1
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Reveguk ZV, Khoroshilov EV, Sharkov AV, Pomogaev VA, Buglak AA, Kononov AI. Excited States in Single-Stranded and i-Motif DNA with Silver Ions. J Phys Chem B 2024. [PMID: 38657136 DOI: 10.1021/acs.jpcb.4c01127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.
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Affiliation(s)
- Zakhar V Reveguk
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9 , 199034 St. Petersburg, Russia
| | - Evgeny V Khoroshilov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991 Moscow, Russia
| | - Andrey V Sharkov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991 Moscow, Russia
| | - Vladimir A Pomogaev
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9 , 199034 St. Petersburg, Russia
- Department of Physics, Tomsk State University, Tomsk 634050, Russia
| | - Andrey A Buglak
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9 , 199034 St. Petersburg, Russia
| | - Alexei I Kononov
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9 , 199034 St. Petersburg, Russia
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2
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Kohl FR, Zhang Y, Charnay AP, Martínez-Fernández L, Kohler B. Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA. J Chem Phys 2021; 153:105104. [PMID: 32933288 DOI: 10.1063/5.0020463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC20, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC20 and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC20 silver ion complex that is not seen in dC20 in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.
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Affiliation(s)
- Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Aaron P Charnay
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
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3
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Sadeghan AA, Soltaninejad H, Dadmehr M, Hamidieh AA, Asadollahi MA, Hosseini M, Ganjali MR, Hosseinkhani S. Fluorimetric detection of methylated DNA of Sept9 promoter by silver nanoclusters at intrastrand 6C-loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119081. [PMID: 33128948 DOI: 10.1016/j.saa.2020.119081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Methylation of DNA at carbon 5 of cytosines is the most common epigenetic modification of human genome. Due to its critical role in many normal cell processes such as growth and development, any aberrant methylation pattern in a particular locus may lead to abnormal functions and diseases such as cancer. Development of methods to detect methylation state of DNA which may eliminate labor-intensive chemical or enzymatic treatments has received considerable attention in recent years. Herein, we report a DNA methylation detection procedure based on fluorescence turn-on strategy. Target sequence was selected from Sept9 promoter region that has been reported as one of the most frequently methylated sites in colorectal cancer. Probe DNA was designed to be complementary to this sequence with an additional six cytosines in the middle to form an internal loop to host silver nanoclusters. The fluorescence intensity of the synthesized silver nanoclusters with the duplexes of probe-non-methylated target was significantly different from that of probe-methylated target. The fluorescence enhanced with increasing the methylated DNA concentration with a linear relation in the range of 1.0 × 10-8 M to 5.0 × 10-7 M with the detection limit of 8.2 × 10-9 M, and quenched with non-methylated ones. The method was very specific in the presence of non-complementary sequences with maximum similarity of 40%. Circular dichroism spectra indicated that silver ions significantly affected the structure of methylated and non-methylated DNA into different extents which could further influence the nanocluster fluorescence. Finally, a method was introduced to meet the concerns in the applicability of the proposed method in real situation.
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Affiliation(s)
- Amir Amiri Sadeghan
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Soltaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | | | - Amir Ali Hamidieh
- Pediatric Cell Therapy Research Center, Tehran University of Medical Scienses, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular - Cellular Sciences Institute, Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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4
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Guo M, Huang B, Yi Q, Luo Z. Gas-phase synthesis and deposition of metal-bipyridine complex [M-bpy 1-2] + (M = Ag, Cu). Phys Chem Chem Phys 2021; 23:16334-16340. [PMID: 34313273 DOI: 10.1039/d1cp02399c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controllable synthesis of organometallic clusters in the gas phase is a topic of reasonable interest with precisely tunable properties depending on sizes, compositions, and intra-cluster charge-transfer interactions. Here, we have prepared small Agn+ and Cun+ clusters by using a customized magnetron sputtering (MagS) source and observed the gas-phase reactions with 2,2'-bipyridine. It is found that the small silver and copper clusters readily react with bipyridine and form products of [M-bpy1-2]+ (M = Ag, Cu). Quantum chemistry calculations reveal that the bipyridine in both [Ag-bpy1-2]+ and [Cu-bpy1-2]+ takes on cis-conformation with altered N-C-C-N dihedral angles, which is in contrast to the trans-conformation of a free 2,2'-bipyridine molecule itself. In order to unveil the principle of conformational transition, we have fully studied the interactions between the nitrogen atoms of bipyridine and the cationic Ag+ and Cu+, calculated the donor-acceptor orbital overlaps, and analyzed the correlation of their frontier molecular orbital energy levels. Furthermore, by using a soft-landing strategy, we have managed to deposit the [Cu-bpy2]+ complex onto the glass substrates coated with Ag nanoparticles, and recorded the surface-enhanced Raman scattering spectra.
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Affiliation(s)
- Mengdi Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
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5
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Taccone MI, Cruz-Ortiz AF, Dezalay J, Soorkia S, Broquier M, Grégoire G, Sánchez CG, Pino GA. UV Photofragmentation of Cold Cytosine–M+ Complexes (M+: Na+, K+, Ag+). J Phys Chem A 2019; 123:7744-7750. [DOI: 10.1021/acs.jpca.9b06495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martín I. Taccone
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Andrés F. Cruz-Ortiz
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Michel Broquier
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de I’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Cristián G. Sánchez
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Gustavo A. Pino
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
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6
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Sadeghan AA, Soltaninejad H, Hosseinkhani S, Hosseini M, Ganjali MR, Asadollahi MA. Fluorescence enhancement of silver nanocluster at intrastrand of a 12C-loop in presence of methylated region of sept 9 promoter. Anal Chim Acta 2018; 1038:157-165. [DOI: 10.1016/j.aca.2018.07.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 02/06/2023]
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7
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Chen X, Makkonen E, Golze D, Lopez-Acevedo O. Silver-Stabilized Guanine Duplex: Structural and Optical Properties. J Phys Chem Lett 2018; 9:4789-4794. [PMID: 30079734 DOI: 10.1021/acs.jpclett.8b01908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag+-mediated guanine duplex with two nucleobases per strand, G2-Ag2+-G2. We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G2-Ag2+-G2 is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.
