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Bhai S, Ganguly B. Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study. RSC Adv 2020; 10:40969-40982. [PMID: 35519218 PMCID: PMC9057718 DOI: 10.1039/d0ra07526d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/26/2020] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg2+-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model DTTD (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The DTTTTD mispair dimer is more energetically stable by ∼36.0 kcal mol−1 than the corresponding canonical DATGCD base pairs. The Hg⋯Hg metallophilic interaction was observed with the DTTTTD mispair and not the canonical base pairs. The DATGCD (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg2+ ion. The DTTTTD mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger Vmin value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg2+ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as DTTTTP (thymine–thymine dimer model with hybrid DNA and PNA backbone) and PTTTTP (thymine–thymine dimer model with PNA backbone). The calculated results showed that the PTTTTP PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for DTTTTD and PTTTTP at the B3LYP-D3/6-31G* level of theory showed that PTTTTP is ∼3.0 kcal mol−1 more stable than DTTTTD. The metallophilic interaction of Hg2+ ions in the PTTTTP mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in DTTTTD. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of PTTTTP compared to the corresponding DTTTTD and can be a signature to identify the formation of metal-mediated nucleic acid systems. Hg2+-mediated PNA–PNA mispair duplex (PTTTTP) is more energetically favoured compared to DNA–DNA mispair duplex (DTTTTD).![]()
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Affiliation(s)
- Surjit Bhai
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
- Academy of Scientific and Innovative Research (AcSIR)
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
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2
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Farrokhzadeh A, Akher FB, Honarparvar B, Van Heerden FR. Modulation of the induced π-stacking interactions between the active site cytosine moiety of HIV-integrase and inhibitors containing substituted-methylbenzene: Physical nature of the positional and substituent effects. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.126950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Mandal S, Hebenbrock M, Müller J. A dinuclear silver(I)-mediated base pair in DNA formed from 1, N 6 -ethenoadenine and thymine. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.05.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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4
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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5
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Šebesta F, Brela MZ, Diaz S, Miranda S, Murray JS, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A, Burda JV. The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study. J Comput Chem 2017; 38:2680-2692. [PMID: 28925001 DOI: 10.1002/jcc.24911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Silvia Diaz
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Sebastian Miranda
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
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6
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Hensel S, Eckey K, Scharf P, Megger N, Karst U, Müller J. Excess Electron Transfer through DNA Duplexes Comprising a Metal‐Mediated Base Pair. Chemistry 2017; 23:10244-10248. [DOI: 10.1002/chem.201702241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Susanne Hensel
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Kevin Eckey
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Philipp Scharf
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Nicole Megger
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
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7
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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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8
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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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9
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The effect of chemical modification of DNA base on binding of HgII and AgI in metal-mediated base pairs. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Dairaku T, Furuita K, Sato H, Kondo Y, Kojima C, Ono A, Tanaka Y. Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By (1)H NMR Spectroscopy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:877-900. [PMID: 26576739 DOI: 10.1080/15257770.2015.1088160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently, we discovered novel silver(I)-mediated cytosine-cytosine base pair (C-Ag(I)-C) in DNA duplexes. To understand the properties of these base pairs, we searched for a DNA sequence that can be used in NMR structure determination. After extensive sequence optimizations, a non-symmetric 15-base-paired DNA duplex with a single C-Ag(I)-C base pair flanked by 14 A-T base pairs was selected. In spite of its challenging length for NMR measurements (30 independent residues) with small sequence variation, we could assign most non-exchangeable protons (254 out of 270) and imino protons for structure determination.
