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Schlosser J, Ihmels H. Photocontrolled Binding of Styrylnaphthyridine Ligands to Abasic Site-Containing DNA by Reversible [2+2] Cycloaddition and Cycloreversion. Chemistry 2024; 30:e202400423. [PMID: 38545937 DOI: 10.1002/chem.202400423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Indexed: 04/25/2024]
Abstract
Five novel styrylnaphthyridine derivatives were synthesized and shown to operate as photoswitchable, selective ligands for abasic site-containing DNA (AP-DNA), which is an important therapeutic and diagnostic target. These compounds associate with AP-DNA with binding constants of 0.5-8.4×104 M-1 as shown by photometric and fluorimetric titrations. Specifically, these ligands bind preferentially to AP-DNA relative to regularly paired duplex DNA. As a special feature, the association of these ligands with DNA can be controlled by means of a reversible [2+2] photocycloaddition. Upon irradiation at 420 nm the photodimer is formed, which does not bind to AP-DNA. In turn, the naphthyridine is regained with excitation at 315 nm. Most notably, this photoinduced deactivation and release of the DNA ligand can be performed in situ in the presence of AP-DNA, thus providing a tool for on-demand delivery of a DNA binder. Overall, these results provide a promising starting point for the development of functional AP-DNA ligands whose bioactivity can be modulated by light with local and temporal control.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
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Wang J, Wang X, Wu S, Che R, Luo P, Meng C. Fluorescent trimethyl-substituted naphthyridine as a label-free signal reporter for one-step and highly sensitive fluorescent detection of DNA in serum samples. Biosens Bioelectron 2017; 87:984-990. [DOI: 10.1016/j.bios.2016.09.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 01/02/2023]
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Yu H, Canoura J, Guntupalli B, Lou X, Xiao Y. A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva. Chem Sci 2017; 8:131-141. [PMID: 28451157 PMCID: PMC5308383 DOI: 10.1039/c6sc01833e] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/28/2016] [Indexed: 12/25/2022] Open
Abstract
Sensors employing split aptamers that reassemble in the presence of a target can achieve excellent specificity, but the accompanying reduction of target affinity mitigates any overall gains in sensitivity. We for the first time have developed a split aptamer that achieves enhanced target-binding affinity through cooperative binding. We have generated a split cocaine-binding aptamer that incorporates two binding domains, such that target binding at one domain greatly increases the affinity of the second domain. We experimentally demonstrate that the resulting cooperative-binding split aptamer (CBSA) exhibits higher target binding affinity and is far more responsive in terms of target-induced aptamer assembly compared to the single-domain parent split aptamer (PSA) from which it was derived. We further confirm that the target-binding affinity of our CBSA can be affected by the cooperativity of its binding domains and the intrinsic affinity of its PSA. To the best of our knowledge, CBSA-5335 has the highest cocaine affinity of any split aptamer described to date. The CBSA-based assay also demonstrates excellent performance in target detection in complex samples. Using this CBSA, we achieved specific, ultra-sensitive, one-step fluorescence detection of cocaine within fifteen minutes at concentrations as low as 50 nM in 10% saliva without signal amplification. This limit of detection meets the standards recommended by the European Union's Driving under the Influence of Drugs, Alcohol and Medicines program. Our assay also demonstrates excellent reproducibility of results, confirming that this CBSA-platform represents a robust and sensitive means for cocaine detection in actual clinical samples.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
| | - Juan Canoura
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
| | - Xinhui Lou
- Department of Chemistry , Capital Normal University , Xisanhuan North Rd. 105 , Beijing , 100048 , China
| | - Yi Xiao
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
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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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Wang J, Song J, Wang X, Wu S, Zhao Y, Luo P, Meng C. An ATMND/SGI based label-free and fluorescence ratiometric aptasensor for rapid and highly sensitive detection of cocaine in biofluids. Talanta 2016; 161:437-442. [PMID: 27769429 DOI: 10.1016/j.talanta.2016.08.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 07/30/2016] [Accepted: 08/16/2016] [Indexed: 12/27/2022]
Abstract
A label-free ratiometric fluorescence aptasensor has been developed for the rapid and sensitive detection of cocaine in complex biofluids. The fluorescent aptasensor is composed of a non-labeled GC-38 cocaine aptamer which serves as a basic sensing unit and two fluorophores, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) and SYBR Green I (SGI) which serves as a signal reporter and a build-in reference, respectively. The detection principle is based on a specific cocaine mediated ATMND displacement reaction and the corresponding change in the fluorescence ratio of ATMND to SGI. Due to the high affinity of the non-labeled aptamer, the good precision originated from the ratiometric method, and the good fluorescence quantum yield of the fluorophore, the aptasensor shows good analytical performance with respect to cocaine detection. Under optimal conditions, the aptasensor shows a linear range of 0.10-10μM and a low limit of detection of 56nM, with a fast response of 20s. The low limit of detection is comparable to most of the fluorescent aptasensors with signal amplification strategies and much lower than all of the unamplified cocaine aptasensors. Practical sample analysis in a series of complex biofluids, including urine, saliva and serum, also indicates the good precision, stability, and high sensitivity of the aptasensor, which may have great potential for the point-of-care screening of cocaine in complex biofluids.
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Affiliation(s)
- Jiamian Wang
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
| | - Jie Song
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
| | - Xiuyun Wang
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
| | - Shuo Wu
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China.
| | - Yanqiu Zhao
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
| | - Pinchen Luo
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
| | - Changgong Meng
- School of Chemistry, Dalian University of Technology, Dalian 116023, PR China
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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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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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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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