1
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Yang C, Wang F, Zhou Q, Jie J, Su H. Fluorescence Quenching Dynamics of 2-Amino-7-methyl-1,8-naphthyridine in Abasic-Site-Containing DNA Duplexes for Nucleobase Recognition. J Phys Chem Lett 2023; 14:10585-10591. [PMID: 37976464 DOI: 10.1021/acs.jpclett.3c02170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Dramatic fluorescence quenching of small heterocyclic ligands trapped in the abasic site (AP) of DNA has been implemented as an unprecedented strategy recognizing single-base mutations in sequence analysis of cancer genes. However, the key mechanisms governing selective nucleobase recognition remain to be disentangled. Herein, we perform fluorescence quenching dynamics studies for 2-amino-7-methyl-1,8-naphthyridine (AMND) in well-designed AP-containing DNA single/double strands. The primary mechanism is discovered, showing that AMND only targets cytosine to form a pseudo-base pair, and therefore, fluorescence quenching of AMND arises through the DNA-mediated electron transfer (ET) between excited state AMND* and flanking nucleobases, most favorably with flanking guanines. Subtle dynamic conformational variations induced by different flanking nucleobases are revealed and found to modulate efficiencies of electron transfer and fluorescence quenching. These findings provide critical mechanistic insights for guiding the design of photoinduced electron transfer (PET)-based fluorescent ligands as sensitive single-base recognition reporters.
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Affiliation(s)
- Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Fang Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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2
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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3
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Xu L, Chen Z, Zhang F, Luo Z, Zheng S, Zhu Z, Huang B. The cis configuration of amino-modified tetraphenylethene for selective detection of single-stranded guanine-rich DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:120987. [PMID: 35149483 DOI: 10.1016/j.saa.2022.120987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
The selectivity and sensitivity of amino-functionalized tetraphenylethene probes (namely Z-N2TPE and E-N2TPE) for ssDNA detection in aqueous solution were investigated. Both Z-N2TPE and E-N2TPE showed high selectivity to guanine-rich ssDNA. The sensitivity was found to be positively related to the DNA length, indicating the longer DNA could binding more probes to cause aggregation induced fluorescence. Z-N2TPE and E-N2TPE could detect guanine-rich ssDNA as short as 5 nt and 10 nt respectively. Theoretical simulation calculation shows that the amino group of the probe could simultaneously bind with guanine and phosphate ester, which contribute to high selectivity. And the cis probe could bind DNA with higher affinity than the trans one, since the two amino groups of Z-N2TPE could synergistically bind DNA while E-N2TPE could bind DNA with only one amino group.
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Affiliation(s)
- Li Xu
- Hubei University of Chinese Medicine, Department of Pharmacy, Wuhan 430200, China.
| | - Zhuo Chen
- Hubei University of Chinese Medicine, Department of Pharmacy, Wuhan 430200, China
| | - Fangdan Zhang
- Hubei University of Chinese Medicine, Department of Pharmacy, Wuhan 430200, China
| | - Zihan Luo
- Hubei University of Chinese Medicine, Department of Pharmacy, Wuhan 430200, China
| | - Sijia Zheng
- Hubei University of Chinese Medicine, Department of Pharmacy, Wuhan 430200, China
| | - Zece Zhu
- Wuhan Textile University, Department of Chemistry and Chemical Engineering, State Key Laboratory of New Textile Materials and Advanced Processing Technologies, Wuhan 4320200, China
| | - Bing Huang
- University of Vienna, Faculty of Physics, 1090 Vienna, Austria
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4
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NISHIZAWA S, LEE ETT, YOSHINO Y, YAJIMA S, ROKUGAWA M, SATO Y. Molecular Design of Fluorogenic Probes for Targeting rRNA: Indicator in FID Assay and Dye for Imaging of Nucleolar RNA in Living Cells. BUNSEKI KAGAKU 2021. [DOI: 10.2116/bunsekikagaku.70.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Sciences, Tohoku University
| | | | - Yukina YOSHINO
- Department of Chemistry, Graduate School of Sciences, Tohoku University
| | - Sayaka YAJIMA
- Department of Chemistry, Graduate School of Sciences, Tohoku University
| | - Masafumi ROKUGAWA
- Department of Chemistry, Graduate School of Sciences, Tohoku University
| | - Yusuke SATO
- Department of Chemistry, Graduate School of Sciences, Tohoku University
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5
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Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.
