the photophysics of Cyt and its analogues under biologically relevant conditions and may help in understanding the photostability as well as photo-damages of the bases and related DNAs.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzheng, Guangdong, P. R. China
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Thanassoulas A, Barthélémy P, Navailles L, Sigaud G. From nucleobases to nucleolipids: an ITC approach on the thermodynamics of their interactions in aqueous solutions. J Phys Chem B 2014; 118:6570-85. [PMID: 24911942 DOI: 10.1021/jp411459w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hybrid constructions based on nucleosides and lipophilic components, known as nucleolipids, have become an extremely interesting class of molecules, especially for their potential biomedical applications. In this matter, it seemed important to define the nature and estimate the strength of their interaction with polynucleotides by different ways. We report in this work a systematic investigation through isothermal titration calorimetry of the thermodynamics of the association and dissociation of adenine and thymine derivatives, not previously performed. Then we use the results obtained on these simple systems as a basis for comparison with the binding of phospholipids functionalized with adenosine and thymidine to polyadenylic or polyuridylic acids applying the same experimental technique.
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Ribeiro RF, Marenich AV, Cramer CJ, Truhlar DG. The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry. Phys Chem Chem Phys 2011; 13:10908-22. [PMID: 21566800 DOI: 10.1039/c0cp02784g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and π-π stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.
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Affiliation(s)
- Raphael F Ribeiro
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
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Singer M, Jäschke A. Reversibly photoswitchable nucleosides: synthesis and photochromic properties of diarylethene-functionalized 7-deazaadenosine derivatives. J Am Chem Soc 2010; 132:8372-7. [PMID: 20481531 DOI: 10.1021/ja1024782] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photochromic nucleosides were designed that combine the structural features and molecular recognition properties of nucleic acids with the light-sensitivity of diarylethenes. Target compounds 1a-c consist of a 7-deazaadenosine unit that is linked to a thiophene as the second aryl functionality via a 1,2-cyclopentenyl linker. These nucleoside analogues undergo a reversible electrocyclic rearrangement, generating strongly colored closed-ring isomers upon irradiation with UV-light, while exposure to light in the visible range triggers the cycloreversion to the colorless opened-ring form. UV-vis spectroscopy, HPLC, and (1)H NMR measurements revealed recognition of complementary thymidine and up to 97% conversion to the thermally stable closed-ring isomers after illumination with UV-light. The required wavelength for ring closure was found to vary depending on the substituents attached to the thiophene moiety. In a first design step, we used this important feature of diarylethenes to shift the switching wavelength from initially 300 nm (1a) to 405 nm (1cH(+)). In a second step, we generated a pair of orthogonal switches, differing enough in their respective switching wavelengths to be controlled independently in the same sample. Finally, a molecular switch was developed that showed both photochromism and acidichromism, thereby illustrating the possibility to gate the spectral properties to multiple stimuli. These new photochromic nucleosides represent useful building blocks for the generation of light-sensitive nucleic acids either by inducing conformational changes upon isomerization or by exploring the different spectral properties of the closed and opened isomers, for example, for use as reversible fluorescence quenchers.
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Affiliation(s)
- Marco Singer
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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Kyogoku Y, Lord RC, Rich A. The effect of substituents on the hydrogen bonding of adenine and uracil derivatives. Proc Natl Acad Sci U S A 2010; 57:250-7. [PMID: 16591461 PMCID: PMC335497 DOI: 10.1073/pnas.57.2.250] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y Kyogoku
- SPECTROSCOPY LABORATORY AND DEPARTMENT OF CHEMISTRY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
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Bangerter BW, Chan SI. A proton magnetic resonance study of the interaction of adenosine with polyuridylic Acid: evidence for both adenine-uracil base-stacking and base-pairing. Proc Natl Acad Sci U S A 2010; 60:1144-51. [PMID: 16591673 PMCID: PMC224893 DOI: 10.1073/pnas.60.4.1144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- B W Bangerter
- NOYES LABORATORY OF CHEMICAL PHYSICS, CALIFORNIA INSTITUTE OF TECHNOLOGY, PASADENA
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Kim SH, Rich A. The structure of a crystalline complex containing one phenobarbital molecule and two adenine derivatives. Proc Natl Acad Sci U S A 2010; 60:402-8. [PMID: 16591644 PMCID: PMC225061 DOI: 10.1073/pnas.60.2.402] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- S H Kim
- DEPARTMENT OF BIOLOGY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY, CAMBRIDGE, MASSACHUSETTS
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11
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Hopmann RFW. A Chemical Relaxation Study of Base Pairing through Self-Association of Uracil and its Hetero-Association with Adenine. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19730770113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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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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Zendlová L, Hobza P, Kabelác M. Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study. J Phys Chem B 2007; 111:2591-609. [PMID: 17302446 DOI: 10.1021/jp065418j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.
