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Nowak-Karnowska J, Głuszyńska A, Kosman J, Dembska A. Fluorescence Turn-Off Ligand for Parallel G-Quadruplexes. Molecules 2024; 29:3907. [PMID: 39202986 PMCID: PMC11357100 DOI: 10.3390/molecules29163907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Parallel-stranded G-quadruplex structures are found to be common in the human promoter sequences. We tested highly fluorescent 9-methoxyluminarine ligand (9-MeLM) binding interactions with different parallel G-quadruplexes DNA by spectroscopic methods such as fluorescence and circular dichroism (CD) titration as well as UV melting profiles. The results showed that the studied 9-MeLM ligand interacted with the intramolecular parallel G-quadruplexes (G4s) with similar affinity. The binding constants of 9-methoxyluminarine with different parallel G4s were determined. The studies upon oligonucleotides with different flanking sequences on c-MYC G-quadruplex suggest that 9-methoxyluminarine may preferentially interact with 3'end of the c-MYC promoter. The high decrease in 9-MeLM ligand fluorescence upon binding to all tested G4s indicates that 9-methoxyluminarine molecule can be used as a selective fluorescence turn-off probe for parallel G-quadruplexes.
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Affiliation(s)
- Joanna Nowak-Karnowska
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (J.N.-K.); (A.G.)
| | - Agata Głuszyńska
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (J.N.-K.); (A.G.)
| | - Joanna Kosman
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (J.N.-K.); (A.G.)
- Laboratory of Molecular Assays and Imaging, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Anna Dembska
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (J.N.-K.); (A.G.)
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2
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Kim S, Shin WH, Kang Y, Kim H, Lee JY. Direct visualization of replication and R-loop collision using single-molecule imaging. Nucleic Acids Res 2024; 52:259-273. [PMID: 37994723 PMCID: PMC10783495 DOI: 10.1093/nar/gkad1101] [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: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
R-loops are three-stranded nucleic acid structures that can cause replication stress by blocking replication fork progression. However, the detailed mechanism underlying the collision of DNA replication forks and R-loops remains elusive. To investigate how R-loops induce replication stress, we use single-molecule fluorescence imaging to directly visualize the collision of replicating Phi29 DNA polymerase (Phi29 DNAp), the simplest replication system, and R-loops. We demonstrate that a single R-loop can block replication, and the blockage is more pronounced when an RNA-DNA hybrid is on the non-template strand. We show that this asymmetry results from secondary structure formation on the non-template strand, which impedes the progression of Phi29 DNAp. We also show that G-quadruplex formation on the displaced single-stranded DNA in an R-loop enhances the replication stalling. Moreover, we observe the collision between Phi29 DNAp and RNA transcripts synthesized by T7 RNA polymerase (T7 RNAp). RNA transcripts cause more stalling because of the presence of T7 RNAp. Our work provides insights into how R-loops impede DNA replication at single-molecule resolution.
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Affiliation(s)
- Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Woo Hee Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
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3
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Wu M, Yang B, Shi L, Tang Q, Wang J, Liu W, Li B, Jin Y. Peroxidase-Mimicking DNAzymes as Receptors for Label-Free Discriminating Heavy Metal Ions by Chemiluminescence Sensor Arrays. Anal Chem 2023; 95:3486-3492. [PMID: 36733985 DOI: 10.1021/acs.analchem.2c05447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Receptors are crucial to the analytical performance of sensor arrays. Different from the previous receptors in sensor arrays, herein, peroxidase-mimicking DNAzymes were innovatively used as receptors to develop a label-free chemiluminescence sensor array for discriminating various heavy metal ions in complex samples. The peroxidase-mimicking DNAzymes are composed of functional oligonucleotides and hemin, including G-triplex-hemin DNAzyme (G3-DNAzyme), G-quadruplex-hemin DNAzyme (G4-DNAzyme), and the dimer of G-quadruplex-hemin DNAzyme (dG4-DNAzyme). Circular dichroism (CD) spectroscopy demonstrated that different metal ions diversely affect the conformation of G-quadruplex and G-triplex, resulting in a change in the activity of peroxidase-mimicking DNAzyme. Thus, the unique fingerprints formed to easily discriminate seven kinds of heavy metal ions by principal component analysis (PCA) within 20 min. The discrimination of unknown metal ions in tap water further confirmed its ability for discriminating multiple heavy metal ions. Moreover, it will not bring water pollution due to the good biocompatibility of DNA. Therefore, it not only merely offers a label-free, rapid, environment-friendly, and cheap (1.49 $) sensor assay for discriminating metal ions but also comes up with an innovative way for developing sensor arrays.
