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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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2
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del Mundo IMA, Cho EJ, Dalby KN, Vasquez KM. A tunable assay for modulators of genome-destabilizing DNA structures. Nucleic Acids Res 2019; 47:e73. [PMID: 30949695 PMCID: PMC6648359 DOI: 10.1093/nar/gkz237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 11/24/2022] Open
Abstract
Regions of genomic instability are not random and often co-localize with DNA sequences that can adopt alternative DNA structures (i.e. non-B DNA, such as H-DNA). Non-B DNA-forming sequences are highly enriched at translocation breakpoints in human cancer genomes, representing an endogenous source of genetic instability. However, a further understanding of the mechanisms involved in non-B DNA-induced genetic instability is needed. Small molecules that can modulate the formation/stability of non-B DNA structures, and therefore the subsequent mutagenic outcome, represent valuable tools to study DNA structure-induced genetic instability. To this end, we have developed a tunable Förster resonance energy transfer (FRET)-based assay to detect triplex/H-DNA-destabilizing and -stabilizing ligands. The assay was designed by incorporating a fluorophore-quencher pair in a naturally-occurring H-DNA-forming sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. By tuning triplex stability via buffer composition, the assay functions as a dual-reporter that can identify stabilizers and destabilizers, simultaneously. The assay principle was demonstrated using known triplex stabilizers, BePI and coralyne, and a complementary oligonucleotide to mimic a destabilizer, MCRa2. The potential of the assay was validated in a 384-well plate with 320 custom-assembled compounds. The discovery of novel triplex stabilizers/destabilizers may allow the regulation of genetic instability in human genomes.
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Affiliation(s)
- Imee M A del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX, USA
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX, USA
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3
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Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
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Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
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4
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Tutuncu S, Guloglu S, Kucukakdag A, Cetinkol OP. Selective High Binding Affinity of Azacyanines to polyd(A) polyd(T)⋅polyd(T) Triplex: The Effect of Chain Length and Branching on Stabilization, Selectivity and Affinity. ChemistrySelect 2018. [DOI: 10.1002/slct.201802802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Serra Tutuncu
- Biomedical Engineering ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
| | - Sercan Guloglu
- Biochemistry ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
| | - Ayca Kucukakdag
- Department of ChemistryMiddle East Technical University 06800 Çankaya Ankara Turkey
| | - Ozgul Persil Cetinkol
- Biomedical Engineering ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
- Biochemistry ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
- Department of ChemistryMiddle East Technical University 06800 Çankaya Ankara Turkey
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5
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Liu X, Xu N, Gai P, Li F. Triplex DNA formation-mediated strand displacement reaction for highly sensitive fluorescent detection of melamine. Talanta 2018; 185:352-358. [PMID: 29759211 DOI: 10.1016/j.talanta.2018.03.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/11/2018] [Accepted: 03/29/2018] [Indexed: 12/15/2022]
Abstract
Since melamine is a strong hazard to human health, the development of new methods for highly sensitive detection of melamine is highly desirable. Herein, a novel fluorescent biosensing strategy was designed for sensitive and selective melamine assay based on the recognition ability of abasic (AP) site in triplex towards melamine and signal amplification by Mg2+-dependent DNAzyme. In this strategy, the melamine-induced formation of triplex DNA was employed to trigger the strand displacement reaction (SDR). The SDR process converted the specific target recognition into the release and activation of Mg2+-dependent DNAzyme, which could catalyze the cleavage of fluorophore/quencher labeled DNA substrate (FQ), resulting in a significantly increased fluorescent signal. Under the optimal conditions, the fluorescent signal has a linear relationship with the logarithm of the melamine concentration in a wide range of 0.005-50 μM. The detection limit was estimated to be 0.9 nM (0.1ppb), which is sufficiently sensitive for practical application. Furthermore, this strategy exhibits high selectivity against other potential interfering substances, and the practical application of this strategy for milk samples reveals that the proposed strategy works well for melamine assay in real samples. Therefore, this strategy presents a new method for the sensitive melamine assay and holds great promise for sensing applications in the environment and the food safety field.
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Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Ningning Xu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China; Key Laboratory of Applied Mycology of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China.