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Affiliation(s)
- Lucie Zendlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nAm. 2, 166 10 Prague 6, Czech Republic
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Abstract
Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo, Prague, Czech Republic
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Michas J, Paleos CM, Skoulios A, Weber P. Structural Study of Recognizable Adenine and Thymine Nucleobases Functionalized with Long Aliphatic Chains. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10587259408047186] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- J. Michas
- a NRC “Demokritos,” , Aghia Paraskevi , Attiki , Greece
| | - C. M. Paleos
- a NRC “Demokritos,” , Aghia Paraskevi , Attiki , Greece
| | - A. Skoulios
- b Groupe des Matériaux Organiques, Institut de Physique et Chimie des Matériaux , 6, rue Boussingault, Strasbourg , France
| | - P. Weber
- b Groupe des Matériaux Organiques, Institut de Physique et Chimie des Matériaux , 6, rue Boussingault, Strasbourg , France
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Affiliation(s)
- C. M. Paleos
- a National Center for Scientific Research “Demokritos,” , 15310 , Aghia Paraskevi , Athens , Greece
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Gmeiner WH, Anderson J, Sahasrabudhe P. NMR Studies Show Monomeric 5-Fluorouridine Forms Base Pairs of Increased Stability Compared with Uridine in Non-Aqueous Solvents. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/15257779408013224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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Slinchenko O, Rachkov A, Miyachi H, Ogiso M, Minoura N. Imprinted polymer layer for recognizing double-stranded DNA. Biosens Bioelectron 2005; 20:1091-7. [PMID: 15556353 DOI: 10.1016/j.bios.2004.06.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 06/12/2004] [Accepted: 06/14/2004] [Indexed: 11/17/2022]
Abstract
A method of preparing a thin polymer layer able to recognize double-stranded DNA (dsDNA) was developed by using 2-vinyl-4,6-diamino-1,3,5-triazine (VDAT) as a functional monomer for creating a DNA-imprinted polymer. The formation of hydrogen bonds between VDAT and A-T base pairs in dsDNA was confirmed by measuring the effects of VDAT on the melting point and the NMR and CD spectra of dsDNA. An imprinted polymer that can recognize dsDNA of the verotoxin gene was prepared by polymerizing VDAT, acrylamide, a crosslinking agent, and the template verotoxin dsDNA on a silanized glass surface. The specificity of this polymer layer for binding verotoxin dsDNA was investigated by using fluorescent-labelled dsDNAs. The fluorescence intensity of the polymer layer after binding verotoxin dsDNA was twice as high as after binding oligo(dG)-oligo(dC), indicating that verotoxin dsDNA was preferentially bound to the polymer imprinted with verotoxin dsDNA. The kinetics of verotoxin dsDNA binding to the imprinted polymer were analyzed by surface plasmon resonance measurements. The dissociation constant (KD) was low, of the order of 10(-9)M.
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Affiliation(s)
- Olena Slinchenko
- Research Center of Advanced Bionics, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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Affiliation(s)
- Toshio Itahara
- Department of Bioengineering, Faculty of Engineering, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan.
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Itahara T. Effect of a Polymethylene Chain on the Intramolecular Hydrogen Bond between Adenine and Thymine. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Pohorille A, Ross WS, Tinoco I. DNA dynamics in aqueous solution: opening the double helix. THE INTERNATIONAL JOURNAL OF SUPERCOMPUTER APPLICATIONS 2001; 4:81-96. [PMID: 11538365 DOI: 10.1177/109434209000400309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.