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Affiliation(s)
- Takenori Dairaku
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan
| | - Kyoko Furuita
- b Institute for Protein Research, Osaka University , Suita , Osaka , Japan
| | - Hajime Sato
- c Bruker BioSpin K.K. , Yokohama , Kanagawa , Japan
| | - Yoshinori Kondo
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan
| | - Chojiro Kojima
- b Institute for Protein Research, Osaka University , Suita , Osaka , Japan
| | - Akira Ono
- d Department of Material & Life Chemistry , Kangawa University, Kanagawa-ku , Yokohama , Kanagawa , Japan
| | - Yoshiyuki Tanaka
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan.,e Laboratory of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University , Yamashiro-cho , Tokushima , Japan
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11
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Park C, Jang K, Lee S, You J, Lee S, Ha H, Yun K, Kim J, Lee H, Park J, Na S. A highly sensitive, direct and label-free technique for Hg(2+) detection using Kelvin probe force microscopy. NANOTECHNOLOGY 2015; 26:305501. [PMID: 26152847 DOI: 10.1088/0957-4484/26/30/305501] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
For several decades, various nanomaterials have been used in a wide range of industrial fields, research areas, and commercial products. Among many nanomaterials, nano-sized mercury materials are one of the most widely used nanomaterials in real life. However, due to the high toxicity of Hg(2+), it is imperative to develop an effective and practical detection method for Hg(2+) to protect human health and environment. In this study, a highly sensitive, label-free method of detecting Hg(2+) that requires only a single drop of solution was developed. The detection mechanism is based on the different surface potential arising from Hg(2+) binding to mismatched thymine-thymine sequences, creating a very stable base pair. The surface potential is measured with Kelvin probe force microscopy (KPFM) to a molecular resolution. The developed method is capable of detecting 2 fmol of Hg(2+), which is 500 times more sensitive than previously reported techniques. Moreover, our method can selectively detect Hg(2+) and can also be applied to tap water and river water. This KPFM-based Hg(2+) detection method can be used as an early detection technique for practical applications.
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Affiliation(s)
- Chanho Park
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
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12
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Valencia M, Martín-Ortiz M, Gómez-Gallego M, Ramírez de Arellano C, Sierra MA. On the use of metal purine derivatives (M=Ir, Rh) for the selective labeling of nucleosides and nucleotides. Chemistry 2015; 20:3831-8. [PMID: 24677547 DOI: 10.1002/chem.201304091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/11/2013] [Indexed: 12/30/2022]
Abstract
The reactions of neutral or cationic IrIII and RhIII derivatives of phenyl purine nucleobases with unsymmetrical alkynes produce new metallacycles in a predictable manner, which allows for the incorporation of either photoactive (anthracene or pyrene) or electroactive (ferrocene) labels in the nucleotide or nucleoside moiety. The reported methodology (metalation of the purine derivative and subsequent marker insertion) could be used for the postfunctionalization and unambiguous labeling of oligonucleotides.
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13
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Tanaka Y, Kondo J, Sychrovský V, Šebera J, Dairaku T, Saneyoshi H, Urata H, Torigoe H, Ono A. Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs. Chem Commun (Camb) 2015; 51:17343-60. [DOI: 10.1039/c5cc02693h] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.
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Affiliation(s)
- Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima
- Japan
- Graduate School of Pharmaceutical Sciences
| | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Chiyoda-ku
- Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Institute of Physics
| | - Takenori Dairaku
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai
- Japan
| | - Hisao Saneyoshi
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences
- Takatsuki
- Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
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Isobe H, Fujino T. Triazole-linked analogues of DNA and RNA ((TL)DNA and (TL)RNA): synthesis and functions. CHEM REC 2014; 14:41-51. [PMID: 24734308 DOI: 10.1002/tcr.201300023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Click chemistry has provided us with access to DNA and RNA analogues with non-natural triazole internucleoside linkages. The bond periodicity of the oligonucleotides was designed to enforce duplex formation with natural congeners, and the non-cleavable linkages protect the oligomers against nuclease digestion. This account reviews the progress of the triazole-linked analogues over the past five years. Reinforced by their synthetic robustness, these analogues may find various utilities as tools for exploratory research.
