1
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Li Y, Meng Z, Liu Y, Zhang B. Turn-on fluorescent nanoprobe for ATP detection based on DNA-templated silver nanoclusters. RSC Adv 2024; 14:5594-5599. [PMID: 38352688 PMCID: PMC10863603 DOI: 10.1039/d3ra07077h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
A turn-on fluorescence nanoprobe was constructed for the determination of adenosine 5'-triphosphate (ATP) based on DNA-templated silver nanoclusters (DNA-AgNCs). The significant enhancement fluorescence intensity of DNA-AgNCs in the presence of ATP is due to the high special binding affinity between ATP and the aptamer, resulting in the environment of DNA-AgNCs with darkish fluorescence lying at one terminus of DNA slightly altering owing to the change of ATP aptamer conformation. A good linear range runs from 9 to 24 mM with a satisfactory detection limit of 3 μM. Furthermore, the proposed nanoprobe exhibited good performance for ATP detection in diluted fetal bovine serum.
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Affiliation(s)
- Yuxia Li
- Department of Chemistry and Chemical Engineering, Jinzhong University Yuci 030619 P. R. China
| | - Zeting Meng
- Department of Chemistry and Chemical Engineering, Jinzhong University Yuci 030619 P. R. China
| | - Yating Liu
- Department of Chemistry and Chemical Engineering, Jinzhong University Yuci 030619 P. R. China
| | - Baozhu Zhang
- Department of Chemistry and Chemical Engineering, Jinzhong University Yuci 030619 P. R. China
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2
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Burguera S, Frontera A, Bauza A. Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications. Inorg Chem 2023; 62:6740-6750. [PMID: 37083254 PMCID: PMC10155183 DOI: 10.1021/acs.inorgchem.3c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.
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Affiliation(s)
- Sergi Burguera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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3
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Zhang B, Yang Z, Li Y, Ma L, Li F, Lv X, Wen G. A label-free aptasensor for the detection of ATP based on turn-on fluorescence DNA-templated silver nanoclusters. RSC Adv 2022; 12:30024-30029. [PMID: 36321105 PMCID: PMC9582908 DOI: 10.1039/d2ra04636a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
A label-free aptasensor has been fabricated in order to detect adenosine triphosphate (ATP) using turn-on fluorescence DNA-Ag NCs. The fluorescence of the DNA-Ag NCs could increase remarkably with the addition of ATP mainly because ATP specifically interacts with its aptamer to change the microenvironment of the darkish DNA-Ag NCs located at one terminus or two termini due to the conformational alteration of the aptamer structure. The proposed sensor can detect ATP in a linear range of 6-27 mM with a good detection limit of 5.0 μM. Additionally, the proposed method succeeded in detecting ATP in fetal bovine serum.
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Affiliation(s)
- Baozhu Zhang
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Ziyao Yang
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Yuxia Li
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Ling Ma
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Fenfang Li
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Xiuqing Lv
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
| | - Guangming Wen
- Department of Chemistry and Chemical Engineering, Jinzhong UniversityYuci 030619P. R. China
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4
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Bachurin SS, Kletskii ME, Burov ON, Bibov MY, Dobaeva NM, Berezovskiy DP. Oligonucleotides-transformers for molecular biology and nanoengineering. Gene X 2022; 820:146277. [PMID: 35149154 DOI: 10.1016/j.gene.2022.146277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
In the present review, numerous experimental and theoretical data describing the properties of non-canonical DNA structures (NSs) are analyzed. NSs (G-quadruplex, i-motif, hairpin, and triplex) play an important role in epigenetic processes (including the genetic variability of viruses), are prone to energetically low-cost conformational transformations and can very effectively be used in the design of nanoscale devices. Numerous experimental data have been analyzed in connection with the so-called oligonucleotides-transformers (nucleotide sequences that able to fold not only into one, but also into several NSs). These sequences were recently predicted by our calculations using automata and graph theories ("Dafna" algorithm). Possible applications of the oligonucleotides-transformers in nanoengineering and genetic editing of organisms are considered.