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6
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de Carvalho LC, Silveira OJ, Longuinhos R, Nunes RW, Alexandre SS. Optical absorption in complexes of abasic DNA with noble-metal nanoclusters by first principles calculations. Phys Chem Chem Phys 2019; 21:1260-1270. [DOI: 10.1039/c8cp03731k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abasic sites (AP site) in a DNA duplex have been experimentally used to produce fluorescent Ag nanoclusters (NC) with a small number of atoms (n ≤ 6).
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Affiliation(s)
- L. C. de Carvalho
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - O. J. Silveira
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - R. Longuinhos
- Departamento de Física
- Universidade Federal de Lavras
- Caixa Postal 3037
- Lavras
- Brazil
| | - R. W. Nunes
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - S. S. Alexandre
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
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7
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Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non-aminoglycoside Ligand for the Bacterial A-site RNA. Chemistry 2018; 24:13862-13870. [DOI: 10.1002/chem.201802320] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Indexed: 12/31/2022]
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8
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Zhang Y, Ai J, Gu Q, Gao Q, Qi H, Zhang C. Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:286-290. [PMID: 27960142 DOI: 10.1016/j.saa.2016.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.
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Affiliation(s)
- Yonghua Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; School of Chemistry and Chemical Engineer, Luoyang Normal University, Luoyang 471022, China
| | - Junjie Ai
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qiaorong Gu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qiang Gao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
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9
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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10
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Banerjee S, Bright SA, Smith JA, Burgeat J, Martinez-Calvo M, Williams DC, Kelly JM, Gunnlaugsson T. Supramolecular Approach to Enantioselective DNA Recognition Using Enantiomerically Resolved Cationic 4-Amino-1,8-naphthalimide-Based Tröger’s Bases. J Org Chem 2014; 79:9272-83. [DOI: 10.1021/jo501711g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Swagata Banerjee
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Sandra A. Bright
- School
of Biochemistry and Immunology and Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Jayden A. Smith
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Jeremy Burgeat
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Miguel Martinez-Calvo
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - D. Clive Williams
- School
of Biochemistry and Immunology and Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - John M. Kelly
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Thorfinnur Gunnlaugsson
- School
of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
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11
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Benner K, Bergen A, Ihmels H, Pithan PM. Selective Stabilization of Abasic Site-Containing DNA by Insertion of Sterically Demanding Biaryl Ligands. Chemistry 2014; 20:9883-7. [DOI: 10.1002/chem.201403622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/17/2023]
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12
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Sato Y, Kudo M, Toriyabe Y, Kuchitsu S, Wang CX, Nishizawa S, Teramae N. Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids. Chem Commun (Camb) 2014; 50:515-7. [DOI: 10.1039/c3cc47717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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13
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NISHIZAWA S, SATO Y, TERAMAE N. Recent Progress in Abasic Site-binding Small Molecules for Detecting Single-base Mutations in DNA. ANAL SCI 2014; 30:137-42. [DOI: 10.2116/analsci.30.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yusuke SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Norio TERAMAE
- Department of Chemistry, Graduate School of Science, Tohoku University
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14
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Benner K, Ihmels H, Kölsch S, Pithan PM. Targeting abasic site-containing DNA with annelated quinolizinium derivatives: the influence of size, shape and substituents. Org Biomol Chem 2014; 12:1725-34. [DOI: 10.1039/c3ob42140f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comparative analysis showed that the type and degree of annelation as well as methyl or chloro-substitution are relevant structural features that determine the interactions of quinolizinium derivatives with abasic site-containing DNA.