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Affiliation(s)
- A Pohorille
- University of California, Berkeley 94720, USA
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Sherer EC, Bono SJ, Shields GC. Further Quantum Mechanical Evidence that Difluorotoluene Does Not Hydrogen Bond. J Phys Chem B 2001. [DOI: 10.1021/jp010197x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edward C. Sherer
- Department of Chemistry, Hamilton College, 198 College Hill Rd., Clinton, New York 13323, and Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455
| | - Sam J. Bono
- Department of Chemistry, Hamilton College, 198 College Hill Rd., Clinton, New York 13323, and Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455
| | - George C. Shields
- Department of Chemistry, Hamilton College, 198 College Hill Rd., Clinton, New York 13323, and Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455
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Kypr J, Vorlícková M. Dimethylsulfoxide-stabilized conformer of guanine-adenine repeat strand of DNA. Biopolymers 2001; 62:81-4. [PMID: 11288056 DOI: 10.1002/bip.1000] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Circular dichroism spectroscopy and other methods are used to show that the addition of dimethylsulfoxide causes reversible folding of the (GA)(10) strand of DNA into an ordered single-stranded conformer. The ordered conformer melts in a cooperative way and it does not contain protonated adenine. The (TA)(10), (A)(20), and (G)(20) are all unstable in this conformer. To the best of our knowledge, this is the first known ordered conformer of DNA that is stabilized by dimethylsulfoxide. This conformer might be a DNA analog of the protein alpha helix, which is an interesting idea for thinking about the evolution of DNA.
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Affiliation(s)
- J Kypr
- Institute of Biophysics of the Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
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29
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Kabelác M, Hobza P. At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study. Chemistry 2001; 7:2067-74. [PMID: 11411979 DOI: 10.1002/1521-3765(20010518)7:10<2067::aid-chem2067>3.0.co;2-s] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.
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Affiliation(s)
- M Kabelác
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
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30
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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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31
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Molecular recognition in supramolecular structures formed by phosphatidylnucleosides-based amphiphiles. Colloids Surf A Physicochem Eng Asp 2000. [DOI: 10.1016/s0927-7757(99)00466-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Meeker K, Ellis AB. Adsorption of DNA Bases onto a Semiconductor Surface: Evidence for Surface-Mediated Promotion and Detection of Complementary Base Pair Formation. J Phys Chem B 2000. [DOI: 10.1021/jp9941099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kathleen Meeker
- Department of Chemistry, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Arthur B. Ellis
- Department of Chemistry, University of WisconsinMadison, Madison, Wisconsin 53706
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33
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Berti D, Barbaro P, Bucci I, Baglioni P. Molecular Recognition through H-Bonding in Micelles Formed by Dioctylphosphatidyl Nucleosides. J Phys Chem B 1999. [DOI: 10.1021/jp990504n] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Debora Berti
- Department of Chemistry, and C.S.G.I., University of Florence, Via G. Capponi 9, I-50121 Florence, Italy, and Istituto per lo Studio della Stereochimica ed Energetica dei Composti di Coordinazione, Consiglio Nazionale delle Ricerche, Via J.Nardi, 39, I-50132 Florence, Italy
| | - Pierluigi Barbaro
- Department of Chemistry, and C.S.G.I., University of Florence, Via G. Capponi 9, I-50121 Florence, Italy, and Istituto per lo Studio della Stereochimica ed Energetica dei Composti di Coordinazione, Consiglio Nazionale delle Ricerche, Via J.Nardi, 39, I-50132 Florence, Italy
| | - Ilaria Bucci
- Department of Chemistry, and C.S.G.I., University of Florence, Via G. Capponi 9, I-50121 Florence, Italy, and Istituto per lo Studio della Stereochimica ed Energetica dei Composti di Coordinazione, Consiglio Nazionale delle Ricerche, Via J.Nardi, 39, I-50132 Florence, Italy
| | - Piero Baglioni
- Department of Chemistry, and C.S.G.I., University of Florence, Via G. Capponi 9, I-50121 Florence, Italy, and Istituto per lo Studio della Stereochimica ed Energetica dei Composti di Coordinazione, Consiglio Nazionale delle Ricerche, Via J.Nardi, 39, I-50132 Florence, Italy
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Orozco M, Cubero E, Barril X, Colominas C, Luque FJ. Nucleic Acid Bases in Solution. COMPUTATIONAL MOLECULAR BIOLOGY 1999. [DOI: 10.1016/s1380-7323(99)80079-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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35
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Berti D, Baglioni P, Bonaccio S, Barsacchi-Bo G, Luisi PL. Base Complementarity and Nucleoside Recognition in Phosphatidylnucleoside Vesicles. J Phys Chem B 1998. [DOI: 10.1021/jp972954q] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL. The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 1997; 15:69-80. [PMID: 9283981 DOI: 10.1080/07391102.1997.10508947] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.
