1
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Copp W, Karimi A, Yang T, Guarné A, Luedtke NW. Fluorescent molecular rotors detect O6-methylguanine dynamics and repair in duplex DNA. Chem Commun (Camb) 2024; 60:1156-1159. [PMID: 38190113 DOI: 10.1039/d3cc04782b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Alkylation at the O6 position of guanine is a common and highly mutagenic form of DNA damage. Direct repair of O6-alkylguanines by the "suicide" enzyme O6-methylguanine DNA methyltransferase (MGMT, AGT, AGAT) maintains genome stability and inhibits carcinogenesis. In this study, a fluorescent analogue of thymidine containing trans-stilbene (tsT) is quenched by O6-methylguanine residues in the opposite strand of DNA by molecular dynamics that propagate through the duplex with as much as ∼9 Å of separation. Increased fluorescence of tsT or the cytosine analogue tsC resulting from MGMT-mediated DNA repair were distinguishable from non-covalent DNA-protein binding following protease digest. To our knowledge, this is the first study utilizing molecular rotor base analogues to detect DNA damage and repair activities in duplex DNA.
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Affiliation(s)
- William Copp
- Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada
- Centre de Recherche en Biologie Structural, McGill University, H3G 0B1 Montreal, Canada
| | - Ashkan Karimi
- Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada
- Centre de Recherche en Biologie Structural, McGill University, H3G 0B1 Montreal, Canada
| | - Tianxiao Yang
- Centre de Recherche en Biologie Structural, McGill University, H3G 0B1 Montreal, Canada
- Department of Biochemistry, McGill University, H3G 1Y6 Montreal, Canada
| | - Alba Guarné
- Centre de Recherche en Biologie Structural, McGill University, H3G 0B1 Montreal, Canada
- Department of Biochemistry, McGill University, H3G 1Y6 Montreal, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada
- Centre de Recherche en Biologie Structural, McGill University, H3G 0B1 Montreal, Canada
- Department of Pharmacology and Therapeutics, McGill University, H3A-1A3 Montreal, Canada
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2
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Qiu Y, Liu B, Zhou W, Tao X, Liu Y, Mao L, Wang H, Yuan H, Yang Y, Li B, Wang W, Qiu Y. Repair-driven DNA tetrahedral nanomachine combined with DNAzyme for 8-oxo guanine DNA glycosylase activity assay, drug screening and intracellular imaging. Analyst 2024; 149:537-545. [PMID: 38088097 DOI: 10.1039/d3an01521a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
8-oxo guanine DNA glycosylase (8-oxoG DNA glycosylase), a crucial DNA repair enzyme, is essential for maintaining genome integrity and preventing diseases caused by DNA oxidative damage. Imaging 8-oxoG DNA glycosylase in living cells requires a dependable technique. In this study, we designed a DNAzyme-modified DNA tetrahedral nanomachine (DTDN) powered by 8-oxoG restoration. Incorporating a molecular beacon probe (MB), the constructed platform was used for amplified in situ monitoring of 8-oxoG DNA glycosylase. Under normal conditions, duplexing with a complementary strand modified with two 8-oxoG sites inhibited the activity of DNAzyme. The restoration of DNAzyme activity by the repair of intracellular 8-oxoG DNA glycosylase on 8-oxoG bases can initiate a signal amplification reaction. This detection system can detect 8-oxoG DNA glycosylase activity linearly between 0 and 20 U mL-1, with a detection limit as low as 0.52 U mL-1. Using this method, we were able to screen 14 natural compounds and identify 6 of them as 8-oxoG DNA glycosylase inhibitors. In addition, a novel approach was utilized to assess the activity of 8-oxoG DNA glycosylase in living cells. In conclusion, this method provides a universal tool for monitoring the activity of 8-oxoG DNA glycosylase in vitro and in living cells, which holds great promise for elucidating the enzyme's functionality and facilitating drug screening endeavors.