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Affiliation(s)
- Stanislav S Bachurin
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation.
| | - Mikhail E Kletskii
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Oleg N Burov
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Mikhail Yu Bibov
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Natalya M Dobaeva
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Dmitriy P Berezovskiy
- I.M. Sechenov First Moscow State Medical University (Sechenov University), build. 4, 2 Bolshaya Pirogovskaya Str, Moscow 119435, Russian Federation
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5
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Dairaku T, Kawai R, Nozawa-Kumada K, Yoshida K, Ono T, Kondo Y, Kondo J, Ono A, Tanaka Y, Kashiwagi Y. Chemical reduction of Ag + to Ag employing organic electron donors: evaluation of the effect of Ag +-mediated cytosine-cytosine base pairing on the aggregation of Ag nanoparticles. Dalton Trans 2021; 50:12208-12214. [PMID: 35226008 DOI: 10.1039/d1dt01927a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ag+-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)2]+ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag+-cytosine (C-Ag+-C) base pairing on the degree of AgNP aggregation in solution. As an aprotic solvent, DMSO was expected to dissolve the [Ag(cytidine)2]+ complex, and powerful reducing agents, such as organic electron donors. In this study, the chemical reduction of a cytidine/Ag+ system using a powerful reducing agent tetrakis(dimethylamino)ethylene (TDAE) was investigated. 1H/13C/15N NMR spectroscopic evidence was obtained to identify the iminium dication (TDAE2+), which is an oxidised form of TDAE. The results were compared with those obtained using another organic electron donor, tetrathiafulvalene (TTF), which exhibits a relatively lower reduction activity than TDAE. AgNPs prepared via redox reaction between [Ag(cytidine)2]+ and organic electron donors (TDAE and TTF) were characterised using UV-Vis spectroscopy and nanoparticle tracking analysis. It was found that the formation of C-Ag+-C base pairing inhibited the aggregation of AgNPs in solution. In addition, in the presence of cytidine, the total concentration of the AgNP solution was affected by the reduction activity of the reducing agent.
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Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Rika Kawai
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Kanako Nozawa-Kumada
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kentaro Yoshida
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Tetsuya Ono
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yoshitomo Kashiwagi
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
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6
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Dairaku T, Kawai R, Kanaba T, Ono T, Yoshida K, Sato H, Nozawa-Kumada K, Kondo Y, Kondo J, Ono A, Tanaka Y, Kashiwagi Y. Effect of cytosine-Ag +-cytosine base pairing on the redox potential of the Ag +/Ag couple and the chemical reduction of Ag + to Ag by tetrathiafulvalene. Dalton Trans 2021; 50:7633-7639. [PMID: 33973617 DOI: 10.1039/d1dt00975c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.
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Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Rika Kawai
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Teppei Kanaba
- Application, Bruker Japan K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0022, Japan
| | - Tetsuya Ono
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Kentaro Yoshida
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Hajime Sato
- Application, Bruker Japan K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0022, Japan
| | - Kanako Nozawa-Kumada
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yoshitomo Kashiwagi
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
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7
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Hossain MN, Ahmad S, Kraatz H. Consecutive Silver(I) Ion Incorporation into Oligonucleotides containing Cytosine‐Cytosine Mispairs. Chempluschem 2020; 86:224-231. [DOI: 10.1002/cplu.202000607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/25/2020] [Indexed: 12/18/2022]
Affiliation(s)
- M. Nur Hossain
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
| | - Syed Ahmad
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
- Department of Chemistry University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
- Department of Chemistry University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
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8
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Srivastava R. Nucleobase Pair-Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study. ACS OMEGA 2020; 5:18808-18817. [PMID: 32775882 PMCID: PMC7408194 DOI: 10.1021/acsomega.0c01931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Nucleobase pair-metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine-adenine hydrogen bonding, adenine-thymine (AT), adenine-uracil, adenine-adenine stacking pairs, and Watson-Crick AT stacking pairs and studied their interaction with the coinage metal dimer M2 and M2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M-M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase-M2 2+ complexes are stronger as compared to nucleobase-M2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase-Cu2 complexes and nucleobase-Ag2 2+/Au2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.