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Zhang JR, Huang WT, Zeng AL, Luo HQ, Li NB. Ethynyl and π-stacked thymine-Hg2+-thymine base pairs enhanced fluorescence quenching via photoinduced electron transfer and simple and sensitive mercury ion sensing. Biosens Bioelectron 2014; 64:597-604. [PMID: 25310495 DOI: 10.1016/j.bios.2014.09.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
Ethynyl triggered enhanced fluorescence quenching effect was first reported based on photoinduced electron transfer (PET) between fluorophore and ethynyl. Ethynyl and 6-carboxyl-fluorescein (FAM) were labeled at the 5'- and 3'-termini of a poly d(T) sequence containing three thymine units, respectively. In the presence of Hg(2+), Hg(2+) binds to two thymine residues through T-Hg(2+)-T interactions and the formed T-Hg(2+)-T base pairs bring FAM and ethynyl from two matched sequences into close proximity. On the one hand, π-stacked T-Hg(2+)-T mediates and accepts electron transfer of the excited state of FAM and quenches the fluorescence through PET. On the other hand, π-stacked interactions between ethynyl and FAM also provide a de-excitation process for the excited state of FAM via PET and trigger an enhanced fluorescence quenching. On the basis of fluorescence quenching, a simple, rapid, and sensitive Hg(2+) sensor was constructed; under optimum conditions, a good linear relationship was obtained over the concentration range of 5-150 nM for Hg(2+) and a very low detection limit (0.42 nM) was reached. The developed system was further designed as a cysteine (Cys) sensor based on fluorescence recovery resulted from the strong interaction between Cys and Hg(2+); the proposed Cys sensor has a linear range of 10-550 nM and a detection limit of 2.5 nM. The two sensors were used for analysis of real samples and the satisfactory results were achieved.
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Affiliation(s)
- Jian Rong Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wei Tao Huang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ai Lian Zeng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Nian Bing Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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Marino T. DFT investigation of the mismatched base pairs (T-Hg-T)3, (U-Hg-U)3, d(T-Hg-T)2, and d(U-Hg-U)2. J Mol Model 2014; 20:2303. [DOI: 10.1007/s00894-014-2303-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
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Kratochvílová I, Golan M, Vala M, Špérová M, Weiter M, Páv O, Šebera J, Rosenberg I, Sychrovský V, Tanaka Y, Bickelhaupt FM. Theoretical and Experimental Study of Charge Transfer through DNA: Impact of Mercury Mediated T-Hg-T Base Pair. J Phys Chem B 2014; 118:5374-81. [DOI: 10.1021/jp501986a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Irena Kratochvílová
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Faculty of Nuclear Physics
and Physical Engineering, Czech Technical University in Prague, Zikova 1, 160 00 Prague 6, Czech Republic
| | - Martin Golan
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Physics,
Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Martin Vala
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Miroslava Špérová
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Martin Weiter
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Jakub Šebera
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale
Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and
Materials (IMM), Radboud University Nijmegen, Comeniuslaan 4, 6525 HP Nijmegen, The Netherlands
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Yamaguchi H, Šebera J, Kondo J, Oda S, Komuro T, Kawamura T, Dairaku T, Kondo Y, Okamoto I, Ono A, Burda JV, Kojima C, Sychrovský V, Tanaka Y. The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation. Nucleic Acids Res 2014; 42:4094-9. [PMID: 24371287 PMCID: PMC3973346 DOI: 10.1093/nar/gkt1344] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 12/16/2022] Open
Abstract
We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T-Hg(II)-T base pair formation. The positive ΔS value arises owing to the Hg(II) dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg(II) and revealed arrangement of T-Hg(II)-T base pairs in metallo-DNA.
