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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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Ganguly S, Murugan NA, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
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Affiliation(s)
- Sudakshina Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
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PC12 cells proliferation and morphological aspects: Inquiry into raffinose-grafted graphene oxide in silk fibroin-based scaffold. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 121:111810. [DOI: 10.1016/j.msec.2020.111810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/15/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022]
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Han Y, Yang W, Luo X, He X, Zhao H, Tang W, Yue T, Li Z. Carbon dots based ratiometric fluorescent sensing platform for food safety. Crit Rev Food Sci Nutr 2020; 62:244-260. [PMID: 32876496 DOI: 10.1080/10408398.2020.1814197] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Food safety has become a major global concern and the rapid detection of food nutritional ingredients and contaminants has aroused much more attention. Nanomaterials-based fluorescent sensing holds great potential in designing highly sensitive and selective detection strategies for food safety analysis. Carbon dots (CDs) possess tremendous prospects in fluorescent sensing food ingredients and contaminants due to their superior properties of chemical and photostability, highly fluorescence with tunability, and no/low-toxicity. Numerous endeavors are demanded to contribute to overcoming the challenge of lower sensitivity and selectivity of the sensors interfered by various components in intricate food matrices to ensure food safety and human health. Nanohybrid CDs based ratiometric fluorescent sensing with self-calibration is regarded as an efficient strategy for the CDs based sensors for the specific recognition of target analyte in the food matrices. This work is devoted to reviewing the development of nanohybrid CDs based ratiometric fluorescent sensing platform and the perspectives of the platform for food safety. The applications of nanohybrid CDs in sensing are summarized and the sensing mechanisms are briefly discussed.
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Affiliation(s)
- Yong Han
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Weixia Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xueli Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xie He
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Haiping Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Wenzhi Tang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
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Morsy NM, Hassan AS, Hafez TS, Mahran MRH, Sadawe IA, Gbaj AM. Synthesis, antitumor activity, enzyme assay, DNA binding and molecular docking of Bis-Schiff bases of pyrazoles. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-02004-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sarkar S, Rajdev P, Singh PC. Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies. Phys Chem Chem Phys 2020; 22:15582-15591. [PMID: 32613973 DOI: 10.1039/d0cp01548b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ionic liquids (ILs) have been extensively used for stabilization and long-term DNA storage. However, molecular level understanding of the role of the hydrogen bond of DNA with ILs in its stabilization is still inadequate. Two ILs, namely, 1,1,3,3-tetramethylguanidinium acetate (TMG) and 2,2-diethyl-1,1,3,3-tetramethylguanidinium acetate (DETMG), have been synthesized, of which TMG has a hydrogen bonding N-H group whereas DETMG does not contain any hydrogen bonding site. It has been found that both TMG and DETMG cations interact in the groove region of DNA; however, their mode of interaction is distinctly different, which causes the stabilization of DNA in the presence of TMG, whereas the effect is opposite in the case of DETMG. It is apparent from the data that only the accommodation of ILs in the groove region is not enough for the stabilization of DNA. MD simulation and spectroscopic studies combinedly indicate that the hydrogen bonding capability of the TMG cation enhances the hydrogen bonding between the Watson-Crick base pairs of DNA, resulting in its stabilization. In contrast, the bigger size as well as the absence of the hydrogen bonding site of the DETMG cation perturbs the minor groove width and base pair step parameters of DNA during its intrusion into the minor groove, which decreases the hydrogen bond between the Watson-Crick base pairs of DNA, leading to destabilization.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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