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Affiliation(s)
- Katja Benner
- University of Siegen
- Organic Chemistry II
- Siegen, Germany
| | - Heiko Ihmels
- University of Siegen
- Organic Chemistry II
- Siegen, Germany
| | - Sarah Kölsch
- University of Siegen
- Organic Chemistry II
- Siegen, Germany
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15
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SATO Y, KAGEYAMA T, NISHIZAWA S, TERAMAE N. Competitive Binding of Abasic Site-Binding Ligands and Masking Ligands to DNA Duplexes for the Analysis of Single-Base Mutation. ANAL SCI 2013; 29:15-9. [DOI: 10.2116/analsci.29.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yusuke SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Tomoe KAGEYAMA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Norio TERAMAE
- Department of Chemistry, Graduate School of Science, Tohoku University
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16
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Sato Y, Toriyabe Y, Nishizawa S, Teramae N. 2,4-Diamino-6,7-dimethylpteridine as a fluorescent ligand for binding and sensing an orphan cytosine in RNA duplexes. Chem Commun (Camb) 2013; 49:9983-5. [DOI: 10.1039/c3cc46085a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Wu F, Sun Y, Shao Y, Xu S, Liu G, Peng J, Liu L. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift. PLoS One 2012. [PMID: 23185252 PMCID: PMC3502418 DOI: 10.1371/journal.pone.0048251] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small molecules that can specifically bind to a DNA abasic site (AP site) have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG), a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.
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Affiliation(s)
- Fei Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yanwei Sun
- Chuyang Honors College, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
- * E-mail:
| | - Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Guiying Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Jian Peng
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Lingling Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
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18
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Sato Y, Zhang Y, Nishizawa S, Seino T, Nakamura K, Li M, Teramae N. Competitive assay for theophylline based on an abasic site-containing DNA duplex aptamer and a fluorescent ligand. Chemistry 2012; 18:12719-24. [PMID: 22915350 DOI: 10.1002/chem.201201298] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Indexed: 11/10/2022]
Abstract
A fluorescence assay for theophylline, one of the common drugs for acute and chronic asthmatic conditions, has been developed based on an abasic site-containing DNA duplex aptamer (AP aptamer) in combination with an abasic site-binding fluorescent ligand, riboflavin. The assay is based on the competitive binding of theophylline and riboflavin at the abasic (AP) site of the AP aptamer. In the absence of theophylline, riboflavin binds to the receptor nucleotide opposite the AP site, which leads to fluorescence quenching of the riboflavin. Upon addition of theophylline, competitive binding occurs between theophylline and riboflavin, which results in an effective fluorescence restoration due to release of riboflavin from the AP site. From an examination of the optimization of the AP aptamers, the complex of riboflavin with a 23-mer AP aptamer (5'-TCT GCG TCC AGX GCA ACG CAC AC-3'/5'-GTG TGC GTT GCC CTG GAC GCA GA-3'; X: the AP site (Spacer C3, a propylene residue)) possessing cytosine as a receptor nucleotide was found to show a selective and effective fluorescence response to theophylline; the limit of detection for theophylline was 1.1 μM. Furthermore, fluorescence detection of theophylline was successfully demonstrated with high selectivity in serum samples by using the optimized AP aptamer and riboflavin.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Japan
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19
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Sato Y, Ichihashi T, Nishizawa S, Teramae N. Strong and Selective Binding of Amiloride to an Abasic Site in RNA Duplexes: Thermodynamic Characterization and MicroRNA Detection. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Sato Y, Ichihashi T, Nishizawa S, Teramae N. Strong and Selective Binding of Amiloride to an Abasic Site in RNA Duplexes: Thermodynamic Characterization and MicroRNA Detection. Angew Chem Int Ed Engl 2012; 51:6369-72. [DOI: 10.1002/anie.201201790] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 01/04/2023]
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21
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Mullice LA, Mottram HJ, Hallett AJ, Pope SJA. Gold(I) Complexes Incorporating Emissive Mercapto-Pteridine Ligands: Syntheses, X-ray Structure, Luminescence and Preliminary Cytotoxic Evaluation. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Pang Y, Xu Z, Sato Y, Nishizawa S, Teramae N. Base pairing at the abasic site in DNA duplexes and its application in adenosine aptasensors. Chembiochem 2012; 13:436-42. [PMID: 22271570 DOI: 10.1002/cbic.201100666] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Indexed: 12/21/2022]
Abstract
