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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Zhang X, Liu Q, Jin Y, Li B. Facile and Sensitive Fluorescence Assay of DNA Polymerase Activity Using Cu2+
and Ascorbate as Signal Developers. ChemistrySelect 2019. [DOI: 10.1002/slct.201803850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xingxing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering; Shaanxi Normal University; Xi'an 710062 China
| | - Qiang Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering; Shaanxi Normal University; Xi'an 710062 China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering; Shaanxi Normal University; Xi'an 710062 China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering; Shaanxi Normal University; Xi'an 710062 China
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Su KY, Goodman SD, Lai HM, Yen RS, Hu WY, Cheng WC, Lin LI, Yang YC, Fang WH. Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis. J Vis Exp 2018:57862. [PMID: 29985320 PMCID: PMC6101880 DOI: 10.3791/57862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The maintenance of the genome and its faithful replication is paramount for conserving genetic information. To assess high fidelity replication, we have developed a simple non-labeled and non-radio-isotopic method using a matrix-assisted laser desorption ionization with time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis for a proofreading study. Here, a DNA polymerase [e.g., the Klenow fragment (KF) of Escherichia coli DNA polymerase I (pol I) in this study] in the presence of all four dideoxyribonucleotide triphosphates is used to process a mismatched primer-template duplex. The mismatched primer is then proofread/extended and subjected to MALDI-TOF MS. The products are distinguished by the mass change of the primer down to single nucleotide variations. Importantly, a proofreading can also be determined for internal single mismatches, albeit at different efficiencies. Mismatches located at 2-4-nucleotides (nt) from the 3' end were efficiently proofread by pol I, and a mismatch at 5 nt from the primer terminus showed only a partial correction. No proofreading occurred for internal mismatches located at 6 - 9 nt from the primer 3' end. This method can also be applied to DNA repair assays (e.g., assessing a base-lesion repair of substrates for the endo V repair pathway). Primers containing 3' penultimate deoxyinosine (dI) lesions could be corrected by pol I. Indeed, penultimate T-I, G-I, and A-I substrates had their last 2 dI-containing nucleotides excised by pol I before adding a correct ddN 5'-monophosphate (ddNMP) while penultimate C-I mismatches were tolerated by pol I, allowing the primer to be extended without repair, demonstrating the sensitivity and resolution of the MS assay to measure DNA repair.
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Affiliation(s)
- Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University; Department of Laboratory Medicine, National Taiwan University Hospital
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Nationwide Children's Hospital and the Department of Pediatrics, The Ohio State University
| | - Hung-Ming Lai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University
| | - Rong-Syuan Yen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University
| | - Wei-Yao Hu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University
| | - Wern-Cherng Cheng
- Department of Laboratory Medicine, National Taiwan University Hospital
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University; Department of Laboratory Medicine, National Taiwan University Hospital
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University; Department of Laboratory Medicine, National Taiwan University Hospital
| | - Woei-Horng Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University; Department of Laboratory Medicine, National Taiwan University Hospital;
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Application of single nucleotide extension and MALDI-TOF mass spectrometry in proofreading and DNA repair assay. DNA Repair (Amst) 2017; 61:63-75. [PMID: 29223016 DOI: 10.1016/j.dnarep.2017.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/07/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
Abstract
Proofreading and DNA repair are important factors in maintaining the high fidelity of genetic information during DNA replication. Herein, we designed a non-labeled and non-radio-isotopic simple method to measure proofreading. An oligonucleotide primer is annealed to a template DNA forming a mismatched site and is proofread by Klenow fragment of Escherichia coli DNA polymerase I (pol I) in the presence of all four dideoxyribonucleotide triphosphates. The proofreading excision products and re-synthesis products of single nucleotide extension are subjected to MALDI-TOF mass spectrometry (MS). The proofreading at the mismatched site is identified by the mass change of the primer. We examined proofreading of Klenow fragment with DNAs containing various base mismatches. Single mismatches at the primer terminus can be proofread efficiently. Internal single mismatches can also be proofread at different efficiencies, with the best correction for mismatches located 2-4-nucleotides from the primer terminus. For mismatches located 5-nucleotides from the primer terminus there was partial correction and extension. No significant proofreading was observed for mismatches located 6-9-nucleotides from the primer terminus. We also subjected primers containing 3' penultimate deoxyinosine (dI) lesions, which mimic endonuclease V nicked repair intermediates, to pol I repair assay. The results showed that T-I was a better substrate than G-I and A-I, however C-I was refractory to repair. The high resolution of MS results clearly demonstrated that all the penultimate T-I, G-I and A-I substrates had been excised last 2 dI-containing nucleotides by pol I before adding a correct ddNMP, however, pol I proofreading exonuclease tolerated the penultimate C-I mismatch allowing the primer to be extended by polymerase activity.
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Ma DL, Dong ZZ, Vellaisamy K, Cheung KM, Yang G, Leung CH. Luminescent Strategies for Label-Free G-Quadruplex-Based Enzyme Activity Sensing. CHEM REC 2017; 17:1135-1145. [PMID: 28467681 DOI: 10.1002/tcr.201700014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/30/2022]
Abstract
By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G-quadruplex-based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G-quadruplex-based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label-free probes. These studies showcase the versatility of the G-quadruplex for developing assays for a variety of different enzymes.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Zhen-Zhen Dong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | | | - Ka-Man Cheung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Guanjun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
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Cai B, Yang X, Sun L, Fan X, Li L, Jin H, Wu Y, Guan Z, Zhang L, Zhang L, Yang Z. Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions. Org Biomol Chem 2015; 12:8866-76. [PMID: 25264858 DOI: 10.1039/c4ob01525h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.
