1
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Bora A, Pal R, Mandi CS, Dutta S. DNA abasic sites act as rational therapeutic targets to synergize temozolomide response in both MMR-proficient and deficient cancer. NAR Cancer 2024; 6:zcae034. [PMID: 39055333 PMCID: PMC11270466 DOI: 10.1093/narcan/zcae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
Temozolomide (TMZ) is widely used in cancer treatment, yet resistance to this agent limits its therapeutic effectiveness, particularly in mismatch-repair (MMR) deficient cancer. Concurrently, the Base Excision Repair (BER) pathway exerts a mitigating role. Our results demonstrated that the increasing TMZ concentrations correlate with an elevated accumulation of DNA abasic sites via the BER pathway in both MMR-proficient and deficient cancer cells, implicating abasic sites as promising targets to enhance the TMZ response. Amino-quinoxaline small molecules (RA-1) have been developed, whose hydrophobic core facilitates selective binding to apurinic/apyrimidinic (AP) sites, particularly adenine as the complementary nucleobase opposite to the AP-sites via base stacking. RA-1 effectively cleaves TMZ-induced DNA abasic sites in-vitro at minimal concentrations through Schiff-base formation. Remarkably, the combination of TMZ and RA-1 exerts a notable synergistic effect on both types of cells. The underlying mechanism of this synergy is rooted in the cleavage of TMZ-induced DNA abasic sites, which impairs the BER pathway, leading to the formation of DNA double-strand breaks. Consequently, the ATM-Chk2/ATR-Chk1 signalling pathways are activated, prompting S-phase arrest and ultimately driving apoptosis. These findings provide a compelling rationale for targeting DNA abasic sites to synergistically augment TMZ responses in both MMR-proficient and deficient cancer cells.
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Affiliation(s)
- Achyut Bora
- Nucleic Acids Research Laboratory, Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ritesh Pal
- Nucleic Acids Research Laboratory, Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chandra Sova Mandi
- Nucleic Acids Research Laboratory, Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sanjay Dutta
- Nucleic Acids Research Laboratory, Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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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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3
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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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4
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Ling P, Cheng S, Wang L, Sun X, Gao X, Gao F. Electrochemically classifying DNA structure based on the small molecule-DNA recognition. Bioelectrochemistry 2022; 147:108193. [PMID: 35753199 DOI: 10.1016/j.bioelechem.2022.108193] [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: 04/05/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Herein, we reported the differential binding ability of aminoglycosides to DNA structures using electrochemical method through principal component analysis (PCA) to classify different DNA secondary structures and understand the link between secondary structure and DNA conformation. In these analyses, the DNA with different secondary structure motifs: bulge, internal loop, hairpin loop and stem loop were designed. The aminoglycosides as receptors were modified on the surface of electrode. In the presence of DNA, the DNA will be absorbed on the surface of electrode via the recognition of DNA and aminoglycosides, resulting in the electrochemical signal observed in [Fe(CN)6]3-/4-. Furthermore, the DNA structures labeled with 2-aminopurine (2-AP) at the structural motif of interest were also employed to study the binding affinity between aminoglycosides and different DNA motifs. The PCA suggested that this method may achieve nucleotide-specific classification of two independent secondary structure motifs, and the structure and sequence of DNA and the size and structure of small molecule could affect the binding ability of the aminoglycosides and DNA. This approach presents a new approach to classify DNA structure and offers ideas for designing targeted drugs small molecule compounds for wound dressing and drug delivery.
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Affiliation(s)
- Pinghua Ling
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
| | - Shan Cheng
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Linyu Wang
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xinyu Sun
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xianping Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Feng Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
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5
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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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6
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Theoretical study of lumichrome, 1-methyl-lumichrome and lumiflavin binding ability with thymine. ACTA CHIMICA SLOVACA 2021. [DOI: 10.2478/acs-2021-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Gas-phase geometry and electronic structure of lumichrome, 1-methyl-lumichrome and lumiflavin in the electronic ground state and their excited states were investigated using the Density Functional Theory. Their binding ability with thymine was estimated for model van der Waals dimers with two intermolecular hydrogen bonds. The influence of hydrogen bonds on their photophysical properties was analyzed. Obtained theoretical data were compared with available experimental absorption and fluorescence spectra.
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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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Interaction of an anti-cancer photosensitizer with a genomic DNA: From base pair specificity and thermodynamic landscape to tuning the rate of detergent-sequestered dissociation. J Colloid Interface Sci 2016; 470:211-220. [PMID: 26945117 DOI: 10.1016/j.jcis.2016.02.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
Abstract
A detailed characterization of the binding interaction of a potent cancer cell photosensitizer, norharmane (NHM) with a genomic DNA (herring sperm; hsDNA) is undertaken with particular emphasis on deciphering the strength, mode, dynamics, energetics and kinetics of binding. A major focus of the study underlies a successful exploration of the concept of detergent-sequestered dissociation of drug from the drug-DNA complex. Biophysical techniques such as absorption, steady-state and time-resolved fluorescence spectroscopy, circular dichroism, DNA helix melting, stopped-flow fluorescence kinetics and calorimetry have been used. A primarily intercalative mode of binding of NHM with DNA is shown. However, the overall interaction is governed by more than one type of binding forces. We demonstrate that the essential prerequisite of a slower dissociation rate of drug from DNA helix is achieved by tenable choice surfactants. Our results also highlight an effective tunability of the rate of dissociation of the DNA-intercalated drug via detergent-sequestration. A detailed isothermal titration calorimetric study unveils the key role of hydrophobic force underlying NHM-hsDNA association. This is further substantiated by the enthalpy-entropy compensation behavior. The major entropic contribution in detergent-induced dissociation of NHM from NHM-hsDNA complex is also demonstrated. Our results present not only a comprehensive structural and thermodynamic profile, base pair specificity, association kinetics for binding of NHM with DNA but also explore the thermodynamic and kinetic aspects of dissociation of bound drug. Characterization and tuning of the essential prerequisites for a drug to be efficient in anti-cancer functionality bear direct and widespread significance in contemporary global research.