The binding of nucleosides to abasic site (AP site)-containing DNA duplexes (AP-DNAs) carrying complementary nucleosides opposite the AP site was investigated by thermal denaturation and isothermal titration calorimetric (ITC) experiments. Purine nucleosides show high affinities (K(d) =14.1 μM for adenosine and 41.8 μM for guanosine) for binding to the AP-DNAs, and the interactions are driven primarily by the enthalpy change, similarly to the case of DNA intercalators. In contrast, pyrimidine nucleosides do not show noticeable binding to the AP-DNAs, thus suggesting that stacking interaction at the AP site plays a key role in the binding of purine nucleosides to the AP-DNAs, as revealed by ITC measurements. Next, to apply an AP-DNA as an aptasensor for adenosine, a competitive assay between adenosine and AP-site-binding fluorescent ligand was performed. The assay employs a fluorescent ligand, riboflavin, that binds to the AP site in a DNA duplex, thereby causing fluorescence quenching. By adding adenosine to the riboflavin/AP-DNA complex, the binding of adenosine to the AP site causes release of riboflavin from the AP site, thereby resulting in restoration of riboflavin fluorescence. AP-DNAs can serve as a new class of aptasensors-a limit of detection of 0.7 μM was obtained for adenosine. In contrast to conventional aptasensors for adenosine, the present method shows high selectivity for adenosine over the other nucleotides (AMP, ADP and ATP). The method does not require covalent labelling of fluorophores, and thus it is cost-effective; finally, the method was successfully demonstrated to be applicable for the detection of adenosine in horse serum.
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Affiliation(s)
- Yuanfeng Pang
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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Sato Y, Zhang Y, Seino T, Sugimoto T, Nishizawa S, Teramae N. Highly selective binding of naphthyridine with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes. Org Biomol Chem 2012; 10:4003-6. [DOI: 10.1039/c2ob25513h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Wu F, Shao Y, Ma K, Cui Q, Liu G, Xu S. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site. Org Biomol Chem 2012; 10:3300-7. [DOI: 10.1039/c2ob00028h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Miura S, Nishizawa S, Suzuki A, Fujimoto Y, Ono K, Gao Q, Teramae N. DNA-Binding Small-Ligand-Immobilized Surface Plasmon Resonance Biosensor for Detecting Thymine-Related Single-Nucleotide Polymorphisms. Chemistry 2011; 17:14104-10. [DOI: 10.1002/chem.201101290] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Indexed: 01/28/2023]
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26
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Xu S, Shao Y, Ma K, Cui Q, Liu G, Wu F, Li M. Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe. Analyst 2011; 136:4480-5. [PMID: 21946800 DOI: 10.1039/c1an15652g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.
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Affiliation(s)
- Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
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Sato Y, Nishizawa S, Teramae N. Label-Free Molecular Beacon System Based on DNAs Containing Abasic Sites and Fluorescent Ligands That Bind Abasic Sites. Chemistry 2011; 17:11650-6. [DOI: 10.1002/chem.201100384] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/31/2011] [Indexed: 01/13/2023]
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28
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Xu Z, Sato Y, Nishizawa S, Teramae N. Fluorescent aptasensors based on conformational adaptability of abasic site-containing aptamers in combination with abasic site-binding ligands. Biosens Bioelectron 2011; 26:4733-8. [PMID: 21719270 DOI: 10.1016/j.bios.2011.05.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 05/18/2011] [Accepted: 05/23/2011] [Indexed: 11/30/2022]
Abstract
Aptamers are nucleic acids that can selectively bind to a variety of targets. Aptamers usually undergo conformational transitions from a flexible or disordered structure into a rigid or ordered structure upon target-binding. This study describes a detection method for l-argininamide (l-Arm) and adenosine based on the conformational adaptability of nucleic acid aptamers. An abasic site (AP site) was formed in the stem and close to the target-binding site of a stem-loop aptamer as an anchoring pocket for a fluorescent ligand. 3,5-Diamino-6-chloro-2-pyrazine carbonitrile (DCPC), which can bind to AP site-containing DNA duplexes by pseudo-base pairing, was utilized as a signaling reporter for the target-binding. The binding of a target to an aptamer induces the tight pairing of bases flanking the AP site, so that DCPC can effectively bind to the stem. The binding of DCPC is accompanied by a significant enhancement of its fluorescence. This new sensing method without an antisense DNA strand was demonstrated by using l-Arm and its aptamer as a model. It was confirmed that the method can sensitively detect l-Arm with a detection limit of 2.1 μM. The proposed method was also applied to adenosine detection, where the reported sequence of an adenosine aptamer was slightly modified. The method based on an AP site-containing aptamer and an AP site-binding ligand was applicable to detection of a target in horse serum.