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Affiliation(s)
- Mengmeng Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bing Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qiaorong Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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4
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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5
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Gao X, Sun Z, Wang X, Zhang W, Xu D, Sun X, Guo Y, Xu S, Li F. Construction of a dual-model aptasensor based on G-quadruplexes generated via rolling circle amplification for visual/sensitive detection of kanamycin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156276. [PMID: 35644384 DOI: 10.1016/j.scitotenv.2022.156276] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
A dual-model colorimetric and electrochemical aptasensor was designed using a large number of G-quadruplexes generated by rolling circle amplification (RCA). Specific binding between target and aptamer during RCA yielded large numbers of G-quadruplexes. A colorimetric sensor was fabricated based on the interaction between the G-quadruplex and hemin, which altered the 3,3',5,5'-Tetramethylbenzidine (TMB)-catalyzed color reaction and facilitated the visual and semi-quantitative detection of kanamycin. An electrochemical sensor was constructed based on the strong interaction between the G-quadruplex and the methylene blue electrical signal molecule. Combining nanocomposites multi-walled carbon nanotubes-chitosan/gold nanoparticles (MWCNTs-CS/AuNPs) and RCA realized double-amplified electrochemical signals. Under optimized conditions, a linear relationship was obtained as the logarithm of different concentrations of kanamycin (KAN). The colorimetric aptasensor had a linear range of 1 × 102 nM to 1 × 103 nM with a detection limit of 1.949 nM. The electrochemical aptasensor had wider a linear range from 1 × 10-3 nM to 2.5 × 103 nM and a lower detection limit of 0.333 pM. The sensor combined the advantages of simple colorimetric visualization with the ultra-precision of electrochemical methods. Aptasensor showed good specificity and prevented interference. Furthermore, the prepared dual-model aptasensor facilitated the practical monitoring of KAN in milk.
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Affiliation(s)
- Xiaolin Gao
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Zhicong Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Xiaoyang Wang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Wanqi Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Deyan Xu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Yemin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China
| | - Shicai Xu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Falan Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 12 Zhangzhou Road, Zibo 255049, Shandong Province, China.
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6
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Kosman J, Żukowski K, Csáki A, Fritzsche W, Juskowiak B. Sequence Effect on the Activity of DNAzyme with Covalently Attached Hemin and Their Potential Bioanalytical Application. SENSORS (BASEL, SWITZERLAND) 2022; 22:500. [PMID: 35062461 PMCID: PMC8780643 DOI: 10.3390/s22020500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
In this work we investigated the effect of a DNA oligonucleotide sequence on the activity of a DNAzyme with covalently attached hemin. For this purpose, we synthesized seven DNA-hemin conjugates. All DNA-hemin conjugates as well as DNA/hemin complexes were characterized using circular dichroism, determination of melting temperatures and pKa of hemin. We observed that hemin conjugation in most cases led to the formation of parallel G-quadruplexes in the presence of potassium and increased thermal stability of all studied systems. Although the activity of DNA-hemin conjugates depended on the sequence used, the highest activity was observed for the DNA-hemin conjugate based on a human telomeric sequence. We used this DNAzyme for development of "sandwich" assay for detection of DNA sequence. For this assay, we used electric chip which could conduct electricity after silver deposition catalyzed by DNAzyme. This method was proved to be selective towards DNA oligonucleotides with mismatches and could be used for the detection of the target. To prove the versatility of our DNAzyme probe we also performed experiments with streptavidin-coated microplates. Our research proved that DNAzyme with covalently attached hemin can be used successfully in the development of heterogeneous assays.
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Affiliation(s)
- Joanna Kosman
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
| | - Krzysztof Żukowski
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
| | - Andrea Csáki
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany; (A.C.); (W.F.)