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Affiliation(s)
- Ruby Srivastava
- Bioinformatics, CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500607, India
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9
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Zhang B, Wei C. The sensitive detection of ATP and ADA based on turn-on fluorescent copper/silver nanoclusters. Anal Bioanal Chem 2020; 412:2529-2536. [PMID: 32043202 DOI: 10.1007/s00216-020-02476-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 11/25/2022]
Abstract
A simple turn-on fluorescence strategy is proposed for the detection of ATP based on DNA-stabilized copper/silver nanoclusters (DNA-Cu/Ag NCs). The fluorescence intensity of DNA-Cu/Ag NCs increases significantly in the presence of ATP, because the specific interaction between ATP and its aptamer causes two darkish Cu/Ag NCs to be situated at the 5' and 3' termini close to each other. A limit of detection (LOD) of 7.0 μM is found, in a linear range of 2-18 mM, and the proposed sensor is simple, sensitive, and selective. Additionally, the DNA-Cu/Ag NCs/ATP system is further developed into a sensor for ADA detection and demonstrates a linear response to ADA from 5 to 50 U/L with a LOD of 5 U/L. The proposed method is also shown to be successful in detecting ATP and ADA in a solution of fetal bovine serum.
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Affiliation(s)
- Baozhu Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, Shanxi, China
- College of Chemistry and Chemical Engineering, Jinzhong University, Yuci, 030619, Shanxi, China
| | - Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, Shanxi, China.
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10
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Zhang B, Wei C. An aptasensor for the label-free detection of thrombin based on turn-on fluorescent DNA-templated Cu/Ag nanoclusters. RSC Adv 2020; 10:35374-35380. [PMID: 35515676 PMCID: PMC9056932 DOI: 10.1039/d0ra04609d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/09/2020] [Indexed: 11/21/2022] Open
Abstract
A highly sensitive thrombin aptasensor was constructed based on the alteration of the aptamer conformation induced by the target recognition and the turn-on fluorescence due to the proximity of two darkish DNA-templated copper/silver nanoclusters (DNA-Cu/Ag NCs). Two DNA templates were designed as the functional structures consisting of the Cu/Ag NC-nucleation segment located at two termini or one terminus and the aptamer segment in the middle of a DNA template. Two darkish DNA-Cu/Ag NCs came close to each other when the aptamer combined with the target due to the conformational alteration of the aptamer structure, resulting in an increased fluorescence signal readout. Thrombin was sensitively determined as low as 1.6 nM in the range of 1.6–8.0 nM with a high selectivity. Finally, this sensor succeeded in detecting thrombin in a real fetal bovine serum. A highly sensitive thrombin aptasensor was constructed based on the alteration of the aptamer conformation induced by the target recognition and the turn-on fluorescence due to the proximity of two darkish DNA-templated copper/silver nanoclusters (DNA-Cu/Ag NCs).![]()
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Affiliation(s)
- Baozhu Zhang
- College of Chemistry and Chemical Engineering
- Jinzhong University
- P. R. China
| | - Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Institute of Molecular Science
- Shanxi University
- Taiyuan 030006
- P. R. China
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11
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Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
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12
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Swasey SM, Rosu F, Copp SM, Gabelica V, Gwinn EG. Parallel Guanine Duplex and Cytosine Duplex DNA with Uninterrupted Spines of Ag I-Mediated Base Pairs. J Phys Chem Lett 2018; 9:6605-6610. [PMID: 30380874 DOI: 10.1021/acs.jpclett.8b02851] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes, and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can introduce new functionalities and enhanced stabilities. Here we demonstrate, using mass spectrometry (MS), ion mobility spectrometry (IMS), and fluorescence resonance energy transfer (FRET), that parallel-stranded structures consisting of up to 20 G-AgI-G contiguous base pairs are formed when natural DNA sequences are mixed with silver cations in aqueous solution. FRET indicates that duplexes formed by poly(cytosine) strands with 20 contiguous C-AgI-C base pairs are also parallel. Silver-mediated G-duplexes form preferentially over G-quadruplexes, and the ability of Ag+ to convert G-quadruplexes into silver-paired duplexes may provide a new route to manipulating these biologically relevant structures. IMS indicates that G-duplexes are linear and more rigid than B-DNA. DFT calculations were used to propose structures compatible with the IMS experiments. Such inexpensive, defect-free, and soluble DNA-based nanowires open new directions in the design of novel metal-mediated DNA nanotechnology.