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Affiliation(s)
- V I Danilov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
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37
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Weisz K, Jähnchen J, Limbach HH. Low-Temperature NMR Studies on the Structure of Uridine Dimers. J Am Chem Soc 1997. [DOI: 10.1021/ja970769k] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Klaus Weisz
- Institut für Organische Chemie der Freien Universität Berlin Takustrasse 3, D-14195 Berlin, Germany
| | - Judith Jähnchen
- Institut für Organische Chemie der Freien Universität Berlin Takustrasse 3, D-14195 Berlin, Germany
| | - Hans-Heinrich Limbach
- Institut für Organische Chemie der Freien Universität Berlin Takustrasse 3, D-14195 Berlin, Germany
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38
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Kim I, Muto Y, Inoue M, Watanabe S, Kitamura A, Yokoyama S, Hosono K, Takaku H, Ono A, Kainosho M, Sakamoto H, Shimura Y. NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific [3-15N]uridine substitutions. Nucleic Acids Res 1997; 25:1565-9. [PMID: 9092663 PMCID: PMC146625 DOI: 10.1093/nar/25.8.1565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
It has been reported that a 183 residue fragment, consisting of the two RNA-binding domains (RBD1- RBD2) of the Drosophila melanogster Sex-lethal (Sxl) protein, strongly binds an oligonucleotide of the target RNA sequence (5'-GUUUUUUUUC-3') that regulates alternative splicing, and forms four or five hydrogen bonds with the imino groups of the RNA. In the present study, we used site-directed mutagenesis to improve the solubility of the didomain fragment of Sxl, and confirmed that this mutant fragment forms hydrogen bonds with the target RNA in the same manner as that of the wild-type fragment. The mutant fragment was shown to bind the cognate RNA sequences GUUUUUUUUC and AUUUUUUUUC more tightly than UUUUUUUUC. By using a [3-15N]uridine phosphoramidite, we synthesized a series of15N-labeled target RNAs, in which one of the uridine residues was specifically replaced by [3-15N]uridine. By observing the imino1H-15N coupling of the labeled uridine residue, we assigned all four of the hydrogen-bonded imino protons to U1, U2, U5 and U6, respectively, of the target RNA. The imino protons of U2 and U6 exhibited nuclear Overhauser effects with aliphatic protons of the protein. All these results indicate that the A/G, U1, U2, U5 and U6 residues in the target sequence of (G/A)UUUUUUUU are specifically recognized by the two RNA-binding domains of the Sxl protein.