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Affiliation(s)
- Baobin Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China.
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Guo X, Liu P, Yang X, Wang K, Wang Q, Guo Q, Huang J, Liu J, Song C, Li W. A multiple amplification strategy for nucleic acid detection based on host-guest interaction between the β-cyclodextrin polymer and pyrene. Analyst 2015; 140:2016-22. [PMID: 25672284 DOI: 10.1039/c4an02402h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A multiple amplification strategy has been developed for nucleic acid detection based on host-guest interaction between the β-cyclodextrin polymer (β-CDP) and pyrene. Briefly, the detection system consists of three parts: the polymerase and nicking enzyme-assisted isothermal strand displacement amplification (SDA) activated by a target DNA or microRNA; the exonuclease III-aided cyclic enzymatic amplification (CEA); and the fluorescence enhancement effect based on host-guest interaction between β-CDP and pyrene. This strategy showed a good positive linear correlation with target DNA concentrations in the range from 75 fM to 1 pM with a detection limit of 41 fM. Significantly, our amplification platform was further validated and evaluated successfully by assaying miRNA-21 in human serum. The proposed assay has great potential as a nucleic acid quantification method for use in biomedical research, clinical analysis and disease diagnostics.
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Affiliation(s)
- Xiaochen Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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Ma DL, Lu L, Lin S, He B, Leung CH. A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity. J Mater Chem B 2015; 3:348-352. [DOI: 10.1039/c4tb01569j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A G-triplex luminescent switch-on probe for the detection of nuclease activity.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Bingyong He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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Ma DL, Chan DSH, Leung CH. Group 9 organometallic compounds for therapeutic and bioanalytical applications. Acc Chem Res 2014; 47:3614-31. [PMID: 25369127 DOI: 10.1021/ar500310z] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CONSPECTUS: Compared with organic small molecules, metal complexes offer several distinct advantages as therapeutic agents or biomolecular probes. Carbon atoms are typically limited to linear, trigonal planar, or tetrahedral geometries, with a maximum of two enantiomers being formed if four different substituents are attached to a single carbon. In contrast, an octahedral metal center with six different substituents can display up to 30 different stereoisomers. While platinum- and ruthenium-based anticancer agents have attracted significant attention in the realm of inorganic medicinal chemistry over the past few decades, group 9 complexes (i.e., iridium and rhodium) have garnered increased attention in therapeutic and bioanalytical applications due to their adjustable reactivity (from kinetically liable to substitutionally inert), high water solubility, stability to air and moisture, and relative ease of synthesis. In this Account, we describe our efforts in the development of group 9 organometallic compounds of general form [M(C(∧)N)2(N(∧)N)] (where M = Ir, Rh) as therapeutic agents against distinct biomolecular targets and as luminescent probes for the construction of oligonucleotide-based assays for a diverse range of analytes. Earlier studies by researchers had focused on organometallic iridium(III) and rhodium(III) half-sandwich complexes that show promising anticancer activity, although their precise mechanisms of action still remain unknown. More recently, kinetically-inert group 9 complexes have arisen as fascinating alternatives to organic small molecules for the specific targeting of enzyme activity. Research in our laboratory has shown that cyclometalated octahedral rhodium(III) complexes were active against Janus kinase 2 (JAK2) or NEDD8-activating enzyme (NAE) activity, or against NO production leading to antivasculogenic activity in cellulo. At the same time, recent interest in the development of small molecules as modulators of protein-protein interactions has stimulated our research group to investigate whether kinetically-inert metal complexes could also be used to target protein-protein interfaces relevant to the pathogenesis of certain diseases. We have recently discovered that cyclometalated octahedral iridium(III) and rhodium(III) complexes bearing C(∧)N ligands based on 2-phenylpyridine could function as modulators of protein-protein interactions, such as TNF-α, STAT3, and mTOR. One rhodium(III) complex antagonized STAT3 activity in vitro and in vivo and displayed potent antitumor activity in a mouse xenograft model of melanoma. Notably, these studies were among the first to demonstrate the direct inhibition of protein-protein interfaces by kinetically-inert group 9 metal complexes. Additionally, we have discovered that group 9 solvato complexes carrying 2-phenylpyridine coligands could function as inhibitors and probes of β-amyloid fibrillogenesis. Meanwhile, the rich photophysical properties of iridium complexes have made them popular tools for the design of luminescent labels and probes. Luminescent iridium(III) complexes benefit from a high quantum yield, responsive emissive properties, long-lived phosphorescence lifetimes, and large Stokes shift values. Over the past few years, our group has developed a number of kinetically-inert, organometallic iridium(III) complexes bearing various C(∧)N and N(∧)N ligands that are selective for G-quadruplex DNA, which is a DNA secondary structure formed from planar stacks of guanine tetrads stabilized by Hoogsteen hydrogen bonding. These complexes were then employed to develop G-quadruplex-based, label-free luminescence switch-on assays for nucleic acids, enzyme activity, small molecules, and metal ions.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine Institute
of Chinese Medical Sciences, University of Macau, Macao SAR, China
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Lu L, Shiu-Hin Chan D, Kwong DWJ, He HZ, Leung CH, Ma DL. Detection of nicking endonuclease activity using a G-quadruplex-selective luminescent switch-on probe. Chem Sci 2014. [DOI: 10.1039/c4sc02032d] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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G-quadruplexes as sensing probes. Molecules 2013; 18:14760-79. [PMID: 24288003 PMCID: PMC6270327 DOI: 10.3390/molecules181214760] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 01/09/2023] Open
Abstract
Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K+, Ca2+, Ag+, Hg2+, Cu2+, Pb2+, Sr2+, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.
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