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Affiliation(s)
- Steven M Swasey
- Department of Chemistry and Biochemistry , Univerisity of California Santa Barbara , Santa Barbara , California 93117 , United States
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie , Université de Bordeaux, CNRS & Inserm (IECB, UMS3033, US001) , 2 rue Robert Escarpit , 33607 Pessac , France
| | - Stacy M Copp
- Center for Integrated Nanotechnologies , Los Alamos National Laboratories , Los Alamos , New Mexico 87545 , United States
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle , Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB , 2 rue Robert Escarpit , 33607 Pessac , France
| | - Elisabeth G Gwinn
- Department of Physics , Univerisity of California Santa Barbara , Santa Barbara , California 93117 , United States
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13
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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14
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Maity SK, Lönnberg T. Oligonucleotides Incorporating Palladacyclic Nucleobase Surrogates. Chemistry 2018; 24:1274-1277. [DOI: 10.1002/chem.201705797] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Sajal Kumar Maity
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
| | - Tuomas Lönnberg
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
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15
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Chen X, Karpenko A, Lopez-Acevedo O. Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block. ACS OMEGA 2017; 2:7343-7348. [PMID: 30023548 PMCID: PMC6045379 DOI: 10.1021/acsomega.7b01089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/19/2017] [Indexed: 05/10/2023]
Abstract
The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.
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Affiliation(s)
- Xi Chen
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Alexander Karpenko
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Olga Lopez-Acevedo
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
- Facultad
de Ciencias Básicas, Universidad
de Medellín, Carrera
87 No. 30-65, Medellín 050026, Colombia
- E-mail:
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16
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Ahn JK, Kim HY, Baek S, Park HG. A new s-adenosylhomocysteine hydrolase-linked method for adenosine detection based on DNA-templated fluorescent Cu/Ag nanoclusters. Biosens Bioelectron 2017; 93:330-334. [DOI: 10.1016/j.bios.2016.08.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 01/26/2023]
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17
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Kamal A, She Z, Sharma R, Kraatz HB. A study of the interactions of Hg(II) with T-T mispair containing hairpin loops. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Wang YM, Liu JW, Duan LY, Liu SJ, Jiang JH. Aptamer-based fluorometric determination of ATP by using target-cycling strand displacement amplification and copper nanoclusters. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2337-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Mohapatra B, Pratibha, Verma S. Directed adenine functionalization for creating complex architectures for material and biological applications. Chem Commun (Camb) 2017; 53:4748-4758. [PMID: 28393940 DOI: 10.1039/c7cc00222j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this feature article, targeted design strategies are outlined for modified adenine nucleobase derivatives in order to construct metal-mediated discrete complexes, ring-expanded purine skeletons, linear and catenated coordination polymers, shape-selective MOFs, and purine-capped nanoparticles, with a wide range of applications from gas and solvent adsorption to bioimaging agents and anticancer metallodrugs. The success of such design strategies could be ascribed to the rich chemistry of purine and pyrimidine derivatives, versatile coordination behavior, ability to bind a host of metal ions, which could be further tuned by the introduction of additional functionalities, and their inherent propensity to hydrogen bond and exhibit π-π interactions. These noncovalent interactions produce stable frameworks and network solids that are useful as advanced materials, and the biocompatibility of these ligand complexes provides an impetus for assessing novel biological applications.
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Affiliation(s)
- Balaram Mohapatra
- Department of Chemistry Indian Institute of Technology Kanpur, Kanpur, India.