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Affiliation(s)
- Hiroshi Yamaguchi
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jakub Šebera
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jiro Kondo
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuji Oda
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoyuki Komuro
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takuya Kawamura
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshinori Kondo
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Itaru Okamoto
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Ono
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jaroslav V. Burda
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Vladimír Sychrovský
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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19
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Characterization of an electrochemical mercury sensor using alternating current, cyclic, square wave and differential pulse voltammetry. Anal Chim Acta 2014; 810:79-85. [DOI: 10.1016/j.aca.2013.12.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 11/22/2022]
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Lotfi Zadeh Zhad HR, Lai RY. A Hg(ii)-mediated “signal-on” electrochemical glutathione sensor. Chem Commun (Camb) 2014; 50:8385-7. [DOI: 10.1039/c4cc03329a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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A reusable and sensitive biosensor for total mercury in canned fish based on fluorescence polarization. Talanta 2013; 117:81-6. [PMID: 24209314 DOI: 10.1016/j.talanta.2013.08.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/21/2022]
Abstract
In this work, we developed a sensitive and selective sensor technique for total mercury (Hg) detection in canned fish samples based on the fluorescence polarization (FP) method. The detection principle was that ssDNA containing thymine (T) bases was modified on magnetic nanoparticles (MNPs), which were used as enhancement probe. In the presence of Hg(2+), the ssDNA on MNPs can hybridize with the fluorophore labeled aptamer owing to the specific interaction between T bases and Hg(2+). The formation of thymine-Hg(2+)-thymine (T-Hg(2+)-T) complexes leads to the molar mass increase of fluorophore molecules, resulting in the enhancement of FP signal. The increase of FP was in a good linearity with the concentration of Hg(2+) in range of 2.0 nM-1.0 mM and the limit of detection was 0.49 nM (3.29 SB/m, according to the recent recommendation of IUPAC). Moreover, the proposed biosensor can be reused for 6 cycling times and was successfully applied in monitoring Hg(2+) in real samples.
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Šebera J, Burda J, Straka M, Ono A, Kojima C, Tanaka Y, Sychrovský V. Formation of a thymine-Hg(II)-thymine metal-mediated DNA base pair: proposal and theoretical calculation of the reaction pathway. Chemistry 2013; 19:9884-94. [PMID: 23766024 DOI: 10.1002/chem.201300460] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/24/2013] [Indexed: 11/07/2022]
Abstract
A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg(II) ion, which results in the formation of a (T)N3-Hg(II)-N3(T) metal-mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg(II)-N3(T) bond is triggered by deprotonation of the imino N3 atom in thymine with a hydroxo ligand on the Hg(II) ion. The formation of the second Hg(II)-N3(T) bond proceeds through water-assisted tautomerization of the remaining, metal-nonbonded thymine base or through thymine deprotonation with a hydroxo ligand of the Hg(II) ion already coordinated to the thymine base. The thermodynamic parameters ΔGR =-9.5 kcal mol(-1), ΔHR =-4.7 kcal mol(-1), and ΔSR =16.0 cal mol(-1) K(-1) calculated with the ONIOM (B3LYP:BP86) method for the reaction agreed well with the isothermal titration calorimetric (ITC) measurements by Torigoe et al. [H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010, 16, 13218-13225]. The peculiar positive reaction entropy measured previously was due to both dehydration of the metal and the change in chemical bonding. The mercury reactant in the theoretical model contained one hydroxo ligand in accord with the experimental pKa value of 3.6 known for an aqua ligand of a Hg(II) center. The chemical modification of T:T mismatched to the T-Hg(II)-T metal-mediated base pair was modeled for the middle base pair within a trinucleotide B-DNA duplex, which ensured complete dehydration of the Hg(II) ion during the reaction.
