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Switzer C. A DNA tetraplex composed of two continuously hydrogen-bonded helical arrays of isoguanine (isoG). Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Aparicio F, Mayoral MJ, Montoro-García C, González-Rodríguez D. Guidelines for the assembly of hydrogen-bonded macrocycles. Chem Commun (Camb) 2019; 55:7277-7299. [DOI: 10.1039/c9cc03166a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.
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Affiliation(s)
- F. Aparicio
- Nanostructured Molecular Systems and Materials (MSMn) group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - M. J. Mayoral
- Nanostructured Molecular Systems and Materials (MSMn) group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - C. Montoro-García
- Nanostructured Molecular Systems and Materials (MSMn) group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - D. González-Rodríguez
- Nanostructured Molecular Systems and Materials (MSMn) group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
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3
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Shumayrikh N, Huang YC, Sen D. Heme activation by DNA: isoguanine pentaplexes, but not quadruplexes, bind heme and enhance its oxidative activity. Nucleic Acids Res 2015; 43:4191-201. [PMID: 25824944 PMCID: PMC4417173 DOI: 10.1093/nar/gkv266] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 02/13/2015] [Accepted: 03/17/2015] [Indexed: 12/31/2022] Open
Abstract
Guanine-rich, single-stranded, DNAs and RNAs are able to fold to form G-quadruplexes that are held together by guanine base quartets. G-quadruplexes are known to bind ferric heme [Fe(III)-protoporphyrin IX] and to strongly activate such bound hemes toward peroxidase (1-electron oxidation) as well as oxygenase/peroxygenase (2-electron oxidation) activities. However, much remains unknown about how such activation is effected. Herein, we investigated whether G-quadruplexes were strictly required for heme activation or whether related multi-stranded DNA/RNA structures such as isoguanine (iG) quadruplexes and pentaplexes could also bind and activate heme. We found that iG-pentaplexes did indeed bind and activate heme comparably to G-quadruplexes; however, iG-quadruplexes did neither. Earlier structural and computational studies had suggested that while the geometry of backbone-unconstrained iG-quintets templated by cations such as Na(+) or NH4 (+) was planar, that of iG-quartets deviated from planarity. We hypothesize that the binding as well as activation of heme by DNA or RNA is strongly supported by the planarity of the nucleobase quartet or quintet that interacts directly with the heme.
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Affiliation(s)
- Nisreen Shumayrikh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yu Chuan Huang
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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Emilie-Laure Z. Large mixed complexes involving uracil, cytosine, thymine and/or 1-methyl uracil around Ca2+ ions: an electrospray ionization/MS study. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:438-447. [PMID: 23584937 DOI: 10.1002/jms.3175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Abstract
We investigated the possible formation of mixed B(n)B'(n')Ca(2+) complexes where B and B' are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1-methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers.
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Affiliation(s)
- Zins Emilie-Laure
- Laboratoire de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, CNRS, UMR 7075, 4 place Jussieu, F-75005, Paris, France
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Jiang D, Seela F. Oligonucleotide duplexes and multistrand assemblies with 8-aza-2'-deoxyisoguanosine: a fluorescent isoG(d) shape mimic expanding the genetic alphabet and forming ionophores. J Am Chem Soc 2010; 132:4016-24. [PMID: 20192268 DOI: 10.1021/ja910020n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
8-Aza-2'-deoxyisoguanosine (4) is the first fluorescent shape mimic of 2'-deoxyisoguanosine (1a); its fluorescence is stronger in alkaline medium than under neutral conditions. Nucleoside 4, which was synthesized from 8-aza-2'-deoxyguanosine via a 4,6-diamino intermediate after selective deamination, was incorporated in oligodeoxyribonucleotides using phosphoramidite 11. Duplexes with 4 x m(5)iC(d) (5-methyl-2'-deoxyisocytidine) base pairs are more stable than those incorporating dG-dC pairs, thereby expanding the genetic alphabet by a fluorescent orthogonal base pair. As demonstrated by T(m) measurements, the base pair stability decreases in the order m(5)iC(d) x 4 >> dG x 4 > dT x 4 > or = dC x 4 >> dA x 4. A better base pairing selectivity of 4 against the canonical nucleosides dT, dC, dA, and dG is observed than for the degenerated base pairing of 1a. The base pair stability changes can be monitored by nucleobase anion fluorescence sensing. The fluorescence change correlates to the DNA base pair stability. Oligonucleotide 5'-d(T(4)4(4)T(4)) (22), containing short runs of nucleoside 4, forms stable multistranded assemblies (ionophores) with K(+) in the central cavity. They are quite stable at elevated temperature but are destroyed at high pH value.
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Affiliation(s)
- Dawei Jiang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Zins EL, Pepe C, Schröder D. Decameric uracil complexes around Li+. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:740-749. [PMID: 20564575 DOI: 10.1002/jms.1764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings.
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Affiliation(s)
- Emilie-Laure Zins
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 16610 Prague 6, Czech Republic.
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Pierce SE, Wang J, Jayawickramarajah J, Hamilton AD, Brodbelt JS. Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats. Chemistry 2010; 15:11244-55. [PMID: 19746468 DOI: 10.1002/chem.200901047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.
