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Zheng J, Zhang W, Gong Y, Liang W, Leng Y. A novel near-infrared polymethine dye biosensor for rapid and selective detection of lithocholic acid. Biosens Bioelectron 2024; 259:116383. [PMID: 38749286 DOI: 10.1016/j.bios.2024.116383] [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: 03/09/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
Lithocholic acid (LCA), a secondary bile acid, has emerged as a potential early diagnostic biomarker for various liver diseases. In this study, we introduce a novel near-infrared (NIR) polymethine dye-based biosensor, capable of sensitive and selective detection of LCA in phosphate buffer and artificial urine (AU) solutions. The detection mechanism relies on the formation of J-aggregates resulting from the interplay of 3,3-Diethylthiatricarbocyanine iodide (DiSC2(7)) dye molecules and LCA, which induces a distinctive red shift in both absorption and fluorescence spectra. The biosensor demonstrates a detection limit for LCA of 70 μM in PBS solution (pH 7.4), while in AU solution, it responds to an LCA concentration as low as ∼60 μM. Notably, the proposed biosensor exhibits outstanding selectivity for LCA, effectively distinguishing it from common interferents such as uric acid, ascorbic acid, and glucose. This rapid, straightforward, and cost-effective spectrometer-based method underscores its potential for early diagnosis of liver diseases by monitoring LCA concentrations.
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Affiliation(s)
- Jianlu Zheng
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-Ku, Tokyo, 153-8505, Japan
| | - Wencui Zhang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Equipe Chimie des Polymères, Institut Parisien de Chimie Moléculaire (UMR-CNRS 8232), Sorbonne Université, 75252, Paris, France
| | - Yanli Gong
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Wenlang Liang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yongxiang Leng
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
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Chiral stacking of cyanine or porphyrin as cationic fluorescent dyes in the presence of anionic polysaccharide of hyaluronic acid. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2049-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Alia JD, Flack JA. Unspecified verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation. RSC Adv 2020; 10:43153-43167. [PMID: 35514896 PMCID: PMC9058138 DOI: 10.1039/d0ra06774a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022] Open
Abstract
The computed vertical energy, Ev,a/f, from the equilibrium geometry of the initial electronic state is frequently considered as representative of the experimental excitation/emission energy, Eabs/fl = hc/λmax. Application of the quantum mechanical version of the Franck–Condon principle does not involve precise specification of nuclear positions before, after, or during an electronic transition. Moreover, the duration of an electronic transition is not experimentally accessible in spectra with resolved vibrational structure. It is shown that computed vibronic spectra based on TDDFT methods and application of quantum mechanical FC analysis predict Eabs = hc/λmax with a 10-fold improvement in accuracy compared to Ev,a for nine cyanine dyes. It is argued that part of the reason for accuracy when this FC analysis is compared to experiment as opposed to Ev,a/f is the unspecified verticality of transitions in the context of the quantum version of the FC principle. Classical FC transitions that preserve nuclear kinetic energy before and after an electronic transition were previously found to occur at a weighted average of final and initial electronic state molecular geometries known as the r-centroid. Inspired by this approach a qualitative method using computed vertical and adiabatic energies and the harmonic approximation is developed and applied yielding a 5-fold improvement in accuracy compared to Ev,a. This improvement results from the dominance of low frequency vibronic transitions in the cyanine dye major band. The model gives insight into the nature of the redshift when qPCR dye EvaGreen is complexed to λDNA and is applicable to the low frequency band of similar non cyanine dyes such as curcumin. It is found that the computed vibronic cyanine dye spectra from time-dependent FC analysis at 0 K and 298 K show decreased intensity at higher temperature suggestive of increased intensity with restricted motion shown when cyanine dyes are used in biomedical imaging. A 2-layer ONIOM model of the DNA minor groove indicates restricted motion of the TC-1 dye excited state in this setting indicative of enhanced fluorescence. Insight into cyanine dye λmax from quantum and classical FC principle; high accuracy with classically inspired approach.![]()
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Affiliation(s)
- Joseph D. Alia
- Division of Science and Mathematics
- University of Minnesota Morris
- USA
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Yu H, Yang W, Alkhamis O, Canoura J, Yang KA, Xiao Y. In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality. Nucleic Acids Res 2019; 46:e43. [PMID: 29361056 PMCID: PMC5934630 DOI: 10.1093/nar/gky026] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/13/2018] [Indexed: 11/13/2022] Open
Abstract