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Affiliation(s)
- Jakub Šebera
- Department of Functional Materials, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i. Na Slovance 2, 182 21 Prague 8, Czech Republic
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Choi JK, Sargsyan G, Olive AM, Balaz M. Highly sensitive and selective spectroscopic detection of mercury(II) in water by using pyridylporphyrin-DNA conjugates. Chemistry 2012; 19:2515-22. [PMID: 23239513 DOI: 10.1002/chem.201202461] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/17/2012] [Indexed: 11/09/2022]
Abstract
Single-labeled pyridylporphyrin-DNA conjugates are reported as highly sensitive and selective spectroscopic sensors for mercury(II) ions in water. The effects of chemical structure (thymine versus adenine), number of nucleotides (monomer versus octamer), and porphyrin metalation (Zn versus free base) on the sensitivity and selectivity of mercury(II) detection are explored. The results indicated that pyridylporphyrin rather than the nucleobase plays a crucial role in mercury(II) sensing, because porphyrin conjugates with both adenosine and thymidine exhibited excellent mercury(II) detection. Mercury(II) recognition was shown in emission quenching, as well as in a redshift of the porphyrin Soret band absorption. The limit of detection (LOD, 3σ/slope) of zinc(II) pyridylporphyrin-5'-oligodeoxythymidine (ZnPorT8) obtained by fluorescence quenching was calculated to be 21.14 nM. Other metal cations (Zn(2+), Cd(2+), Pb(2+), Mn(2+), Ca(2+), Ni(2+), Mg(2+), Fe(2+), Cu(2+), and Na(+)) did not interfere with the emission and absorption sensing of mercury(II). Free-base porphyrin-oligothymine conjugate 2HPorT8 displayed similar sensitivity to ZnPorT8 but different selectivity. The results also implied that the sensing properties of porphyrin-deoxythymidine conjugates could potentially be tuned by porphyrin metalation.
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Affiliation(s)
- Jung Kyu Choi
- Department of Chemistry, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071, USA
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Benda L, Straka M, Sychrovský V, Bouř P, Tanaka Y. Detection of mercury-TpT dinucleotide binding by Raman spectra: a computational study. J Phys Chem A 2012; 116:8313-20. [PMID: 22803635 DOI: 10.1021/jp3045077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.
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Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Praha 6, Czech Republic
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Uchiyama T, Miura T, Takeuchi H, Dairaku T, Komuro T, Kawamura T, Kondo Y, Benda L, Sychrovský V, Bouř P, Okamoto I, Ono A, Tanaka Y. Raman spectroscopic detection of the T-Hg II-T base pair and the ionic characteristics of mercury. Nucleic Acids Res 2012; 40:5766-74. [PMID: 22383582 PMCID: PMC3384328 DOI: 10.1093/nar/gks208] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 11/30/2022] Open
Abstract
Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg(II)-mediated T-T (T-Hg(II)-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg(II). A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift ((18)O-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg(II)-T pair. This resonance includes the N-Hg(II)-bonded state (Hg(II)-N3-C4=O4) and the N-Hg(II)-dissociated state (Hg(II+) N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg(II). Consequently, the Hg(II) nucleus in the T-Hg(II)-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.
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Affiliation(s)
- Tomomi Uchiyama
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Takashi Miura
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Hideo Takeuchi
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Tomoyuki Komuro
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Takuya Kawamura
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Yoshinori Kondo
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Ladislav Benda
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Vladimír Sychrovský
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Petr Bouř
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Itaru Okamoto
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Akira Ono
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Laboratory of Bio-Structural Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic and Department of Material and Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa, Yokohama, Kanagawa-ken 221-8686, Japan
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Abstract
Base-pairing in the naturally occurring DNA and RNA oligonucleotide duplexes is based on π-stacking, hydrogen bonding, and shape complementarity between the nucleobases adenine, thymine, guanine, and cytosine as well as on the hydrophobic-hydrophilic balance in aqueous media. This complex system of multiple supramolecular interactions is the product of a long-term evolutionary process and thus highly optimized to serve its biological functions such as information storage and processing. After the successful implementation of automated DNA synthesis, chemists have begun to introduce artificial modifications inside the core of the DNA double helix in order to study various aspects of base pairing, generate new base pairs orthogonal to the natural ones, and equip the biopolymer with entirely new functions. The idea to replace the hydrogen bonding interactions with metal coordination between ligand-like nucleosides and suitable transition metal ions culminated in the development of a plethora of artificial base-pairing systems termed "metal base-pairs" which were shown to strongly enhance the DNA duplex stability. Furthermore, they show great potential for the use of DNA as a molecular wire in nanoscale electronic architectures. Although single electrons have proven to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides was identified as a serious obstacle. By exchanging some or all of the Watson-Crick base pairs in DNA with metal complexes, this problem may be solved. In the future, these research efforts are supposed to lead to DNA-like materials with superior conductivity for nano-electronic applications. Other fields of potential application such as DNA-based supramolecular architecture and catalysis may be strongly influenced by these developments as well. This text is meant to illustrate the basic concepts of metal-base pairing and give an outline over recent developments in this field.