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Affiliation(s)
- Yun Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenchao Zhou
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Xueqing Tao
- College of Biology, Hunan University, Changsha 410082, China
| | - Yang Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Linxi Mao
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
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3
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Konttinen O, Carmody J, Kurnik M, Johnson KA, Reich N. High fidelity DNA strand-separation is the major specificity determinant in DNA methyltransferase CcrM's catalytic mechanism. Nucleic Acids Res 2023; 51:6883-6898. [PMID: 37326016 PMCID: PMC10359602 DOI: 10.1093/nar/gkad443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/29/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
Strand-separation is emerging as a novel DNA recognition mechanism but the underlying mechanisms and quantitative contribution of strand-separation to fidelity remain obscure. The bacterial DNA adenine methyltransferase, CcrM, recognizes 5'GANTC'3 sequences through a DNA strand-separation mechanism with unusually high selectivity. To explore this novel recognition mechanism, we incorporated Pyrrolo-dC into cognate and noncognate DNA to monitor the kinetics of strand-separation and used tryptophan fluorescence to follow protein conformational changes. Both signals are biphasic and global fitting showed that the faster phase of DNA strand-separation was coincident with the protein conformational transition. Non-cognate sequences did not display strand-separation and methylation was reduced > 300-fold, providing evidence that strand-separation is a major determinant of selectivity. Analysis of an R350A mutant showed that the enzyme conformational step can occur without strand-separation, so the two events are uncoupled. A stabilizing role for the methyl-donor (SAM) is proposed; the cofactor interacts with a critical loop which is inserted between the DNA strands, thereby stabilizing the strand-separated conformation. The results presented here are broadly applicable to the study of other N6-adenine methyltransferases that contain the structural features implicated in strand-separation, which are found widely dispersed across many bacterial phyla, including human and animal pathogens, and some Eukaryotes.
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Affiliation(s)
- Olivia Konttinen
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jason Carmody
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Martin Kurnik
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kenneth A Johnson
- Life Sciences Interdisciplinary Graduate Program, Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Norbert Reich
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
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4
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Wang L, Zhang H, Chen W, Chen H, Xiao J, Chen X. Recent advances in DNA glycosylase assays. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Closing-upon-repair DNA tetrahedron nanoswitch for FRET imaging the repair activity of 8-oxoguanine DNA glycosylase in living cells. Anal Chim Acta 2022; 1196:339481. [DOI: 10.1016/j.aca.2022.339481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 11/19/2022]
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6
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Zhang H, Li F, Wang L, Shao S, Chen H, Chen X. Sensitive homogeneous fluorescent detection of DNA glycosylase by target-triggering ligation-dependent tricyclic cascade amplification. Talanta 2020; 220:121422. [PMID: 32928432 DOI: 10.1016/j.talanta.2020.121422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
Abnormal DNA glycosylases are concerned with the aging process as well as numerous pathologies in humans. Herein, a sensitive fluorescence method utilizing target-induced ligation-dependent tricyclic cascade amplification reaction was developed for the detecting DNA glycosylase activity. The presence of DNA glycosylase triggered the cleavage of damaged base in hairpin substrate, successively activating ligation-dependent strand displacement amplification (SDA) and exponential amplification reaction (EXPAR) for the generation of large amount of reporter probes. The resultant reporter probes bound with the signal probes to form stable dsDNA duplexes. And then the signal probes could be digested circularly in the dsDNA duplexes by T7 exonuclease, leading to the generation of an enhanced fluorescence signal. Due to the high efficiency of tricyclic cascade amplification and the low background signal deriving from the inhibition of nonspecific amplification, this method exhibited a detection limit of 0.14 U/mL and a dynamic range from 0.16 to 8.0 U/mL. Moreover, it could be applied for detecting DNA glycosylase activity in human serum with good selectivity and high sensitivity, and even quantifying other types of enzyme with 5'-PO4 residue cleavage product by rationally designing the corresponding substrate. Importantly, this method could be performed in homogenous solution without any complicated separation steps, providing a new strategy for DNA glycosylase-related biomedical research.
