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Kotera N, Granzhan A, Teulade-Fichou MP. Comparative study of affinity and selectivity of ligands targeting abasic and mismatch sites in DNA using a fluorescence-melting assay. Biochimie 2016; 128-129:133-7. [PMID: 27523781 DOI: 10.1016/j.biochi.2016.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/08/2016] [Indexed: 11/29/2022]
Abstract
Recently, several families of small-molecule ligands have been developed to selectively target DNA pairing defects, such as abasic sites and mismatched base pairs, with the aim to interfere with the DNA repair and the template function of the DNA. However, the affinity and selectivity (with respect to well-matched DNA) of these ligands has barely been evaluated in a systematic way. Herein, we report a comparative study of binding affinity and selectivity of a representative panel of 16 ligands targeting abasic sites and a T-T mismatch in DNA, using a fluorescence-monitored melting assay. We demonstrate that bisintercalator-type macrocyclic ligands are characterized by moderate affinity but exceptionally high selectivity with respect to well-matched DNA, whereas other reported ligands show either modest selectivity or rather low affinity in identical conditions.
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Affiliation(s)
- Naoko Kotera
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
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2
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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3
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Ahn JK, Park KS, Won BY, Park HG. A novel electrochemical method to detect theophylline utilizing silver ions captured within abasic site-incorporated duplex DNA. Biosens Bioelectron 2015; 67:590-4. [DOI: 10.1016/j.bios.2014.09.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/20/2014] [Accepted: 09/22/2014] [Indexed: 01/03/2023]
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4
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Kotera N, Poyer F, Granzhan A, Teulade-Fichou MP. Efficient inhibition of human AP endonuclease 1 (APE1) via substrate masking by abasic site-binding macrocyclic ligands. Chem Commun (Camb) 2015; 51:15948-51. [DOI: 10.1039/c5cc06084b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bis-naphthalene macrocycles bind to abasic sites in DNA, leading to efficient inhibition of their cleavage by human AP endonuclease 1 (APE1).
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Affiliation(s)
- Naoko Kotera
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Florent Poyer
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Anton Granzhan
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
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5
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Park KS, Oh SS, Soh HT, Park HG. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline. NANOSCALE 2014; 6:9977-9982. [PMID: 24901073 DOI: 10.1039/c4nr00625a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon 305-701, Republic of Korea.
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Siters KE, Sander SA, Morrow JR. Selective Binding of Zn 2+Complexes to Non-Canonical Thymine or Uracil in DNA or RNA. PROGRESS IN INORGANIC CHEMISTRY: VOLUME 59 2014. [DOI: 10.1002/9781118869994.ch03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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7
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Pradhan T, Jung HS, Jang JH, Kim TW, Kang C, Kim JS. Chemical sensing of neurotransmitters. Chem Soc Rev 2014; 43:4684-713. [DOI: 10.1039/c3cs60477b] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review focuses on the chemosensors for neurotransmitters published for the last 12 years, covering biogenic amines (dopamine, epinephrine, norepinephrine, serotonin, histamine and acetylcholine), amino acids (glutamate, aspartate, GABA, glycine and tyrosine), and adenosine.
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Affiliation(s)
- Tuhin Pradhan
- Department of Chemistry
- Korea University
- Seoul 130-701, Korea
- Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology
- and Department of Chemistry
| | - Hyo Sung Jung
- Department of Chemistry
- Korea University
- Seoul 130-701, Korea
| | - Joo Hee Jang
- Department of Chemistry
- Korea University
- Seoul 130-701, Korea
| | - Tae Woo Kim
- The East-West Medical Science
- Kyung Hee University
- Yongin 446-701, Korea
| | - Chulhun Kang
- The East-West Medical Science
- Kyung Hee University
- Yongin 446-701, Korea
| | - Jong Seung Kim
- Department of Chemistry
- Korea University
- Seoul 130-701, Korea
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8
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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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9
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Gahlon HL, Sturla SJ. Hydrogen bonding or stacking interactions in differentiating duplex stability in oligonucleotides containing synthetic nucleoside probes for alkylated DNA. Chemistry 2013; 19:11062-7. [PMID: 23801518 DOI: 10.1002/chem.201204593] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 04/17/2013] [Indexed: 01/01/2023]
Abstract
Oligonucleotides that hybridize to modified DNA are useful chemical tools to probe the noncovalent interactions that stabilize DNA duplexes. In an effort to better understand the interactions that influence the specificity of hybridization probes for O(6)-alkylguanine lesions, we examined a series of synthetic nucleoside analogues (BIM, Benzi, and Peri) with respect to their ability to stabilize duplex DNA comprised of native or damaged DNA oligonucleotides. The base-modified nucleoside analogues contained systematically varied hydrogen-bonding and π-stacking properties. The nucleoside probes were incorporated into DNA and paired opposite canonical bases (A, T, C, or G), O(6) -methylguanine (O(6)-MeG), O(6)-benzylguanine (O(6)-BnG), or a stable abasic site analogue (tetrahydrofuran, THF). On the basis of the free energy of duplex formation, the highest degree of stabilization was observed when Peri was paired opposite O(6)-MeG. The thermodynamic data suggest that the smaller probes stabilize DNA duplexes more through hydrogen bonding, whereas the larger probes, with a greater capacity to π stack, contribute to duplex stabilization more on the basis of base stacking. These results demonstrate that increased helix stability could be achieved when BIM, Benzi, or Peri were paired opposite damage-containing DNA rather than unmodified DNA (that is, O(6)-MeG rather than G). This knowledge is expected to be useful in the design and development of nucleoside analogues for uses in DNA-based technologies.
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Affiliation(s)
- Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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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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11
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Zhu Z, Ravelet C, Perrier S, Guieu V, Fiore E, Peyrin E. Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules. Anal Chem 2012; 84:7203-11. [PMID: 22793528 DOI: 10.1021/ac301552e] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.
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Affiliation(s)
- Zhenyu Zhu
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
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12
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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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