Aptamer-based sensors offer a powerful tool for molecular detection, but the practical implementation of these biosensors is hindered by costly and laborious sequence engineering and chemical modification procedures. We report a simple strategy for directly isolating signal-reporting aptamers in vitro through systematic evolution of ligands by exponential enrichment (SELEX) that transduce binding events into a detectable change of absorbance via target-induced displacement of a small-molecule dye. We first demonstrate that diethylthiatricarbocyanine (Cy7) can stack into DNA three-way junctions (TWJs) in a sequence-independent fashion, greatly altering the dye's absorbance spectrum. We then design a TWJ-containing structured library and isolate an aptamer against 3,4-methylenedioxypyrovalerone (MDPV), a synthetic cathinone that is an emerging drug of abuse. This aptamer intrinsically binds Cy7 within its TWJ domain, but MDPV efficiently displaces the dye, resulting in a change in absorbance within seconds. This assay is label-free, and detects nanomolar concentrations of MDPV. It also recognizes other synthetic cathinones, offering the potential to detect newly-emerging designer drugs, but does not detect structurally-similar non-cathinone compounds or common cutting agents. Moreover, we demonstrate that the Cy7-displacement colorimetric assay is more sensitive than a conventional strand-displacement fluorescence assay. We believe our strategy offers an effective generalized approach for the development of sensitive dye-displacement colorimetric assays for other small-molecule targets.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, FL 33199, USA
| | - Weijuan Yang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, FL 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, FL 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, FL 33199, USA
| | - Kyung-Ae Yang
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, FL 33199, USA
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Liu K, Wen Y, Shi T, Li Y, Li F, Zhao YL, Huang C, Yi T. DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene. Chem Commun (Camb) 2015; 50:9141-4. [PMID: 24989898 DOI: 10.1039/c4cc02783c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Thiazole orange-modified diarylethene (1) shows weak fluorescence but no photochromism in aqueous solution. When binding with DNA, the fluorescence of 1 is enhanced drastically and the photochromic reactivity is unlocked. This kind of DNA-responsive photoswitchable system can be used for imaging nucleic acids within cells.
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Affiliation(s)
- Keyin Liu
- Department of Chemistry, and Concerted Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China.
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Choi JK, Reed A, Balaz M. Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA. Dalton Trans 2014; 43:563-7. [PMID: 24129690 DOI: 10.1039/c3dt52210e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.
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Affiliation(s)
- Jung Kyu Choi
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA.
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Metelev V, Zhang S, Tabatadze D, Kumar ATN, Bogdanov A. The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores. MOLECULAR BIOSYSTEMS 2013; 9:2447-53. [PMID: 23925269 PMCID: PMC3929952 DOI: 10.1039/c3mb70108e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a general phenomenon of the formation of either a fluorescent or an entirely quenched oligodeoxynucleotide (ODN) duplex system by hybridizing pairs of complementary ODNs with identical chemical composition. The ODNs carried internucleoside tether-linked cyanines, where the cyanines were chosen to form a Förster's resonance energy transfer (FRET) donor-acceptor pair. The fluorescent and quenched ODN duplex systems differed only in that the cyanines linked to the respective ODNs were linked either closer to the 5'- or 3'-ends of the molecule. In either case, however, the dyes were separated by an identical number (7 or 8) of base pairs. Characterization by molecular modeling and energy minimization using a conformational search algorithm in a molecular operating environment (MOE) revealed that linking of the dyes closer to the 5'-ends resulted in their reciprocal orientation across the major groove which allowed a closely interacting dye pair to be formed. This overlap between the donor and acceptor dye molecules resulted in changes in absorbance spectra consistent with the formation of H-aggregates. Conversely, dyes linked closer to 3'-ends exhibited emissive FRET and formed a pair of dyes that interacted with the DNA helix only weakly. Induced CD spectra analysis suggested that interaction with the double helix was weaker than in the case of the closely interacting cyanine dye pair. Linking the dyes such that the base pair separation was 10 or 0 favored energy transfer with subsequent acceptor emission. Our results suggest that when interpreting FRET measurements from nucleic acids, the use of a "spectroscopic ruler" principle which takes into account the 3D helical context of the double helix will allow more accurate interpretation of fluorescence emission.
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Affiliation(s)
- Valeri Metelev
- The Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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Choi JK, D'Urso A, Balaz M. Chiroptical properties of anionic and cationic porphyrins and metalloporphyrins in complex with left-handed Z-DNA and right-handed B-DNA. J Inorg Biochem 2013; 127:1-6. [PMID: 23831582 DOI: 10.1016/j.jinorgbio.2013.05.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/24/2022]
Abstract
We report the chiroptical signature and binding interactions of cationic (meso-tetrakis(4-N-methylptridyl)porphyrin, 2HT4) and anionic (meso-tetrakis(4-sulfonatophenyl)porphyrin, 2HTPPS) porphyrins and their zinc(II) and nickel(II) derivatives (ZnT4, ZnTPPS, NiT4, and NiTPPS) with right-handed B-form and two forms of left-handed Z-form of alternating guanine-cytosine polydeoxynucleotide poly(dG-dC)2. NiTPPS is able to spectroscopically discriminate between spermine-induced Z-DNA and Co(III)-induced Z-DNA via new induced circular dichroism signal in the visible region of the electromagnetic spectrum.
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Affiliation(s)
- Jung Kyu Choi
- University of Wyoming, Department of Chemistry, Laramie, WY 82071, USA
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