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Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Fengyun Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Lili Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Shuai Shao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Hongli Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
| | - Xingguo Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
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7
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Konttinen O, Carmody J, Pathuri S, Anderson K, Zhou X, Reich N. Cell cycle regulated DNA methyltransferase: fluorescent tracking of a DNA strand-separation mechanism and identification of the responsible protein motif. Nucleic Acids Res 2020; 48:11589-11601. [PMID: 33053173 PMCID: PMC7672430 DOI: 10.1093/nar/gkaa844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 12/23/2022] Open
Abstract
DNA adenine methylation by Caulobacter crescentus Cell Cycle Regulated Methyltransferase (CcrM) is an important epigenetic regulator of gene expression. The recent CcrM-DNA cocrystal structure shows the CcrM dimer disrupts four of the five base pairs of the (5'-GANTC-3') recognition site. We developed a fluorescence-based assay by which Pyrrolo-dC tracks the strand separation event. Placement of Pyrrolo-dC within the DNA recognition site results in a fluorescence increase when CcrM binds. Non-cognate sequences display little to no fluorescence changes, showing that strand separation is a specificity determinant. Conserved residues in the C-terminal segment interact with the phospho-sugar backbone of the non-target strand. Replacement of these residues with alanine results in decreased methylation activity and changes in strand separation. The DNA recognition mechanism appears to occur with the Type II M.HinfI DNA methyltransferase and an ortholog of CcrM, BabI, but not with DNA methyltransferases that lack the conserved C-terminal segment. The C-terminal segment is found broadly in N4/N6-adenine DNA methyltransferases, some of which are human pathogens, across three Proteobacteria classes, three other phyla and in Thermoplasma acidophilum, an Archaea. This Pyrrolo-dC strand separation assay should be useful for the study of other enzymes which likely rely on a strand separation mechanism.
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Affiliation(s)
- Olivia Konttinen
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Jason Carmody
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Sarath Pathuri
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Kyle Anderson
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Xiaofeng Zhou
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norbert Reich
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93103, USA
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
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8
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Qiu Y, Dang W, Fan J, Zhou T, Li B, Liu Y, Qin Y, Tong C, Daniyal M, Wang W, Liu B. DNAzyme and rGO based fluorescence assay for Fpg activity analysis, drug screening, and bacterial imaging. Talanta 2020; 218:121158. [PMID: 32797912 DOI: 10.1016/j.talanta.2020.121158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 05/10/2020] [Indexed: 11/16/2022]
Abstract
Due to the significant role of formamidopyrimidine DNA glycosylase (Fpg) in physiological processes and DNA oxidative damage-related diseases, it is essential to establish sensitive methods for monitoring the Fpg activity in vitro and in vivo so as to illustrate its concrete role in these events. In this work, a sensitive, simple and reliable fluorescence assay was developed by taking the advantages of DNAzyme assisted cascade signal amplification and ultra-high fluorescence quenching efficiency of reduced graphene oxide (rGO). This detection system consisted of DNAzyme, rGO and fluorescence probe allows the activity of Fpg to be detected in a linear range from 0 to 80 U/mL with a detection limit of 0.66 U/mL. With the help of this method, 11 natural compounds were screened, and 7 compounds were identified as activators of Fpg. More importantly, the developed assay was used to monitor the activity of Fpg through fluorescence imaging in living Escherichia coli for the first time. The imaging results visually demonstrated the dynamic activation effect of natural compound Ginsenoside Re on the Fpg of Escherichia coli. In summary, these results indicated that this DNAzyme and rGO based fluorescence assay provides a potent strategy for Fpg quantitative assay in vitro and real-time monitoring in living bacteria, which holds great potential for applying on biological study and Fpg-targeted drug screening.
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Affiliation(s)
- Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China; College of Biology, Hunan University, Changsha, 410082, China
| | - Wenya Dang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Jialong Fan
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ting Zhou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yang Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yan Qin
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Chunyi Tong
- College of Biology, Hunan University, Changsha, 410082, China
| | - Muhammad Daniyal
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, China.