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20
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Aro-Heinilä A, Lönnberg T. Fluorescent Oligonucleotide Probes for Screening High-Affinity Nucleobase Surrogates. Chemistry 2016; 23:1028-1031. [PMID: 27911048 DOI: 10.1002/chem.201605300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/16/2022]
Abstract
Double-helical oligonucleotide probes featuring a single-nucleotide gap opposed by one of the canonical nucleobases and flanked by the fluorescent nucleobase analogue pyrrolocytosine have been synthesized and titrated with PdII chelates of dipicolinamide and its N2 ,N6 -dialkylated derivatives. The fluorometric titrations revealed greatly increased affinity of the PdII chelates for the nucleobases opposing the gap compared to the respective free nucleotides in solution. Owing to the constrained environment of the single-nucleotide gap, the relative stabilities of the various PdII -mediated base pairs were also significantly different from those previously reported at monomer level.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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21
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A mini-review on functional nucleic acids-based heavy metal ion detection. Biosens Bioelectron 2016; 86:353-368. [DOI: 10.1016/j.bios.2016.06.075] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023]
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22
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Taherpour S, Golubev O, Lönnberg T. On the feasibility of recognition of nucleic acid sequences by metal-ion-carrying oligonucleotides. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.01.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Dairaku T, Furuita K, Sato H, Šebera J, Nakashima K, Kondo J, Yamanaka D, Kondo Y, Okamoto I, Ono A, Sychrovský V, Kojima C, Tanaka Y. Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with1H/15N/109Ag NMR Spectroscopy. Chemistry 2016; 22:13028-31. [DOI: 10.1002/chem.201603048] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences; Ohu University; 31-1 Misumido, Tomita-machi, Koriyama Fukushima 963-8611 Japan
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Kyoko Furuita
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Hajime Sato
- Application, Bruker BioSpin K. K.; 3-9 Moriya-cho, Kanagawa-ku, Yokohama Kanagawa 221-0022 Japan
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Katsuyuki Nakashima
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences; Faculty of Science and Technology, Sophia University; 7-1 Kioi-cho, Chiyoda-ku Tokyo 102-8554 Japan
| | - Daichi Yamanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Itaru Okamoto
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
- Czech Technical University in Prague; Faculty of Electrical Engineering, Department of Electrotechnology; Technická 2 166 27 Praha 6 Czech Republic
| | - Chojiro Kojima
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
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24
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Lopatina LI, Karpushkin EA, Zinchenko A, Sergeyev VG. Decoration of DNA scaffold by gold nanoparticles formed in aqueous solutions. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Taniguchi S, Zinchenko A, Murata S. Fabrication of Bimetallic Core–Shell and Alloy Ag–Au Nanoparticles on a DNA Template. CHEM LETT 2016. [DOI: 10.1246/cl.160180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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26
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Thornton L, Dixit V, Assad LO, Ribeiro TP, Queiroz DD, Kellett A, Casey A, Colleran J, Pereira MD, Rochford G, McCann M, O'Shea D, Dempsey R, McClean S, Kia AFA, Walsh M, Creaven B, Howe O, Devereux M. Water-soluble and photo-stable silver(I) dicarboxylate complexes containing 1,10-phenanthroline ligands: Antimicrobial and anticancer chemotherapeutic potential, DNA interactions and antioxidant activity. J Inorg Biochem 2016; 159:120-32. [DOI: 10.1016/j.jinorgbio.2016.02.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/08/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
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27
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Ma L, Liu H, Wu G, Sun N, Meng L, Li Y, Liu Z, Diao A. A dual-channel detection of mercuric ions using a label free G-quadruplex-based DNAzyme molecule. Analyst 2016; 141:3997-4000. [DOI: 10.1039/c6an00795c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have constructed a ‘turn-off’ and label free bio-sensor using a DNAzyme molecule.
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Affiliation(s)
- Long Ma
- Biomolecular Sciences Research Complex
- EaStCHEM School of Chemistry
- University of St Andrews
- Fife KY16 9ST
- UK
| | - Haiyan Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Guanrong Wu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Lingpei Meng
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Yuyin Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Zhenxing Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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28
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Park KS, Lee CY, Park HG. Metal ion triggers for reversible switching of DNA polymerase. Chem Commun (Camb) 2016; 52:4868-71. [DOI: 10.1039/c6cc00454g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new strategy to modulate DNA polymerase activity in a reversible and switchable manner was devised by using the novel interactions between DNA bases and metal ions.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
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29