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany; (A.C.); (W.F.)
| | - Bernard Juskowiak
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
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7
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Yang H, Peng Y, Xu M, Xu S, Zhou Y. Development of DNA Biosensors Based on DNAzymes and Nucleases. Crit Rev Anal Chem 2021; 53:161-176. [PMID: 34225516 DOI: 10.1080/10408347.2021.1944046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Shuxia Xu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China.,College of Ecology and Environment, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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8
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Canesin G, Di Ruscio A, Li M, Ummarino S, Hedblom A, Choudhury R, Krzyzanowska A, Csizmadia E, Palominos M, Stiehm A, Ebralidze A, Chen SY, Bassal MA, Zhao P, Tolosano E, Hurley L, Bjartell A, Tenen DG, Wegiel B. Scavenging of Labile Heme by Hemopexin Is a Key Checkpoint in Cancer Growth and Metastases. Cell Rep 2021; 32:108181. [PMID: 32966797 PMCID: PMC7551404 DOI: 10.1016/j.celrep.2020.108181] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/03/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022] Open
Abstract
Hemopexin (Hx) is a scavenger of labile heme. Herein, we present data defining the role of tumor stroma-expressed Hx in suppressing cancer progression. Labile heme and Hx levels are inversely correlated in the plasma of patients with prostate cancer (PCa). Further, low expression of Hx in PCa biopsies characterizes poorly differentiated tumors and correlates with earlier time to relapse. Significantly, heme promotes tumor growth and metastases in an orthotopic murine model of PCa, with the most aggressive phenotype detected in mice lacking Hx. Mechanistically, labile heme accumulates in the nucleus and modulates specific gene expression via interacting with guanine quadruplex (G4) DNA structures to promote PCa growth. We identify c-MYC as a heme:G4-regulated gene and a major player in heme-driven cancer progression. Collectively, these results reveal that sequestration of labile heme by Hx may block heme-driven tumor growth and metastases, suggesting a potential strategy to prevent and/or arrest cancer dissemination. Canesin et al. describe a role and mechanism for labile heme as a key player in regulating gene expression to promote carcinogenesis via binding to G-quadruplex in the c-MYC promoter. Hemopexin, a heme scavenger, may be used as a strategy to block progression of cancer.
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Affiliation(s)
- Giacomo Canesin
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Annalisa Di Ruscio
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA.
| | - Mailin Li
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | - Simone Ummarino
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | - Andreas Hedblom
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Reeham Choudhury
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Agnieszka Krzyzanowska
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Eva Csizmadia
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Macarena Palominos
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Anna Stiehm
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Alexander Ebralidze
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Shao-Yong Chen
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Mahmoud A Bassal
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Ping Zhao
- College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Emanuela Tolosano
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Laurence Hurley
- College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Anders Bjartell
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Cambridge, MA 02138, USA
| | - Barbara Wegiel
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA.
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9
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Xiang X, Bao Y, Sun L, Zhang Y, Guo X. A stable uncompleted tetramolecular G-quadruplex formed by d(AG nA) under acidic condition. Int J Biol Macromol 2021; 176:66-71. [PMID: 33577823 DOI: 10.1016/j.ijbiomac.2021.02.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/06/2021] [Accepted: 02/07/2021] [Indexed: 01/12/2023]
Abstract
In this work, the effects of terminal adenines on the formation and stability of tetramolecular G-quadruplexes (G4s) have been studied by electrospray ionization mass spectrometry (ESI-MS), UV, CD and NMR spectroscopy. Several evidences suggested that the sequences d(AGnA) (n = 4 or 5) form stable uncompleted tetramolecular G4 at acidic condition which is different from the canonical one in the neutral condition. In addition, hydrolysis of guanine has also been observed in acidic condition that may occur for unpaired strands rather than in complete G4. Thus, a new G4 topology containing incomplete G-quartet is proposed that is very stable and particularly presents in acidic ammonium ions solution. The information presented in this study provides the new insight on the polymorphism of G4s in acidic environment, which may help understand of the special role of adenines on the formation of G4s.
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Affiliation(s)
- Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Likang Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China.