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9
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Li J, Zhang M, Wang H, Wu J, Zheng R, Zhang J, Li Y, Wang Z, Dai Z. Sensitive determination of formamidopyrimidine DNA glucosylase based on phosphate group-modulated multi-enzyme catalysis and fluorescent copper nanoclusters. Analyst 2020; 145:5174-5179. [PMID: 32613972 DOI: 10.1039/d0an00928h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a method for quantifying the activity of formamidopyrimidine DNA glucosylase (Fpg) was designed based on phosphate group (P)-modulated multi-enzyme catalysis and fluorescent copper nanoclusters (CuNCs). By eliminating 8-oxoguanine from double-stranded DNA, Fpg generates a nick with P at both 3' and 5' termini. Subsequently, part of the DNA is digested by 5'P-activated lambda exonuclease (λ Exo), and the generated 3'P disables exonuclease I (Exo I), resulting in the generation of single-stranded DNA containing poly(thymine) (poly(T)). Using poly(T) as templates, CuNCs were prepared to emit intense fluorescence as the readout of this method. However, in the absence of Fpg, the originally modified 5'P triggers the digestion of λ Exo. In this case, fluorescence emission is not obtained because CuNCs cannot be formed without DNA templates. Therefore, the catalysis of λ Exo and Exo I can be tuned by 5'P and 3'P, which can be further used to determine the activity of Fpg. The fluorescent Fpg biosensor works in a "signal-on" manner with the feature of "zero" background noise, and thus shows desirable analytical features and good performance. Besides, Fpg in serum samples and cell lysate could be accurately detected with the biosensor, indicating the great value of the proposed system in practical and clinical analysis.
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Affiliation(s)
- Junyao Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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10
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Wilson DL, Kool ET. Ultrafast Oxime Formation Enables Efficient Fluorescence Light-up Measurement of DNA Base Excision. J Am Chem Soc 2019; 141:19379-19388. [PMID: 31774658 DOI: 10.1021/jacs.9b09812] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
DNA glycosylases constitute a biologically and biomedically important group of DNA repair enzymes responsible for initiating base excision repair (BER). Measuring their activities can be useful for studying the mechanisms DNA damage and repair and for practical applications in cancer diagnosis and drug screening. Previous fluorescence methods for assaying DNA glycosylases are often complex and/or limited in scope to a single enzyme type. Here we report a universal base excision reporter (UBER) fluorescence probe design that implements an unprecedentedly rapid oxime reaction (>150 M-1 s-1) with high specificity for the abasic (AP) site of DNA. The molecular rotor design achieves a robust >250-500-fold increase in fluorescence upon reaction with AP sites in DNA. By using the fluorescence reporter in concert with specific DNA lesion-containing substrates, the UBER probe can be used in a coupled assay in principle with any DNA glycosylase. We demonstrate the utility of the UBER probe by assaying five different glycosylases in real time as well as profiling glycosylase activity in cell lysates. We anticipate that the UBER probe will be of considerable utility to researchers studying DNA repair biology owing to its high level of generalizability, ease of use, and compatibility with biologically derived samples.
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Affiliation(s)
- David L Wilson
- Department of Chemistry, Stanford Cancer Institute and ChEM-H Institute , Stanford University , Stanford , California 94305 , United States
| | - Eric T Kool
- Department of Chemistry, Stanford Cancer Institute and ChEM-H Institute , Stanford University , Stanford , California 94305 , United States
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11
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Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
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12
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Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
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13
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Dang W, Tong C, Yang Y, Liu Y, Liu B, Zhou H, Wang W. A cascade amplification platform assisted with DNAzyme for activity analysis, kinetic study and effector screening of Fpg in vitro. Analyst 2019; 144:1731-1740. [PMID: 30663736 DOI: 10.1039/c8an02253d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
As a highly conserved damage repair protein, Fpg can specifically recognize and digest 8-oxoG from a damaged DNA backbone. Meanwhile, DNAzyme, a single-stranded DNA with enzymatic activity, can cleave RNA in the presence of cofactors. In this study, we established a highly sensitive method for Fpg assay using a DNAzyme-mediated signal cascade amplification strategy. Based on the Fpg-dependent fluorescence response of the "turn-on" manner, we could reliably determine Fpg activity down to 0.14 U mL-1 with a linear response from 0.10 to 40 U mL-1 under optimal conditions. In addition, this strategy was successfully applied to analyze the kinetic parameter of Fpg with Km of 0.061 μM. Furthermore, the developed sensing system was used to screen the regulators of Fpg from natural compounds and antibiotics. These results indicated that all of the 14 natural compounds and 6 kinds of antibiotics deferentially showed an active effect on Fpg in vitro. In summary, these results show that the method not only provides an alternative for monitoring Fpg activity but also shows great potential for drug screening in the future.