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Affiliation(s)
- Guido H Clever
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Göttingen, Germany.
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Lin Z, Li X, Kraatz HB. Impedimetric Immobilized DNA-Based Sensor for Simultaneous Detection of Pb2+, Ag+, and Hg2+. Anal Chem 2011; 83:6896-901. [DOI: 10.1021/ac2014096] [Citation(s) in RCA: 246] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zhenzhen Lin
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Xiaohong Li
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, University of Western Ontario,1151 Richmond Street, London, N6A 5B7, Canada
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Matsui T, Miyachi H, Baba T, Shigeta Y. Theoretical Study on Reaction Scheme of Silver(I) Containing 5-Substituted Uracils Bridge Formation. J Phys Chem A 2011; 115:8504-10. [DOI: 10.1021/jp200871f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Liu S, Clever GH, Takezawa Y, Kaneko M, Tanaka K, Guo X, Shionoya M. Direct Conductance Measurement of Individual Metallo-DNA Duplexes within Single-Molecule Break Junctions. Angew Chem Int Ed Engl 2011; 50:8886-90. [DOI: 10.1002/anie.201102980] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 11/10/2022]
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Liu S, Clever GH, Takezawa Y, Kaneko M, Tanaka K, Guo X, Shionoya M. Direct Conductance Measurement of Individual Metallo-DNA Duplexes within Single-Molecule Break Junctions. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102980] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Isobe H, Yamazaki N, Asano A, Fujino T, Nakanishi W, Seki S. Electron Mobility in a Mercury-mediated Duplex of Triazole-linked DNA (TLDNA). CHEM LETT 2011. [DOI: 10.1246/cl.2011.318] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Benda L, Straka M, Tanaka Y, Sychrovský V. On the role of mercury in the non-covalent stabilisation of consecutive U–HgII–U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids. Phys Chem Chem Phys 2011; 13:100-3. [DOI: 10.1039/c0cp01534b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ono A, Torigoe H, Tanaka Y, Okamoto I. Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 2011; 40:5855-66. [DOI: 10.1039/c1cs15149e] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Miyachi H, Matsui T, Shigeta Y, Hirao K. Effects of mercury(ii) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine–mercury(ii)–thymine nucleobase pairs. Phys Chem Chem Phys 2010; 12:909-17. [DOI: 10.1039/b912807g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Matsui T, Miyachi H, Nakanishi Y, Shigeta Y, Sato T, Kitagawa Y, Okumura M, Hirao K. Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA. J Phys Chem B 2009; 113:12790-5. [PMID: 19708672 DOI: 10.1021/jp9045319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.
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Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan.