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Affiliation(s)
- I Kim
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan
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39
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40
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Schröder G, Sabat M, Baxter I, Kozelka J, Lippert B. cis-[Pt(NH3)2(9-MeA-N7)(9-EtGH-N7)](PF6)2·1.5H2O (9-MeA = 9-Methyladenine; 9-EtGH = 9-Ethylguanine): A Right-Handed Helicoidal Model Compound for the Intrastrand A,G Cross-Link in Duplex DNA. Inorg Chem 1997. [DOI: 10.1021/ic9611296] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guy Schröder
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, URA 400 CNRS, Université René Descartes, F-75270 Paris Cedex 06, France
| | - Michal Sabat
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, URA 400 CNRS, Université René Descartes, F-75270 Paris Cedex 06, France
| | - Ivan Baxter
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, URA 400 CNRS, Université René Descartes, F-75270 Paris Cedex 06, France
| | - Jirí Kozelka
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, URA 400 CNRS, Université René Descartes, F-75270 Paris Cedex 06, France
| | - Bernhard Lippert
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, URA 400 CNRS, Université René Descartes, F-75270 Paris Cedex 06, France
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41
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Newby CS, Coke M. The preparation, characterisation and solubility characteristics of a hydrogen-bonded complex between acyclovir and cytosine. J Pharm Biomed Anal 1996; 15:39-47. [PMID: 8895075 DOI: 10.1016/0731-7085(96)01820-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Acyclovir and cytosine form a Crick-Watson hydrogen-bonded complex in dimethylsulphoxide (DMSO). For the complex formation Acyclovir + cytosine reversible complex the equilibrium constant, K, was determined using NMR spectroscopy to be K = 1.00 +/- 0.07 mol-1 dm3 at 21 degrees C in DMSO. The acyclovir-cytosine complex was formed in DMSO, then diluted with octan-1-ol to leave a 95.3% v/v octan-1-ol/47% v/v DMSO solution, and demonstrated a 12-fold increase in the saturated solubility of acyclovir. This was compared to a solution of acyclovir alone treated in the same manner. This suggests that a complex species of acyclovir with cytosine has a greater lipophilic character than acyclovir alone. Attempts to increase the octan-1-ol/water partition coefficient for acyclovir produced no significant increase with the presence of cytosine. It was argued that no complexation would occur in water due to the rapid exchange of the protons that are involved in the hydrogen-bonded complex. Experiments to isolate the solid acyclovir-cytosine Crick-Watson hydrogen-bonded complex were performed. Spectra and T1 relaxation times obtained during subsequent solid-state 13C NMR experiments provided evidence that a solid complex can be isolated.
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Affiliation(s)
- C S Newby
- Reckitt & Colman Pharmaceuticals, Hull, UK
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42
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Schreiber A, Lüth MS, Erxleben A, Fusch EC, Lippert B. Bis(purine) Complexes of trans-a2PtII: Preparation and X-ray Structures of Bis(9-methyladenine) and Mixed 9-Methyladenine, 9-Methylguanine Complexes and Chemistry Relevant to Metal-Modified Nucleobase Triples and Quartets. J Am Chem Soc 1996. [DOI: 10.1021/ja953595k] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- André Schreiber
- Contribution from the Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany
| | - Marc S. Lüth
- Contribution from the Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany
| | - Andrea Erxleben
- Contribution from the Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany
| | - Edda C. Fusch
- Contribution from the Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany
| | - Bernhard Lippert
- Contribution from the Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany
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43
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Šponer J, Leszczynski J, Hobza P. Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952760f] [Citation(s) in RCA: 348] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
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44
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Santos MA, Ferreira T, Esteves MA, Drew MG, Beland FA, Marques MM. Molecular recognition of guanosine and 2-acetylaminofluorene-modified guanosine. A comparative study. Supramol Chem 1995. [DOI: 10.1080/10610279508233951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Paleos CM, Tsiourvas D. Bildung thermotroper Flüssigkristalle durch intermolekulare Wasserstoffbrückenbindungen. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951071605] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Strazewski P. Calculating the Thermodynamics of Weakly Hydrogen-Bonded Complexes from Heteronuclear NMR Data: Base-pairing stabilities of a 5-methyl(15N2)[O2,O4-17O2]uridine (= (15N2)[O2,O4-17O2]ribosylthymine) derivative, and structural implications. Helv Chim Acta 1995. [DOI: 10.1002/hlca.19950780508] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Barawkar D, Kumar R, Ganesh K. Effect of C5-amino substituent on 2′-deoxyuridine base pairing with 2′-deoxyadenosine: investigation by 1H and 13C NMR spectroscopy. Tetrahedron 1992. [DOI: 10.1016/s0040-4020(01)86598-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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48
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MacPhail RA, Williams LD, Jones DA, Shaw BR. Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization. J Biomol Struct Dyn 1992; 9:881-98. [PMID: 1524704 DOI: 10.1080/07391102.1992.10507964] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This report describes an infrared (IR) spectroscopic study of a model cytosine-guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O6-methylguanosine (O6MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35,724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw,J.Am.Chem.Soc. 112,829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent, but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C = O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O6-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.
