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Jiang L, Teng J, Liu X, Xu L, Yang T, Hu X, Ding S, Li J, Jiang Y, Cheng W. Interaction analysis of RNA G-quadruplex with ligands and in situ imaging application. Anal Biochem 2024; 694:115613. [PMID: 39002744 DOI: 10.1016/j.ab.2024.115613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
RNA G4, as an integral branch of G4 structure, possesses distinct interactions with ligands compared to the common DNA G4, thus the investigation of RNA G4/ligand interactions might be considered as a fresh breakthrough to improve the biosensing performance of G4/ligand system. In this study, we comparatively explored the structural and functional mechanisms of RNA G4 and DNA G4 in the interaction with ligands, hemin and thioflavin T (ThT), utilizing the classical PS2.M sequence as a model. We found that although the catalytic performance of RNA G4/hemin system was lower than DNA G4/hemin, RNA G4/ThT fluorescence system exhibited a significant improvement (2∼3-fold) compared to DNA G4/ThT, and adenine modification could further enhance the signaling. Further, by exploring the interaction between RNA G4 and ThT, we deemed that RNA G4 and ThT were stacked in a bimolecular mode compared to single-molecule binding of DNA G4/ThT, thus more strongly limiting the structural spin in ThT excited state. Further, RNA G4/ThT displayed higher environmental tolerance and lower ion dependence than DNA G4/ThT. Finally, we employed RNA G4/ThT as a highly sensitive label-free fluorescent signal output system for in situ imaging of isoforms BCR-ABL e13a2 and e14a2. Overall, this study successfully screened a high-performance RNA G4 biosensing system through systematic RNA G4/ligands interaction studies, which was expected to provide a promising reference for subsequent G4/ligand research.
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Affiliation(s)
- Lanxin Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jie Teng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China; Department of Laboratory Medicine, West China Second Hospital of Sichuan University, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610066, PR China
| | - Xiaojuan Liu
- Department of Laboratory Medicine, West China Second Hospital of Sichuan University, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610066, PR China
| | - Lulu Xu
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xingping Hu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yongmei Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China; Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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2
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Cao Y, Li W, Pei R. Exploring the catalytic mechanism of multivalent G-quadruplex/hemin DNAzymes by modulating the position and spatial orientation of connected G-quadruplexes. Anal Chim Acta 2022; 1221:340105. [DOI: 10.1016/j.aca.2022.340105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
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3
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Fenati RA, Locock K, Qu Y, Ellis AV. Oxacillin Coupled G-Quadruplexes as a Novel Biofilm-Specific Antibiotic for Staphylococcus aureus Biofilms. ACS APPLIED BIO MATERIALS 2019; 2:3002-3008. [DOI: 10.1021/acsabm.9b00336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Renzo A. Fenati
- School of Chemical and Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Yue Qu
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Clayton, Victoria 3800, Australia
| | - Amanda V. Ellis
- School of Chemical and Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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4
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Shi H, Li D, Xu F, He X, Wang K, Ye X, Tang J, He C. A label-free activatable aptamer probe for colorimetric detection of cancer cells based on binding-triggered in situ catalysis of split DNAzyme. Analyst 2015; 139:4181-4. [PMID: 25037636 DOI: 10.1039/c4an00561a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A novel label-free tailed hairpin-shaped activatable aptamer probe (THAAP) was developed by rationally integrating an aptamer and a split G-quadruplex into one sequence. Based on target recognition-triggered in situ catalysis of split DNAzyme, the THAAP strategy achieved a simple, fast, washing-free, specific and quantitative colorimetric assay of human leukemic CCRF-CEM cells.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
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5
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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6
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Li T, Lohmann F, Famulok M. Interlocked DNA nanostructures controlled by a reversible logic circuit. Nat Commun 2014; 5:4940. [PMID: 25229207 PMCID: PMC4199106 DOI: 10.1038/ncomms5940] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 08/07/2014] [Indexed: 12/04/2022] Open
Abstract
DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.