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6
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Liu X, Song M, Li F. Triplex DNA-based Bioanalytical Platform for Highly Sensitive Homogeneous Electrochemical Detection of Melamine. Sci Rep 2017; 7:4490. [PMID: 28674450 PMCID: PMC5495805 DOI: 10.1038/s41598-017-04812-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/19/2017] [Indexed: 12/01/2022] Open
Abstract
Melamine detection has attracted much attention since the discovery of the damage of melamine to human health. Herein, we have developed a sensitive homogeneous electroanalytical platform for melamine detection, which is relied on the formation of triplex molecular beacon integrated with exonuclease III (Exo III)-mediated signal amplification. The formation of triplex molecular beacon was triggered by the recognition and incorporation of melamine to the abasic (AP) site contained in the triplex stem. The stem of the triplex molecular beacon was designed to have a protruding double-strand DNA, which can be recognized and hydrolyzed by Exo III for releasing methylene blue (MB)-labeled mononucleotide. These released MB molecules exhibit high diffusivity toward indium tin oxide electrode with negative charge, thus producing a significantly increased electrochemical response. Taking advantages of the high binding affinity of the DNA triplex structure containing AP sites towards melamine and the unique features of Exo III, this sensing platform is capable for sensitive and selective melamine assay with a detection limit as low as 8.7 nM. Furthermore, this strategy shows good applicability for melamine assay in real samples. Therefore, this strategy broadens the application of triplex DNA and presents a new method for sensitive detection of melamine.
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Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Mengmeng Song
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
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Tiwari R, Haque L, Bhuiya S, Das S. Third strand stabilization of poly(U)·poly(A)* poly(U) triplex by the naturally occurring flavone luteolin: A multi-spectroscopic approach. Int J Biol Macromol 2017; 103:692-700. [PMID: 28545966 DOI: 10.1016/j.ijbiomac.2017.05.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 01/17/2023]
Abstract
Naturally occurring flavonoid luteolin (LTN) was found to interact with double stranded poly(A).poly(U) and triple stranded poly(U)·poly(A)*poly(U) with association constants of the order of 104M-1. The association was monitored by various spectroscopic and viscometric techniques. Non-cooperative binding was observed for the association of LTN with two different polymorphic forms of RNA. Intercalation mode of binding was confirmed by fluorescence quenching and viscometric experiments. Thermal melting profiles indicated greater stabilization of the Hoogsteen base paired third strand (∼16°C) compared to Watson-Crick double strand (∼5°C) of RNA by LTN. Since the interaction of naturally occurring small molecules with RNA is an active area of research, this study has led to great openings to explore LTN as RNA targeted therapeutic agent.
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Affiliation(s)
- Richa Tiwari
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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Yang H, Yao W, Wang Y, Shi L, Su R, Wan D, Xu N, Lian W, Chen C, Liu S. High-throughput screening of triplex DNA binders from complicated samples by 96-well pate format in conjunction with peak area-fading UHPLC-Orbitrap MS. Analyst 2017; 142:670-675. [DOI: 10.1039/c6an01974a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Screening triplex DNA binders from complicated samples in a high-throughput fashion with good reproducibility without the requirement of an extra releasing step.
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Affiliation(s)
- Hongmei Yang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| | - Wenbin Yao
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Yihan Wang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Lei Shi
- High Temperature Reactor Holdings Co
- Ltd
- China Nuclear Engineering Group Co
- Beijing 100037
- China
| | - Rui Su
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Debin Wan
- Department of Entomology and Comprehensive Cancer Center
- University of California
- Davis
- USA
| | - Niusheng Xu
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- China
| | - Wenhui Lian
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Changbao Chen
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Shuying Liu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
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9
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Chen Z, Lu M. Target-responsive aptamer release from manganese dioxide nanosheets for electrochemical sensing of cocaine with target recycling amplification. Talanta 2016; 160:444-448. [PMID: 27591636 DOI: 10.1016/j.talanta.2016.07.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 12/30/2022]
Abstract
A novel electrochemical sensing platform based on manganese dioxide (MnO2) nanosheets was developed for sensitive screening of target cocaine with the signal amplification. Ferrocene-labeled cocaine aptamers were initially immobilized onto MnO2 nanosheets-modified screen-printed carbon electrode because of π-stacking interaction between nucleobases and nanosheets. The immobilized ferrocene-aptamer activated the electrical contact with the electrode, thereby resulting in the sensor circuit to switch on. Upon target cocaine introduction, the analyte reacted with the aptamer and caused the dissociation of ferrocene-aptamer from the electrode, thus giving rise to the detection circuit to switch off. The released aptamer was cleaved by DNase I with target recycling. Under optimal conditions, the decreasing percentage of the electronic signal relative to background current increased with the increasing cocaine concentration in the dynamic range of 0.1-20nM, and the detection limit was 32pM. The reproducibility, selectivity and method accuracy were acceptable. Importantly, this concept offers promise for rapid, simple, and cost-effective analysis of cocaine biological samples without the needs of sample separation and multiple washing steps.
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Affiliation(s)
- Zongbao Chen
- Key Laboratory of Applied Organic Chemistry, College of Jiangxi Province, Department of Chemistry, Shangrao Normal University, Shangrao 334001, Jiangxi, PR China
| | - Minghua Lu
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, Henan, PR China.
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Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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Abstract
Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.
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Affiliation(s)
- Zhiqin Yuan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Cho-Chun Hu
- Department of Applied Science
- National Taitung University
- Taitung 95002
- Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry
- National Taiwan University
- Taipei 106
- Taiwan
| | - Chao Lu
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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