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9
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Gophane DB, Sigurdsson ST. TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy. Beilstein J Org Chem 2015; 11:219-27. [PMID: 25815073 PMCID: PMC4362019 DOI: 10.3762/bjoc.11.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/15/2015] [Indexed: 02/04/2023] Open
Abstract
Three 2´-deoxynucleosides containing semi-flexible spin labels, namely (T)A, (U)A and (U)C, were prepared and incorporated into deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; (T)A directly and (U)A as well as (U)C through a urea linkage. (T)A and (U)C showed a minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while (U)A destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label (T)A varied with different base-pairing partners in duplex DNA, with the (T)A•T pair being the least mobile. Furthermore, (T)A showed decreased mobility under acidic conditions for the sequences (T)A•C and (T)A•G, to the extent that the EPR spectrum of the latter became nearly superimposable to that of (T)A•T. The reduced mobility of the (T)A•C and (T)A•G mismatches at pH 5 is consistent with the formation of (T)AH(+)•C and (T)AH(+)•G, in which protonation of N1 of A allows the formation of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels (U)A and (U)C were more mobile than (T)A, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a DNA duplex. (U)A and (U)C had similar mobility order for the different base pairs, with the lowest mobility when paired with C and the highest when paired with T.
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Affiliation(s)
- Dnyaneshwar B Gophane
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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10
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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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11
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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12
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Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 2014; 59:64-74. [PMID: 24690563 DOI: 10.1016/j.bios.2014.03.014] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 01/16/2023]
Abstract
Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.
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Affiliation(s)
- Chunjing Feng
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Shuang Dai
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China.
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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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14
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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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15
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Wong CH, Richardson SL, Ho YJ, Lucas AMH, Tuccinardi T, Baranger AM, Zimmerman SC. Investigating the binding mode of an inhibitor of the MBNL1·RNA complex in myotonic dystrophy type 1 (DM1) leads to the unexpected discovery of a DNA-selective binder. Chembiochem 2012; 13:2505-9. [PMID: 23097190 DOI: 10.1002/cbic.201200602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 01/12/2023]
Affiliation(s)
- Chun-Ho Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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16
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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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17
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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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18
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Shelke SA, Sigurdsson ST. Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç. Nucleic Acids Res 2011; 40:3732-40. [PMID: 22210856 PMCID: PMC3333849 DOI: 10.1093/nar/gkr1210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The influence of structural changes of an abasic site in duplex DNA on noncovalent and site-directed spin labeling (NC-SDSL) of the spin label ç were examined with electron paramagnetic resonance (EPR) spectroscopy. The binding affinities of ç to sixteen different DNA duplexes containing all possible sequences immediately flanking the abasic site were determined and the results showed that the binding of ç is highly flanking-sequence dependent. In general, a 5′-dG nucleotide favors the binding of the spin label. In particular, 5′-d(G__T) was the best binding sequence whereas 5′-d(C__T) showed the lowest affinity. Changing the structure of the abasic site linker from a tetrahydrofuran analog (F) to the anucleosidic C3-spacer (C3) does not appreciably affect the binding of ç to the abasic site. For efficient binding of ç, the abasic site needs to be located at least four base pairs away from the duplex end. Introducing a methyl substituent at N3 of ç did not change the binding affinity, but a decreased binding was observed for both N3-ethyl and -propyl groups. These results will guide the design of abasic site receptors and spin label ligands for NC-SDSL of nucleic acids.
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Affiliation(s)
- Sandip A Shelke
- Department of Chemistry, University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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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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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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Ma K, Cui Q, Liu G, Wu F, Xu S, Shao Y. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition. NANOTECHNOLOGY 2011; 22:305502. [PMID: 21719966 DOI: 10.1088/0957-4484/22/30/305502] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.
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Affiliation(s)
- Kun Ma
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
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23
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Roy B, Saha A, Nandi AK. Melamine sensing through riboflavin stabilized gold nanoparticles. Analyst 2011; 136:67-70. [DOI: 10.1039/c0an00599a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Falconer RJ, Collins BM. Survey of the year 2009: applications of isothermal titration calorimetry. J Mol Recognit 2010; 24:1-16. [DOI: 10.1002/jmr.1073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010; 49:7984-6. [DOI: 10.1002/anie.201002637] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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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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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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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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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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