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Ma L, Wu G, Li Y, Qin P, Meng L, Liu H, Li Y, Diao A. A reversible metal ion fueled DNA three-way junction molecular device for "turn-on and -off" fluorescence detection of mercury ions (II) and biothiols respectively with high selectivity and sensitivity. NANOSCALE 2015; 7:18044-18048. [PMID: 26487480 DOI: 10.1039/c5nr04688b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We constructed a reversible molecular device in the nanoscale based on a DNA three-way junction (3WJ) fueled by Hg(2+) binding and sequestration. It is highly responsive to external stimuli, which brings about optically detectable global structural changes. Such a DNA device can serve as a novel "turn-on and -off" fluorescent sensor for Hg(2+) and biothiol detection with high selectivity and sensitivity.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China. and Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanrong Wu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yufeng Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Ping Qin
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Lingpei Meng
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Haiyan Liu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yuyin Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Aipo Diao
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
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30
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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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31
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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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32
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Ahn JK, Park KS, Won BY, Park HG. A novel electrochemical method to detect theophylline utilizing silver ions captured within abasic site-incorporated duplex DNA. Biosens Bioelectron 2015; 67:590-4. [DOI: 10.1016/j.bios.2014.09.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/20/2014] [Accepted: 09/22/2014] [Indexed: 01/03/2023]
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33
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Ihara T, Ohura H, Shirahama C, Furuzono T, Shimada H, Matsuura H, Kitamura Y. Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation. Nat Commun 2015; 6:6640. [DOI: 10.1038/ncomms7640] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
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34
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A DNA-templated silver nanocluster probe for label-free, turn-on fluorescence-based screening of homo-adenine binding molecules. Biosens Bioelectron 2015; 64:618-24. [DOI: 10.1016/j.bios.2014.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
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35
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Hsu HC, Ho MC, Wang KH, Hsu YF, Chang CW. DNA stabilized silver nanoclusters as the fluorescent probe for studying the structural fluctuations and the solvation dynamics of human telomeric DNA. NEW J CHEM 2015. [DOI: 10.1039/c4nj02065k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silver nanoclusters can be utilized as a fluorescent probe for studying the structural fluctuation and the solvation dynamics of human telomeric DNA.
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Affiliation(s)
- Hung-Chi Hsu
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058
- Taiwan
| | - Meng-Chieh Ho
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058
- Taiwan
| | - Kai-Hung Wang
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058
- Taiwan
| | - Ying-Feng Hsu
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058
- Taiwan
| | - Chih-Wei Chang
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058
- Taiwan
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36
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Park KS, Oh SS, Soh HT, Park HG. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline. NANOSCALE 2014; 6:9977-9982. [PMID: 24901073 DOI: 10.1039/c4nr00625a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon 305-701, Republic of Korea.
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37
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Li W, Zhao X, Zhang J, Fu Y. Cu(II)-coordinated GpG-duplex DNA as peroxidase mimetics and its application for label-free detection of Cu2+ ions. Biosens Bioelectron 2014; 60:252-8. [PMID: 24813915 DOI: 10.1016/j.bios.2014.04.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/12/2014] [Accepted: 04/17/2014] [Indexed: 02/01/2023]
Abstract
Herein a facile method is proposed to construct DNA-based peroxidase mimetics simply assembled by polymorphic DNA and Cu(2+) ions. The Cu(II)-catalyzed oxidation of TMB in the presence of H2O2 can be significantly accelerated through Cu(II)-coordination with DNA scaffolds, of which a colorimetric change can be discerned by naked-eye. The reaction rates of DNA-Cu(II) complexes are directly associated with sequence composition as well as the secondary structure of DNA scaffold, e.g., the reaction rate decreases in the following order: GpG-duplex ≈ G-rich coil > G-quadruplex > C-rich coil > i-motif. It is the first report to explore a colorimetric Cu(2+) sensing system on the basis of peroxidase mimicking activities of polymorphic DNA-Cu(II) complexes. One of our most intriguing results is that the GpG-duplex DNA demonstrates the ability to sense Cu(2+) ions in aqueous solution without significant interference from other metal ions. The Cu(2+) detection limit of 1.2 nM is achieved with a linear response range of 1.2-100 nM, and the developed sensing system is potentially applicable for quantitative determination of Cu(2+) in drinking water samples.
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Affiliation(s)
- Wei Li
- Key Laboratory for Green Chemical Technology MOE, Key Laboratory of Systems Bioengineering MOE, Tianjin University, Tianjin 300072, People׳s Republic of China
| | - Xuyin Zhao
- Key Laboratory for Green Chemical Technology MOE, Key Laboratory of Systems Bioengineering MOE, Tianjin University, Tianjin 300072, People׳s Republic of China
| | - Jinli Zhang
- Key Laboratory for Green Chemical Technology MOE, Key Laboratory of Systems Bioengineering MOE, Tianjin University, Tianjin 300072, People׳s Republic of China
| | - Yan Fu
- Key Laboratory for Green Chemical Technology MOE, Key Laboratory of Systems Bioengineering MOE, Tianjin University, Tianjin 300072, People׳s Republic of China.
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