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Affiliation(s)
- Zhiai Xu
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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29
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Jing B, Li QZ, Gong BA, Liu ZB, Li WZ, Cheng JB, Sun JZ. The prominent enhancing effect and mechanism of the methyl group in the X···Y (X=O, S, H3CO, H3CS, (H3C)2O, (H3C)2S; Y=HCN, HNC) hydrogen-bonded complex. Mol Phys 2011. [DOI: 10.1080/00268976.2011.554899] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Nagaraju M, Narahari Sastry G. Effect of alkyl substitution on H-bond strength of substituted amide-alcohol complexes. J Mol Model 2010; 17:1801-16. [DOI: 10.1007/s00894-010-0886-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/20/2010] [Indexed: 11/28/2022]
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31
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Sato Y, Tian J, Ichihashi T, Chinda Y, Xu Z, Pang Y, Nishizawa S, Teramae N. Enhancement in fluorescence response by a quencher for amiloride upon binding to thymine opposite an abasic site in a DNA duplex. Anal Chim Acta 2010; 675:49-52. [DOI: 10.1016/j.aca.2010.06.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 11/27/2022]
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32
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Nishizawa S, Sato Y, Xu Z, Morita K, Li M, Teramae N. Abasic site-based DNA aptamers for analytical applications. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.484865] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Rajendar B, Rajendran A, Ye Z, Kanai E, Sato Y, Nishizawa S, Sikorski M, Teramae N. Effect of substituents of alloxazine derivatives on the selectivity and affinity for adenine in AP-site-containing DNA duplexes. Org Biomol Chem 2010; 8:4949-59. [DOI: 10.1039/c0ob00057d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Thiagarajan V, Rajendran A, Satake H, Nishizawa S, Teramae N. NBD-Based Green Fluorescent Ligands for Typing of Thymine-Related SNPs by Using an Abasic Site-Containing Probe DNA. Chembiochem 2009; 11:94-100. [DOI: 10.1002/cbic.200900530] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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35
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Sankaran NB, Sato Y, Sato F, Rajendar B, Morita K, Seino T, Nishizawa S, Teramae N. Small-Molecule Binding at an Abasic Site of DNA: Strong Binding of Lumiflavin for Improved Recognition of Thymine-Related Single Nucleotide Polymorphisms. J Phys Chem B 2009; 113:1522-9. [DOI: 10.1021/jp808576t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. B. Sankaran
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Fuyuki Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Burki Rajendar
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Kotaro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Takehiro Seino
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
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36
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Sato Y, Nishizawa S, Yoshimoto K, Seino T, Ichihashi T, Morita K, Teramae N. Influence of substituent modifications on the binding of 2-amino-1,8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization. Nucleic Acids Res 2009; 37:1411-22. [PMID: 19136458 PMCID: PMC2655693 DOI: 10.1093/nar/gkn1079] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Here, we report on a significant effect of substitutions on the binding affinity of a series of 2-amino-1,8-naphthyridines, i.e., 2-amino-1,8-naphthyridine (AND), 2-amino-7-methyl-1,8-naphthyridine (AMND), 2-amino-5,7-dimethyl-1,8-naphthyridine (ADMND) and 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), all of which can bind to cytosine opposite an AP site in DNA duplexes. Fluorescence titration experiments show that the binding affinity for cytosine is effectively enhanced by the introduction of methyl groups to the naphthyridine ring, and the 1:1 binding constant (106 M−1) follows in the order of AND (0.30) < AMND (2.7) < ADMND (6.1) < ATMND (19) in solutions containing 110 mM Na+ (pH 7.0, at 20°C). The thermodynamic parameters obtained by isothermal titration calorimetry experiments indicate that the introduction of methyl groups effectively reduces the loss of binding entropy, which is indeed responsible for the increase in the binding affinity. The heat capacity change (ΔCp), as determined from temperature dependence of the binding enthalpy, is found to be significantly different between AND (−161 cal/mol K) and ATMND (−217 cal/mol K). The hydrophobic contribution appears to be a key force to explain the observed effect of substitutions on the binding affinity when the observed binding free energy (ΔGobs) is dissected into its component terms.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, CREST, Japan Science and Technology Agency, Aoba-ku, Sendai 980-8578, Japan
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37