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Highly sensitive fluorescent sensor for mercury ion based on photoinduced charge transfer between fluorophore and pi-stacked T-Hg(II)-T base pairs. Talanta 2009; 79:775-9. [PMID: 19576444 DOI: 10.1016/j.talanta.2009.05.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 05/04/2009] [Accepted: 05/04/2009] [Indexed: 11/21/2022]
Abstract
A novel and simple oligodeoxyribonucleotide-based sensor with single fluorophore-labeled for mercury ion sensing was reported. An oligodeoxyribonucleotide poly(dT) was labeled with fluorescein as donor. Based on the specific binding of Hg(II) to T-T mismatch base pairs, the formation of pi-stacked [T-Hg(II)-T] with "sandwich" structure on the addition of Hg(II) ions facilitates the electron transfer via photoinduced charge transfer (PCT), which creates an additional nonradiative decay channel for excited fluorophore and triggers the fluorescence to be quenched. The pi-stacked [T-Hg(II)-T] functioned not only as mercury ion recognition but also as an electron acceptor to quench the donor. A linear relationship was observed over the range of 0-1.0 microM with the detection limit of 20 nM for mercury ions. The fluorescence quenching phenomenon and quenching mechanism, reliability and selectivity of the system were investigated in detail.
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Matsui T, Miyachi H, Sato T, Shigeta Y, Hirao K. Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study. J Phys Chem B 2008; 112:16960-5. [DOI: 10.1021/jp8080707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hideaki Miyachi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takeshi Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yasuteru Shigeta
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kimihiko Hirao
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
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41
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Affiliation(s)
- Jens Müller
- Faculty of Chemistry, Dortmund University of Technology, Otto‐Hahn‐Str. 6, 44227 Dortmund, Germany, Fax: +49 231 755 3797
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He W, Franzini RM, Achim C. Metal-Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding. PROGRESS IN INORGANIC CHEMISTRY 2008. [DOI: 10.1002/9780470144428.ch8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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Affiliation(s)
- Jirí Sponer
- Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic
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Kirin SI, Yennawar HP, Williams ME. Synthesis and Characterization of CuII Complexes with Amino Acid Substituted Di(2-pyridyl)amine Ligands. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kirin SI, Ohr K, Yennawar HP, Morgan CM, Levine LA, Williams ME. Synthesis and X-ray single crystal structure analysis of an inorganic nucleoside analog. INORG CHEM COMMUN 2007. [DOI: 10.1016/j.inoche.2007.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ito T, Nikaido G, Nishimoto SI. Effects of metal binding to mismatched base pairs on DNA-mediated charge transfer. J Inorg Biochem 2007; 101:1090-3. [PMID: 17537514 DOI: 10.1016/j.jinorgbio.2007.04.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 11/21/2022]
Abstract
Photoinduced hole transfer reaction in DNA duplex bearing cytosine-cytosine (CC) or thymine-thymine (TT) mismatched base pairs as metal-ion binding sites was studied using polyacrylamide gel electrophoresis. Site-specific binding of silver (I) ion to a CC mismatched base pair as well as non-specific binding to multiple sites of nucleobases in the DNA suppressed hole migration through the sequence. In the case of mercury (II) binding to duplex DNA containing single TT mismatch at N3 of the pyrimidine rings, little effect on the efficiency of hole transfer was observed, which is in accordance with a recent theoretical prediction. On the other hand, addition of Hg(II) to duplex containing tandem TT base pairs remarkably reduced hole transfer efficiency, although the calculation has suggested such binding could form high degree of electronic coupling between the hole carrier bases.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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Joseph J, Schuster GB. Long-Distance Radical Cation Hopping in DNA: The Effect of Thymine−Hg(II)−Thymine Base Pairs. Org Lett 2007; 9:1843-6. [PMID: 17417861 DOI: 10.1021/ol070135a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymine-Hg(II)-thymine base pairs have been incorporated in an oligonucleotide duplex to study their effect on DNA-mediated charge transport. The introduction of a formally charged Hg atom inside the DNA base core does not significantly alter the charge hopping and trapping properties, as discussed in this paper. Hg(II) replaces the protons normally found on thymines within the complex and acts like a "big proton" in terms of its role in DNA charge transport.
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Affiliation(s)
- Joshy Joseph
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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