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Affiliation(s)
- Wenya Dang
- College of Biology, Hunan University, Changsha, 410082, China.
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14
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Lee CY, Kim HY, Kim S, Park KS, Park HG. A simple and sensitive detection of small molecule-protein interactions based on terminal protection-mediated exponential strand displacement amplification. Analyst 2019; 143:2023-2028. [PMID: 29634063 DOI: 10.1039/c8an00099a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein describe a simple and sensitive strategy to detect a small molecule-protein interaction based on terminal protection-mediated exponential strand displacement amplification (eSDA). In principle, the small molecule linked to a DNA probe protects the DNA probe against the exonuclease I-catalyzed degradation after its binding to the corresponding target protein. The protected DNA probe then serves as a template to promote eSDA. Consequently, a large number of duplexes are produced, which leads to a high fluorescence from a double-stranded DNA specific fluorescent dye, SYBR Green I. As a model system to prove this sensing strategy, the interaction between biotin and streptavidin (SA), which is known to be the strongest among the non-covalent biological interactions, was selected and its analytical performance was thoroughly investigated. As a result, SA was sensitively detected with the limit of detection of 16 pM. In addition, the practical applicability of this method was successfully demonstrated by reliably determining the SA in human serum.
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Affiliation(s)
- Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21 + program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
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15
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Song J, Yin F, Li X, Dong N, Zhu Y, Shao Y, Chen B, Jiang W, Li CZ. Sensitive detection of formamidopyrimidine-DNA glycosylase activity based on target-induced self-primed rolling circle amplification and magnetic nanoprobes. Analyst 2019. [PMID: 29517783 DOI: 10.1039/c7an02032e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We developed a novel approach to determine formamidopyrimidine DNA glycosylase (FPG) activity by taking advantage of target-induced self-primed rolling circle amplification (RCA) and magnetic nanoprobes. Herein, a unique nick (8-oxoguanine, 8-oxoG) was positioned in duplex DNA containing P-circle and P1, which together serve as a FPG substrate, RCA template, and RCA primer probe. The presence of FPG specifically binds 8-oxoG and cleaves the P-circle into two parts, producing 5'-phosphoryl termini. A phosphodiester bond between the 5'-phosphoryl and 3'-hydroxyl termini was formed with the addition of T4 DNA ligase, producing an unnicked circular strand. Using the unnicked strand as the RCA template, the P1 hybridized with the circle probe as a primer will trigger the RCA process. The RCA reaction produces amounts of long tandem-repeat DNA tiles with multiple recognizing regions for the FAM modified DNA probes (FP) and biotin-modified DNA probes (BP). With the streptavidin-biotin interaction, the BPs and FPs can be easily immobilized on the surface of streptavidin-modified magnetic microbeads (MBs). Due to the RCA enhanced and highly-concentrated fluorescence accumulation on the MBs, an ultralow detection limit of 1.033 U mL-1 for FPG was obtained. Combined with the high tolerance capability of human blood serum owing to magnetic isolation, the FPG assays in human blood serum were also obtained using fluorescence and confocal laser scanning microscopy. These results indicate that this robust self-primed RCA combined with magnetic nanoprobes is an excellent candidate for quantitatively monitoring the FPG activity responsible for DNA oxidative damage-related clinical diagnosis and therapy.