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Affiliation(s)
- Xi Chen
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
| | - Esko Makkonen
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
| | - Dorothea Golze
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
- Department of Electrical Engineering and Automation , Aalto University , P.O. Box 13500, 00076 Aalto , Finland
| | - Olga Lopez-Acevedo
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales , Universidad de Antioquia UdeA ; Calle 70 No. 52-21 , 050010 Medellín , Colombia
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8
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Cruz-Ortiz AF, Rossa M, Berthias F, Berdakin M, Maitre P, Pino GA. Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H + Pair. J Phys Chem Lett 2017; 8:5501-5506. [PMID: 29064704 DOI: 10.1021/acs.jpclett.7b02140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gas phase protonated guanine-cytosine (CGH+) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH+ pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm-1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.
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Affiliation(s)
- Andrés F Cruz-Ortiz
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Maximiliano Rossa
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Francis Berthias
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Matías Berdakin
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
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9
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Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA Films Containing the Artificial Nucleobase Imidazole Mediate Charge Transfer in a Silver(I)-Responsive Way. Angew Chem Int Ed Engl 2017; 56:6098-6102. [DOI: 10.1002/anie.201700248] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Current address: Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
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10
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Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA-Filme mit der künstlichen Nucleobase Imidazol vermitteln Ladungstransfer in einer Silber(I)-abhängigen Weise. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
- Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
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11
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UV fragmentation and ultrafast dynamics of trinuclear silver/1-methylthymine and silver/1-methyluracil metal-base pairs in an ion trap. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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MacAleese L, Hermelin S, Hage KE, Chouzenoux P, Kulesza A, Antoine R, Bonacina L, Meuwly M, Wolf JP, Dugourd P. Sequential Proton Coupled Electron Transfer (PCET): Dynamics Observed over 8 Orders of Magnitude in Time. J Am Chem Soc 2016; 138:4401-7. [DOI: 10.1021/jacs.5b12587] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Luke MacAleese
- Institut
Lumière Matière, UMR5306 Université Claude Bernard
Lyon1-CNRS, Université de Lyon 69622 Villeurbanne
cedex, France
| | - Sylvain Hermelin
- Group
of Applied Physics (GAP) Biophotonics, Université de Genève, Chemin
de Pinchat 22, CH-1211 Geneva, Switzerland
| | - Krystel El Hage
- Department
of Chemistry, University of Basel, Klingelbergstr 80, CH-4056 Basel, Switzerland
| | - Pierre Chouzenoux
- Institut
Lumière Matière, UMR5306 Université Claude Bernard
Lyon1-CNRS, Université de Lyon 69622 Villeurbanne
cedex, France
| | - Alexander Kulesza
- Institut
Lumière Matière, UMR5306 Université Claude Bernard
Lyon1-CNRS, Université de Lyon 69622 Villeurbanne
cedex, France
| | - Rodolphe Antoine
- Institut
Lumière Matière, UMR5306 Université Claude Bernard
Lyon1-CNRS, Université de Lyon 69622 Villeurbanne
cedex, France
| | - Luigi Bonacina
- Group
of Applied Physics (GAP) Biophotonics, Université de Genève, Chemin
de Pinchat 22, CH-1211 Geneva, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstr 80, CH-4056 Basel, Switzerland
| | - Jean-Pierre Wolf
- Group
of Applied Physics (GAP) Biophotonics, Université de Genève, Chemin
de Pinchat 22, CH-1211 Geneva, Switzerland
| | - Philippe Dugourd
- Institut
Lumière Matière, UMR5306 Université Claude Bernard
Lyon1-CNRS, Université de Lyon 69622 Villeurbanne
cedex, France
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13
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Gao J, Berden G, Rodgers MT, Oomens J. Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals. Phys Chem Chem Phys 2016; 18:7269-77. [PMID: 26894838 DOI: 10.1039/c6cp00234j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.
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Affiliation(s)
- Juehan Gao
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.
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14
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Taccone MI, Féraud G, Berdakin M, Dedonder-Lardeux C, Jouvet C, Pino GA. Communication: UV photoionization of cytosine catalyzed by Ag+. J Chem Phys 2015; 143:041103. [DOI: 10.1063/1.4927469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Martín I. Taccone
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Geraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Matías Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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15
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Silver (I) as DNA glue: Ag(+)-mediated guanine pairing revealed by removing Watson-Crick constraints. Sci Rep 2015; 5:10163. [PMID: 25973536 PMCID: PMC4431418 DOI: 10.1038/srep10163] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/01/2015] [Indexed: 12/23/2022] Open
Abstract
Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag+ is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg2+. In contrast to prior studies of Ag+ incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag+-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag+ bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag+-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.
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16
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Berdakin M, Steinmetz V, Maitre P, Pino GA. On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory. Phys Chem Chem Phys 2015; 17:25915-24. [DOI: 10.1039/c5cp02221e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single water molecule hydration stabilizes two quasi-isoenergetic complexes of cytosine⋯Ag+.
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Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Philippe Maitre
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
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17
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Sen A, Dessent CEH. Communication: Photoactivation of nucleobase bound platinumIImetal complexes: Probing the influence of the nucleobase. J Chem Phys 2014; 141:241101. [DOI: 10.1063/1.4904259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Ananya Sen
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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