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Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: A case study with isoxanthopterin and its derivatives. Bioorg Med Chem 2009; 17:351-9. [DOI: 10.1016/j.bmc.2008.10.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 10/27/2008] [Accepted: 10/27/2008] [Indexed: 11/21/2022]
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38
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Smirani W, Rzaigui M. 2,5-Dimethyl-anilinium chloride monohydrate. Acta Crystallogr Sect E Struct Rep Online 2008; 65:o83. [PMID: 21581721 PMCID: PMC2967991 DOI: 10.1107/s1600536808041287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 12/06/2008] [Indexed: 12/05/2022]
Abstract
In the title compound, C8H12N+·Cl−·H2O, the crystal packing is influenced by O—H⋯Cl, N—H⋯Cl and N—H⋯O hydrogen bonds, resulting in a two-dimensional network propagating parallel to (001).
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Affiliation(s)
- Wajda Smirani
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna, Bizerte, Tunisia
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39
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Zhao C, Rajendran A, Dai Q, Nishizawa S, Teramae N. A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes. ANAL SCI 2008; 24:693-5. [PMID: 18544854 DOI: 10.2116/analsci.24.693] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A fluorescent pyrazine derivative, 3,5-diamino-6-chloro-2-pyrazine carbonitrile (DCPC), is presented as a promising light-up ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), DCPC can bind to thymine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-GTGTG CGTTG ANA TGGAC GCAGA-3'/3'-CACAC GCAAC TXT ACCTG CGTCT-5', X = abasic site, N = target nucleotide) with a dissociation constant of 2.6 microM. The binding of DCPC is accompanied by a significant enhancement of its fluorescence (lambda(max), 412 nm), and the response is highly selective to thymine base. These binding and sensing properties allow a clear detection of thymine-related mutations present in polymerase chain reaction (PCR) amplification products.
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Affiliation(s)
- Chunxia Zhao
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba, Sendai, Japan
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40
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Li Q, Wang N, Yu Z. Solvent effect on the role of methyl groups in formation of O···HO hydrogen bond in dimethyl ether–methanol complex. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.04.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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41
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Li Q, An X, Luan F, Li W, Gong B, Cheng J. Regulating Function of Methyl Group in Strength of CH···O Hydrogen Bond: A High-Level Ab Initio Study. J Phys Chem A 2008; 112:3985-90. [DOI: 10.1021/jp800562k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qingzhong Li
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Xiulin An
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Feng Luan
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Wenzuo Li
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Baoan Gong
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Jianbo Cheng
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
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42
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Ye Z, Rajendar B, Qing D, Nishizawa S, Teramae N. 6,7-Dimethyllumazine as a potential ligand for selective recognition of adenine opposite an abasic site in DNA duplexes. Chem Commun (Camb) 2008:6588-90. [DOI: 10.1039/b816876h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Rajendar B, Nishizawa S, Teramae N. Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms. Org Biomol Chem 2008; 6:670-3. [DOI: 10.1039/b719786a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Rajendar B, Sato Y, Nishizawa S, Teramae N. Improvement of base selectivity and binding affinity by controlling hydrogen bonding motifs between nucleobases and isoxanthopterin: Application to the detection of T/C mutation. Bioorg Med Chem Lett 2007; 17:3682-5. [PMID: 17470392 DOI: 10.1016/j.bmcl.2007.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Revised: 04/03/2007] [Accepted: 04/13/2007] [Indexed: 11/20/2022]
Abstract
At an abasic site in an oligo-DNA duplex, isoxanthopterin (IX)(dagger) can bind to thymine (T) and cytosine (C) with strong affinity compared to adenine and guanine, but the base selectivity for T against C is moderate. In order to improve both binding affinity and base selectivity for T against C, a methyl group is introduced to IX, which is known as 3-methyl isoxanthopterin (3-MIX),(dagger) by which binding affinity for C is expected to decrease. Indeed, 3-MIX specifically binds to T more strongly than IX and loses its binding affinity for C. The improved binding ability of 3-MIX for T would be suitable for the practical use in SNP typing related to T.