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Affiliation(s)
- R A MacPhail
- Department of Chemistry, Duke University, Durham, NC 27706
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49
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Oida T, Humphreys WG, Guengerich FP. Preparation and characterization of oligonucleotides containing S-[2-(N7-guanyl)ethyl]glutathione. Biochemistry 1991; 30:10513-22. [PMID: 1657147 DOI: 10.1021/bi00107a021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
S-[2-(N7-Guanyl)ethyl]glutathione is the major adduct derived from modification of DNA with 1,2-dibromoethane in biological systems and is postulated to be a mutagenic lesion [Humphreys, W. G., Kim, D.-H., Cmarik, J. L., Shimada, T., & Guengerich, F. P. (1990) Biochemistry 29, 10342-10350]. Oligonucleotides containing this modified base were prepared by treatment of oligonucleotides with S-(2-chloroethyl)glutathione and purified by chromatography. The self-complementary oligonucleotide d(ATGCAT), when thus modified at the single guanine, appeared to associate with itself as judged by UV measurements, but CD and NMR measurements indicated a lack of hybridization, with a decrease in the melting temperature of greater than 10 degrees C. The same lack of self-association was noted when d(ATGCAT) was modified to contain an N-acetyl-S-[2-(N7-guanyl)ethyl]cysteine methyl ester moiety. The oligomer d-(C1A2T3G4C5C6T7) was modified to contain a single S-[2-(N7-guanyl)ethyl]glutathione moiety at the central position, and UV, CD, and 1H NMR studies indicated that this oligomer hybridized to its normal complement d(A8G9G10C11A12T13G14), although the binding was considerably weakened by adduction (imino proton NMR spectroscopy in the presence of H2O indicated that the hydrogen bond signals seen in the oligomer were all broadened upon modification). All proton resonances were identified using two-dimensional 1H NMR spectroscopy. Adduct formation affected the chemical shifts of the base and 1', 2', and 2" protons of T3 and C5, the 2" proton of C6, and the 8 and 1' protons of C11, while little effect was observed on other protons. No cross-peaks were detected between the glutathione and oligomer moieties in two-dimensional nuclear Overhauser enhanced NMR studies. These results suggest that a rather local structural perturbation occurs in the DNA oligomer upon modification and that the glutathione moiety appears to be relatively unperturbed by its placement in the duplex. When the cytosine in the normal d(AGGCATG) complement to d-(CATGCCT) was changed to each of the other three potential bases at the central position, no hybridization with the oligomer d(CATGCCT) containing S-[2-(N7-guanyl)ethyl]glutathione was detected. We conclude that these N7-guanyl derivatives destabilize hybridization and that bases other than cytosine do not appear to show preferential thermodynamic bonding to these adducts, at least in the sequences examined to date.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- T Oida
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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50
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Abstract
Spectrophotometric and radioactive techniques were used to measure the water solubility of retinaldehyde, retinol (vitamin A), and retinoic acid under physiological conditions. Hydration decreases the molar extinction coefficient of these substances and shifts their absorption peak bathochromically (10 nm for retinal and approximately 1 nm for the rest). We find their solubility to be about 0.1 microM at room temperature, pH 7.3 (with experimental values being 0.11 microM for retinaldehyde, 0.06 microM for retinol, and 0.21 microM for retinoic acid). To prevent oxidative degradation of retinol, which is the most labile retinoid, our argon-saturated buffer solutions contained physiological levels of ascorbate or alpha-tocopherol. To the best of our knowledge, water solubility of these compounds has not yet been previously reported. Although the measured solubilities are relatively low, they are significant and may account for the movement of retinoids through the aqueous phase as observed by others during exchange with binding proteins and during intervesicular transfer in the absence of binding proteins. Diffusion of uncomplexed retinoids through the aqueous phase can be a major pathway for transport over subcellular distances.
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Affiliation(s)
- E Z Szuts
- Laboratory of Sensory Physiology, Marine Biological Laboratory, Woods Hole, Massachusetts 02543
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