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10
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Increasing the activity of DNAzyme based on the telomeric sequence: 2’-OMe-RNA and LNA modifications. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract2’-OMe-RNA analogues and LNA point modifications of DNA oligonucleotides were applied for the modulation of the G-quadruplex topology and enhancement of peroxidase activity of the resulting DNAzymes. The effect of the 2’-OMe-RNA analogue was studied for full length modified oligonucleotides with various sequences. In the case of LNA-point modification, we have chosen a telomeric DNA sequence and investigated various numbers of modifications. Our main goal was to prove that the application of these modifications can influence the activity of DNAzyme, especially those, which normally form poor DNAzymes. As an example, we have chosen the telomeric HT22 sequence which is known to form DNAzyme characterized by low activity. In all cases, the DNAzymes formed by a telomeric sequence with the application of the 2’-OMe-RNA analogue as well as LNA-point modification, showed significantly higher peroxidase activity. We were also able to shift the formation of hybrid or antiparallel topology to parallel topology. These results are important for the development of probes for biological applications as well as for the design of probes based on DNA sequences that normally form DNAzymes with low activity. This paper also provides information on how the application of nucleotide analogues can transform the topology of G-quadruplexes.
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11
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Lv M, Guo Y, Ren J, Wang E. Exploration of intramolecular split G-quadruplex and its analytical applications. Nucleic Acids Res 2019; 47:9502-9510. [PMID: 31504779 PMCID: PMC6765144 DOI: 10.1093/nar/gkz749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/13/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Distinct from intermolecular split G-quadruplex (Inter-SG), intramolecular split G-quadruplex (Intra-SG) which could be generated in a DNA spacer-inserted G-quadruplex strand has not been systematically explored. Not only is it essential for the purpose of simplicity of DNA-based bioanalytical applications, but also it will give us hints how to design split G-quadruplex-based system. Herein, comprehensive information is provided about influences of spacer length and split mode on the formation of Intra-SG, how to adjust its thermodynamic stability, and selection of optimal Intra-SG for bioanalysis. For instances, non-classical Intra-SG (e.g. 2:10, 4:8 and 5:7) displays lower stability than classical split strands (3:9, 6:6 and 9:3), which is closely related to integrity of consecutive guanine tract; as compared to regular Intra-SG structures, single-thymine capped ones have reduced melting temperature, providing an effective approach to adjustment of stability. It is believed that the disclosed rules in this study will contribute to the effective application of split G-quadruplex in the field of DNA technology in the future.
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Affiliation(s)
- Mengmeng Lv
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuchun Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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12
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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13
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Abstract
G-quadruplex DNAzymes are short DNA aptamers with repeating G4 quartets bound in a non-covalent complex with hemin. These G4/Hemin structures exhibit versatile peroxidase-like catalytic activity with a wide range of potential applications in biosensing and biotechnology. Current efforts are aimed at gaining a better understanding of the molecular mechanism of DNAzyme catalysis as well as devising strategies for improving their catalytic efficiency. Multimerisation of discrete units of G-quadruplexes to form multivalent DNAzyes is an emerging design strategy aimed at enhancing the peroxidase activities of DNAzymes. While this approach holds promise of generating more active multivalent G-quadruplex DNAzymes, few examples have been studied and it is not clear what factors determine the enhancement of catalytic activities of multimeric DNAzymes. In this study, we report the design and characterisation of multimers of five G-quadruplex sequences (AS1411, Bcl-2, c-MYC, PS5.M and PS2.M). Our results show that multimerisation of G-quadruplexes that form parallel structure (AS1411, Bcl-2, c-MYC) leads to significant rate enhancements characteristic of cooperative and/or synergistic interactions between the monomeric units. In contrast, multimerisation of DNA sequences that form non-parallel structures (PS5.M and PS2.M) did not exhibit similar levels of synergistic increase in activities. These results show that design of multivalent G4/Hemin structures could lead to a new set of versatile and efficient DNAzymes with enhanced capacity to catalyse peroxidase-mimic reactions.