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Affiliation(s)
- Burki Rajendar
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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45
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Rajendran A, Nair BU. Unprecedented dual binding behaviour of acridine group of dye: A combined experimental and theoretical investigation for the development of anticancer chemotherapeutic agents. Biochim Biophys Acta Gen Subj 2006; 1760:1794-801. [PMID: 16997475 DOI: 10.1016/j.bbagen.2006.08.011] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 07/27/2006] [Accepted: 08/15/2006] [Indexed: 11/17/2022]
Abstract
Acridine group of dyes are well known in the field of development of probes for nucleic acid structure and conformational determination because of their relevance in the development of novel chemotherapeutic agents, footprinting agents and for gene manipulation in biotechnology and medicine. Here, we report the interaction of 9-N,N-dimethylaniline decahydroacridinedione (DMAADD), a new class of dye molecule with calf thymus DNA (CT-DNA) which has been studied extensively by means of traditional experimental and theoretical techniques. The changes in the base stacking of CT-DNA upon the binding of DMAADD are reflected in the circular dichroic (CD) spectral studies. Competitive binding study shows that the enhanced emission intensity of ethidium bromide (EB) in presence of DNA was quenched by the addition of DMAADD indicating that it displaces EB from its binding site in DNA and the apparent binding constant has been estimated to be (3.3+/-0.2)x10(5) M(-1). This competitive binding study and further fluorescence experiments reveal that DMAADD is a moderate binder of CT-DNA, while viscosity measurements show that the mode of binding is partial intercalation. Generally, one would expect increase in the melting temperature (T(m)) of DNA in presence of intercalators. Interestingly, an unusual decrease in melting temperature (DeltaT(m) of -4+/-0.2 degrees C) of DNA by the addition of DMAADD was observed. From our knowledge such a decreasing trend in melting point was not reported before for all the possible modes of binding. Molecular modeling gave the pictorial view of the binding model which clearly shows that of the various mode of binding, the dye prefers the major groove binding to the sites rich in GC residues and to the sites rich in AT residues it prefers intercalation mode of binding either through major or minor groove with the inclusion of the N,N-dimethylaniline (DMA) group inside the double helix which has been stacked in between the bases, under physiological relevant pH of 7.5.
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Affiliation(s)
- Arivazhagan Rajendran
- Chemical Laboratory, Department of Physical and Inorganic Chemistry Division, Central Leather Research Institute, Adyar, Chennai, India
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46
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Satake H, Nishizawa S, Teramae N. Ratiometric Fluorescence Detection of Pyrimidine/Purine Transversion by Using a 2-Amino-1,8-naphthyridine Derivative. ANAL SCI 2006; 22:195-7. [PMID: 16512406 DOI: 10.2116/analsci.22.195] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A new class of abasic site-binding fluorescence ligands, Naph-NBD in which 7-nitrobenzo-2-oxa-1,3-diazole (NBD) is connected to 2-amino-7-methyl-1,8-naphthyridine (Naph) by a propylene linker, is presented for the ratiometric assay for SNPs typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), Naph-NBD is found to selectively recognize pyrimidine bases over purine bases opposite the abasic site in DNA duplexes (K11/M(-1): T, 8.1 x 10(6); C, 2.5 x 10(6): G, 0.33 x 10(6); A, 0.27 x 10(6)). The binding of Naph-NBD is accompanied by significant quenching of the fluorescence from the naphthyridine moiety (lambda max, 409 nm), while the emission from the NBD (lamda max, 544 nm) is relatively unaffected. Such a fluorescence response of Naph-NBD allows the emission ratio detection of pyrimidine/purine transversion.
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Affiliation(s)
- Hiroyuki Satake
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan
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