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Affiliation(s)
- Sarah E Pierce
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
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Zins EL, Rochut S, Pepe C. Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:813-820. [PMID: 19199276 DOI: 10.1002/jms.1561] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters.
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Affiliation(s)
- Emilie-Laure Zins
- Laboratoire de Dynamique, Interactions et Réactivité, Université Pierre et Marie Curie, 4 place Jussieu, 75 005 Paris, CNRS, UMR 7075, France.
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Zins EL, Rochut S, Pepe C. Theoretical and experimental studies of cationized uracil complexes in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:40-49. [PMID: 18698558 DOI: 10.1002/jms.1468] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.
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Affiliation(s)
- Emilie-Laure Zins
- Université Pierre et Marie Curie, Paris 6, Laboratoire de Dynamique, Interactions et Réactivité, CNRS, UMR 7075, Paris, France.
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Meng F, Zhao X. Theoretical study of inosine tetrad and octamer interacting with alkali metal ions. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Gu J, Wang J, Leszczynski J. Isoguanine octamer: From bowl to ball. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gu J, Wang J, Leszczynski J. Iso-guanine quintet complexes coordinated by mono valent cations (Na+, K+, Rb+, and Cs+). J Comput Chem 2007; 28:1790-5. [PMID: 17394242 DOI: 10.1002/jcc.20623] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The geometric structures, the interaction energies, the vibrational characteristics, and the electronic structures of the complexes of the isoguanine (isoG) quintet coordinated with mono valent cations (Na(+), K(+), Rb(+), and Cs(+)) have been studied based on the nonplanar models. The geometry of the local minimum structure of the Na(+)-isoG quintet complex deviates significantly from the planar structure. The geometric characteristics of the Na(+)-isoG quintet complex support the experimental findings that Na(+) is unlikely to induce the formation of the isoG quintet-based pentaplexes. Similar to the guanine tetraplexes, the ionic selectivity of the isoG quintet-based pentaplexes is largely dominated by the hydration energy of the cations. After hydration correction, the positive value of the free energy difference for the formation of the Na(+)-isoG quintet complex (DeltaG(f)) suggests that the isoG quintet is unable to capture the hydrated Na(+). The negative values of DeltaG(f) for the K(+) and Rb(+) complexes implies that both ions have the tendency to be inserted into the isoG pentaplexes. This study suggests that, to elucidate the high Cs(+) selectivity of isoG pentaplexes, it is necessary to extend the model from the isoG quintet to the isoG decamer.
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Affiliation(s)
- Jiande Gu
- Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
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Meyer M, Steinke T, Sühnel J. Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions. J Mol Model 2006; 13:335-45. [PMID: 17013632 DOI: 10.1007/s00894-006-0148-5] [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] [Received: 12/01/2005] [Accepted: 06/26/2006] [Indexed: 11/30/2022]
Abstract
Isoguanine tetraplexes and pentaplexes contain two or more stacked polyads with intercalating metal ions. We report here the results of a density functional study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na(+), K(+) and Rb(+) ions at the B3LYP level. In comparison to single polyad metal ion complexes, there is a trend towards increased non-planarity of the polyads in the sandwich complexes. In general, the pentad sandwiches have relatively planar polyad structures, whereas the tetrad complexes contain highly non-planar polyad building blocks. As in other sandwich complexes and in metal ion complexes with single polyads, the metal ion-base interaction energy plays an essential role. In iG sandwich structures, this interaction energy is slightly larger than in the corresponding guanine sandwich complexes. Because the base-base interaction energy is even more increased in passing from guanine to isoguanine, the isoguanine sandwiches are thus far the only examples where the base-base interaction energy is larger than the base-metal ion interaction energy. Stacking interactions have been studied in smaller models consisting of two bases, retaining the geometry from the complete complex structures. From the data obtained at the B3LYP and BH&H levels and with Møller-Plesset perturbation theory, one can conclude that the B3LYP method overestimates the repulsion in stacked base dimers. For the complexes studied in this work, this is only of minor importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal ion preference K(+) approximately Rb(+) > Na(+) is found for tetrad complexes. On the other hand, for pentads the ordering is Rb(+) > K(+) > Na(+). In the latter case experimental data are available that agree with this prediction.
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Affiliation(s)
- Michael Meyer
- Revotar Biopharmaceuticals AG, Neuendorfstrasse 24a, 16761, Hennigsdorf, Germany.
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Meyer M, Hocquet A, Sühnel J. Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J Comput Chem 2005; 26:352-64. [PMID: 15648098 DOI: 10.1002/jcc.20176] [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: 01/30/2023]
Abstract
Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum-chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G-tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G-, C-, U-, and T-tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base-base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense.
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Affiliation(s)
- Michael Meyer
- Revotar Biopharmaceuticals AG, Neuendorfstrasse 24a, D-16761 Hennigsdorf, Germany.
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Wang H, Meng F, Xu W, Liu C. The effects of incorporating 2,4-dithiouracil into uracil tetrad: a theoretical study. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Meng F, Xu W, Liu C. Theoretical study of incorporating 6-thioguanine into a guanine tetrad and their influence on the metal ion–guanine tetrad. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.03.128] [Citation(s) in RCA: 5] [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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