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Affiliation(s)
- Tao Li
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
| | - Finn Lohmann
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
| | - Michael Famulok
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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7
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G-quadruplex DNAzyme-based microcystin-LR (toxin) determination by a novel immunosensor. Biosens Bioelectron 2011; 26:4393-8. [DOI: 10.1016/j.bios.2011.04.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/25/2011] [Accepted: 04/25/2011] [Indexed: 01/13/2023]
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Shi Y, Huang WT, Luo HQ, Li NB. A label-free DNA reduced graphene oxide-based fluorescent sensor for highly sensitive and selective detection of hemin. Chem Commun (Camb) 2011; 47:4676-8. [PMID: 21423976 DOI: 10.1039/c0cc05518b] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
G-quadruplex structure aptamer (PS2.M) can capture acridine orange (AO) from reduced graphene oxide (rGO). When the AO-PS2.M/rGO mixture is incubated with hemin, the specific binding of hemin with PS2.M results in a release of AO from PS2.M and return of AO back to rGO. Based on the quenching of fluorescence, the target hemin was detected sensitively and selectively, giving a detection limit of 50 nM.
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Affiliation(s)
- Yan Shi
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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Lai Y, Ma Y, Sun L, Jia J, Weng J, Hu N, Yang W, Zhang Q. A highly selective electrochemical biosensor for Hg2+ using hemin as a redox indicator. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.01.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Kong DM, Xu J, Shen HX. Positive effects of ATP on G-quadruplex-hemin DNAzyme-mediated reactions. Anal Chem 2010; 82:6148-53. [PMID: 20552961 DOI: 10.1021/ac100940v] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Some G-quadruplex-hemin complexes can be used as peroxidase-mimicking DNAzymes, catalyzing H(2)O(2)-mediated reactions such as the oxidation of 2,2'-azinobis (3-ethylbenzothiozoline)-6-sulfonic acid (ABTS) by H(2)O(2). However, some challenges, for example, the relatively low catalytic activity and the disproportionation of the reaction product ABTS*(+), may seriously restrict further development and applications of these complexes. Here, we demonstrated the positive effect of adenosine triphosphate (ATP) on G-quadruplex-hemin DNAzyme-mediated catalytic reactions. The presence of ATP not only improved the catalytic activity of G-quadruplex-hemin DNAzymes, but also inhibited the disproportionation of ABTS*(+). These observations may improve the performance of existing G-quadruplex-hemin DNAzyme-based chemical sensors, for example, the Ag(+)-detection method that uses G-quadruplex-hemin DNAzymes, and widen the application range of G-quadruplex-hemin DNAzymes. We also demonstrated that the phosphate groups, nucleobase, and sugar of ATP determine the reaction-promoting ability of ATP. These observations may be helpful in the design of highly efficient enhancers for G-quadruplex-hemin DNAzymes.
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Affiliation(s)
- De-Ming Kong
- Key Laboratory of Functional Polymer Materials (Nankai University), Ministry of Education, Nankai University, Tianjin 300071, P. R. China.
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Hong Y, Xiong H, Lam J, Häußler M, Liu J, Yu Y, Zhong Y, Sung H, Williams I, Wong K, Tang B. Fluorescent Bioprobes: Structural Matching in the Docking Processes of Aggregation-Induced Emission Fluorogens on DNA Surfaces. Chemistry 2010; 16:1232-45. [DOI: 10.1002/chem.200900778] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Nakayama S, Sintim HO. Colorimetric split G-quadruplex probes for nucleic acid sensing: improving reconstituted DNAzyme's catalytic efficiency via probe remodeling. J Am Chem Soc 2009; 131:10320-33. [PMID: 19621970 DOI: 10.1021/ja902951b] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Split G-rich DNA probes can assemble into active peroxidase-mimicking DNAzymes in the presence of bioanalytes such as DNA, thereby providing a simple and cheap means to detect analytes in biological samples. A comprehensive study designed to reveal the salient probe architectural features and reaction conditions that facilitate facile reconstitution into enzymatically proficient enzymes unveiled these important findings: (a) The loops that connect the G3-tracts in a G-quadruplex structure can be replaced with a stem-loop or loop-stem-loop motif without destabilizing the resulting quadruplex structure; endowing the split G-rich probes with regions of limited complementarity leads to more proficient reconstituted enzymes. (b) The addition of hemin to antiparallel G-quadruplex DNAzymes lead to a blue shift in the CD spectra of the G-quadruplex DNAzymes. (c) The architectures of the DNA motifs that lie adjacent to the G-quadruplex structure influence both the stability and the enzymatic proficiency of the reconstituted enzymes. (d) The nature of the monovalent cation that is present in excess is a key determinant of the turnover number of the G-quadruplex DNAzyme; decomposition of G-quadruplex DNAzymes is slower in buffers that contain ammonium ions than those that contain sodium or potassium ions. These findings are important for the design of bioassays that use peroxidase-mimicking G-quadruplexes as detection labels.