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Affiliation(s)
- Juan Song
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China
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16
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Ahn JK, Kim HY, Park KS, Park HG. A Personal Glucose Meter for Label-Free and Washing-Free Biomolecular Detection. Anal Chem 2018; 90:11340-11343. [PMID: 30152994 DOI: 10.1021/acs.analchem.8b02014] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We developed a label-free and washing-free method for biomolecular detection using a personal glucose meter (PGM). ATP was selected as a model target, and cascade enzymatic reactions promoted by hexokinase and pyruvate kinase were adopted to link the amount of ATP to glucose that is detectable by a hand-held PGM. In principle, the presence of target ATP enables hexokinase to catalyze the conversion of glucose to glucose 6-phosphate by providing a phosphate group to glucose, and thus the amount of glucose is decreased in proportion to the amount of ATP. In addition, adenosine 5'-diphosphate (ADP), which is generated after hexokinase-catalyzed enzymatic reaction, is recovered to ATP by a pyruvate kinase enzyme. The regenerated ATP is again supplemented to catalyze multiple rounds of cascade enzymatic reactions, leading to signal amplification. As a result, the change of glucose amount that is inversely proportional to ATP amount is simply measured by a hand-held PGM. By employing this strategy, we successfully determined ATP down to 49 nM with high selectivity even in real samples such as tap water, human serum, and bovine urine. Importantly, the developed system does not require expensive modification and washing steps but is conveniently operated with a commercially available PGM, which would pave the way for the development of a simple and cost-effective sensing platform.
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Affiliation(s)
- Jun Ki Ahn
- Department of Chemical and Biomolecular Engineering, BK21+ Program , KAIST: Korea Advanced Institute of Science & Technology , 291 Daehak-ro , Yuseong-gu, Daejeon 305-701 , Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering, BK21+ Program , KAIST: Korea Advanced Institute of Science & Technology , 291 Daehak-ro , Yuseong-gu, Daejeon 305-701 , Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering , Konkuk University , Seoul 05029 , Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, BK21+ Program , KAIST: Korea Advanced Institute of Science & Technology , 291 Daehak-ro , Yuseong-gu, Daejeon 305-701 , Republic of Korea
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17
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Abstract
DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.
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Affiliation(s)
- David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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18
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Li P, Kumar S, Park KS, Park HG. Development of a rapid and simple tetracycline detection system based on metal-enhanced fluorescence by europium-doped AgNP@SiO 2 core-shell nanoparticles. RSC Adv 2018; 8:24322-24327. [PMID: 35539166 PMCID: PMC9082042 DOI: 10.1039/c8ra03185a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/26/2018] [Indexed: 12/23/2022] Open
Abstract
We herein describe a rapid and selective sensing platform for tetracycline (Tc), which relies on the metal-enhanced fluorescence (MEF) effect of europium (Eu3+)-doped silver-silica core-shell nanoparticles (AgNP@SiO2). The developed assay utilizes AgNP@SiO2 as a key detection component, which is systematically optimized to have a silica shell thickness suitable for the effective MEF phenomenon. In principle, the AgNP@SiO2, which binds to Eu3+ through the electrostatic interaction, captures Tc by selective chelation with Eu3+, leading to significant fluorescence enhancement of the EuTc complex. Based on this novel strategy, we determined Tc as low as 83.1 nM with a total assay time of less than 10 min, which is comparable to or better than that of the previous fluorescence-based methods. Furthermore, the practical applicability of this strategy was successfully demonstrated by detecting Tc in tap water. This work highlights the unique features of AgNP@SiO2 for MEF-based biosensing applications.
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Affiliation(s)
- Pei Li
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea +82-42-350-3910 +82-42-350-3932
| | - Sathish Kumar
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea +82-42-350-3910 +82-42-350-3932
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University Seoul 05029 Republic of Korea +82-2-450-3742 +82-2-450-3742
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea +82-42-350-3910 +82-42-350-3932
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19
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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