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Fu H, Yang P, Hai J, Li H. Utilization of circular dichroism and electrospray ionization mass spectrometry to understand the formation and conversion of G-quadruplex DNA at the human c-myb proto-oncogene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:70-76. [PMID: 29860170 DOI: 10.1016/j.saa.2018.05.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 06/08/2023]
Abstract
G-quadruplex DNAs are involved in a number of key biological processes, including gene expression, transcription, and apoptosis. The c-myb oncogene contains a number of GGA repeats in its promoter which forms G-quadruplex, thus it could be used as a target in cancer therapeutics. Several in-vitro studies have used Circular Dichroism (CD) spectroscopy or electrospray ionization mass spectrometry (ESI-MS) to demonstrate formation and stability of G-quadruplex DNA structure in the promoter region of human c-myb oncogene. The factors affecting the c-myb G-quadruplex structures were investigated, such as cations (i.e. K+, NH4+ and Na+) and co-solutes (methanol and polyethylene glycol). The results indicated that the presence of cations and co-solutes could change the G-quadruplex structural population and promote its thermodynamic stabilization as indicated by CD melting curves. It indicated that the co-solutes preferentially stabilize the c-myb G-quadruplex structure containing both homo- and hetero-stacking. In addition, protopine was demonstrated as a binder of c-myb G-quadruplex as screened from a library of natural alkaloids using ESI-MS method. CD spectra showed that it could selectively stabilize the c-myb G-quadruplex structure compared to other six G-quadruplexes from tumor-related G-rich sequences and the duplex DNAs (both long and short-chain ones). The binding of protopine could induce the change in the G-quadruplex structural populations. Therefore, protopine with its high binding specificity could be considered as a precursor for the design of drugs to target and regulate c-myb oncogene transcription.
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Affiliation(s)
- Hengqing Fu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Pengfei Yang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinhui Hai
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China.
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15
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Kosman J, Żukowski K, Juskowiak B. Comparison of Characteristics and DNAzyme Activity of G4⁻Hemin Conjugates Obtained via Two Hemin Attachment Methods. Molecules 2018; 23:molecules23061400. [PMID: 29890720 PMCID: PMC6100319 DOI: 10.3390/molecules23061400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022] Open
Abstract
Two conjugation methods using different linkers were applied for the investigation of the spectral characteristics and activity of G-quadruplex (G4)–hemin conjugates. For this purpose, two G-quadruplex-forming DNA sequences were selected, and then conjugated to a hemin molecule via either amine coupling or a click reaction. The products obtained via these two methods differed in their chemistry and the length of the linker between the DNA and hemin molecules. Spectral characteristics revealed that both methods produced conjugates that were more thermally stable than G4/hemin complexes. Despite similar spectral characteristics, the conjugates obtained via these two methods differed in their DNAzyme activity. G4–hemin conjugates obtained through amine coupling exhibited higher activity than conjugates obtained through a click reaction. This was potentially due to the length and chemistry of the linker, which was 30 atoms long following the click reaction, but only six atoms long following amine coupling. A longer connector favors higher flexibility, and hence, reduces the binding of hemin with G4. The aromatic groups present in the linker obtained through the click reaction can also disturb the G4–hemin interaction. However, the conjugation of G4 DNA to hemin via the click reaction was connected to a higher yield, and did not require any sophisticated synthesis equipment.
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Affiliation(s)
- Joanna Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Krzysztof Żukowski
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
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16
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Ai T, Yang Q, Lv Y, Huang Y, Li Y, Geng J, Xiao D, Zhou C. Insight into How Telomeric G-Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin. Chem Asian J 2018; 13:1805-1810. [PMID: 29718585 DOI: 10.1002/asia.201800464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/30/2018] [Indexed: 02/05/2023]
Abstract
The toxic oxidative damage of G-quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label-free and nanopore-based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)n ). The nanopore-based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single-molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (Ka )≈106 m-1 ) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of Ka to approximately 107 m-1 . Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π-π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H2 O2 in the catalytic cycle. Our studies developed a label-free and single-molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative-damage property in cellular oxidative disease and anticancer therapeutics.
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Affiliation(s)
- Tingting Ai
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - You Lv
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuqin Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuzhi Li
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Jia Geng
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P.R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
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17
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Sato H, Shimada N, Masuda T, Maruyama A. Allosteric Control of Peroxidase-Mimicking DNAzyme Activity with Cationic Copolymers. Biomacromolecules 2018; 19:2082-2088. [DOI: 10.1021/acs.biomac.8b00201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hiroki Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Tsukuru Masuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
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18
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Maguire D, Neytchev O, Talwar D, McMillan D, Shiels PG. Telomere Homeostasis: Interplay with Magnesium. Int J Mol Sci 2018; 19:E157. [PMID: 29303978 PMCID: PMC5796106 DOI: 10.3390/ijms19010157] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 12/14/2022] Open
Abstract
Telomere biology, a key component of the hallmarks of ageing, offers insight into dysregulation of normative ageing processes that accompany age-related diseases such as cancer. Telomere homeostasis is tightly linked to cellular metabolism, and in particular with mitochondrial physiology, which is also diminished during cellular senescence and normative physiological ageing. Inherent in the biochemistry of these processes is the role of magnesium, one of the main cellular ions and an essential cofactor in all reactions that use ATP. Magnesium plays an important role in many of the processes involved in regulating telomere structure, integrity and function. This review explores the mechanisms that maintain telomere structure and function, their influence on circadian rhythms and their impact on health and age-related disease. The pervasive role of magnesium in telomere homeostasis is also highlighted.