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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Li T, Dong S, Wang E. G-quadruplex aptamers with peroxidase-like DNAzyme functions: which is the best and how does it work? Chem Asian J 2009; 4:918-922. [PMID: 19422006 DOI: 10.1002/asia.200900019] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Some G-quadruplex DNA aptamers have been found to strongly bind hemin to form DNAzymes with peroxidase-like activity. To help determine the most suitable DNAzymes and to understand how they work, five previously reported G-quadruplex aptamers were compared for their binding affinity and then the potential catalytic mechanism of their corresponding hemin-G-quadruplex DNAzymes was explored. Among these aptamers, a G-quadruplex named AGRO100 was shown to possess the highest hemin-binding affinity and the best DNAzyme function. This means that AGRO100 is the most ideal candidate for DNAzyme-based analysis. Furthermore, we found the peroxidase-like activity of DNAzyme to be primarily dependent on the concentration of H(2)O(2) and independent of that of the peroxidase substrate (that is, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt). Accordingly, a reaction mechanism for DNAzyme-catalyzed peroxidation is proposed. This study provides new insights into the G-quadruplex-based DNAzymes and will help us to further extend their applications in the analytical field.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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Li T, Wang E, Dong S. A grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. PLoS One 2009; 4:e5126. [PMID: 19357767 PMCID: PMC2663033 DOI: 10.1371/journal.pone.0005126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 03/13/2009] [Indexed: 11/19/2022] Open
Abstract
Nucleic acid aptamers are generally obtained by in vitro selection. Some have G-rich consensus sequences with ability to fold into the four-stranded structures known as G-quadruplexes. A few G-quadruplex aptamers have proven to bind hemin to form a new class of DNAzyme with the peroxidase-like activity, which can be significantly promoted by appending an appropriate base-pairing duplex onto the G-quadruplex structures of aptamers. Knowing the structural role of base pairing, here we introduce a novel grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. To demonstrate this strategy, three existing G-quadruplex aptamers are chosen as the first generation. A base-pairing DNA duplex is grafted onto the G-quadruplex motif of the first generation aptamers. Consequently, three new aptamers with the quadruplex/duplex DNA structures are produced as the second generation. The hemin-binding affinities and DNAzyme functions of the second generation aptamers are characterized and compared with the first generation. The results indicate three G-quadruplex aptamers obtained by the grafting strategy have more excellent properties than the corresponding original aptamers. Our findings suggest that, if the structures and functions of existing aptamers are thoroughly known, the grafting strategy can be facilely utilized to improve the aptamer properties and thereby producing better next-generation aptamers. This provides a simple but effective approach to the design of nucleic acid aptamers and DNAzymes.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
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15
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Li T, Shi L, Wang E, Dong S. Silver-Ion-Mediated DNAzyme Switch for the Ultrasensitive and Selective Colorimetric Detection of Aqueous Ag+and Cysteine. Chemistry 2009; 15:3347-50. [DOI: 10.1002/chem.200900056] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Li T, Dong S, Wang E. Label-Free Colorimetric Detection of Aqueous Mercury Ion (Hg2+) Using Hg2+-Modulated G-Quadruplex-Based DNAzymes. Anal Chem 2009; 81:2144-9. [DOI: 10.1021/ac900188y] [Citation(s) in RCA: 422] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
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Li T, Li B, Wang E, Dong S. G-quadruplex-based DNAzyme for sensitive mercury detection with the naked eye. Chem Commun (Camb) 2009:3551-3. [DOI: 10.1039/b903993g] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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