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Affiliation(s)
- Donogh Maguire
- Emergency Medicine Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK.
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow G4 0SF, UK.
| | - Ognian Neytchev
- Section of Epigenetics, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK.
| | - Dinesh Talwar
- The Scottish Trace Element and Micronutrient Reference Laboratory, Department of Biochemistry, Royal Infirmary, Glasgow G31 2ER, UK.
| | - Donald McMillan
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow G4 0SF, UK.
| | - Paul G Shiels
- Section of Epigenetics, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK.
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19
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Shahbazi N, Hosseinkhani S, Khajeh K, Ranjbar B. Structural and functional study of a simple, rapid, and label-free DNAzyme-based DNA biosensor for optimization activity. Biopolymers 2017; 107. [DOI: 10.1002/bip.23028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 03/23/2017] [Accepted: 04/26/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Narges Shahbazi
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biochemistry, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Khosro Khajeh
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biochemistry, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Bijan Ranjbar
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
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20
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Xu L, Shen X, Li B, Zhu C, Zhou X. G-quadruplex based Exo III-assisted signal amplification aptasensor for the colorimetric detection of adenosine. Anal Chim Acta 2017. [PMID: 28622804 DOI: 10.1016/j.aca.2017.05.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine. The strategy employed two unlabeled hairpin DNA oligonucleotides (HP1 and HP2), where HP1 contained the aptamer towards adenosine and HP2 embedded the guanine-rich sequence (GRS). In the presence of adenosine, hairpin HP1 could form specific binding with adenosine and trigger the unfolding of HP1's hairpin structure. The resulting adenosine-HP1 complex could hybridize with HP2, generating the Exo III recognition site. After Exo III-assisted degradation, the GRS was released from HP2, and the adenosine-HP1 was released back to the solution to combine another HP2, inducing the cycling amplification. After multiple circulations, the released ample GRSs were induced to form G-quadruplex, further catalyzing the oxidation of TMB, yielding a color change which was finally mirrored in the absorbance change. On the contrary, the absence of adenosine failed to unfold HP1, remaining color unchanged eventually. Thanks to the amplification strategy, the limit of detection was lowered to 17 nM with a broad linear range from 50 nM to 6 μM. The proposed method was successfully applied to the detection of adenosine in biological samples and satisfying recoveries were acquired.
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Affiliation(s)
- Lei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Xin Shen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Bingzhi Li
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Chunhong Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Xuemin Zhou
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China.
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21
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Kosman J, Stanislawska A, Gluszynska A, Juskowiak B. Conjugation of hemin to G-quadruplex forming oligonucleotide using click chemistry. Int J Biol Macromol 2017; 101:799-804. [PMID: 28366862 DOI: 10.1016/j.ijbiomac.2017.03.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022]
Abstract
Peroxidase-mimicking DNAzyme is one of the systems that recently gained a great interest. It has been successfully applied for designing numerous bioassays. The success of this system is connected to its advantages over a protein enzyme, horseradish peroxidase. Promising strategy for further improvement of performance of DNAzyme with peroxidase-like activity was proposed recently. It was based on the covalent attachment of hemin moiety to the G-quadruplex scaffold. We report here the first attempt of conjugating hemin to the G-quadruplex DNA using click chemistry approach. We modified hemin molecule through attachment of an azide-terminated linker to the porphyrin carboxylic group. Two click chemistry approaches were examined to conjugate the azide-modified hemin to a G-quadruplex oligonucleotide: copper-catalyzed and Cu-free cycloaddition reactions. Using Cu-free click reaction, we successfully synthesized G-quadruplex-hemin conjugate that exhibited promising peroxidase activity.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - A Stanislawska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - A Gluszynska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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