1
|
Göse M, Magill EE, Hughes-Games A, Shaw SJ, Diffin FM, Rawson T, Nagy Z, Seidel R, Szczelkun MD. Short-range translocation by a restriction enzyme motor triggers diffusion along DNA. Nat Chem Biol 2024; 20:689-698. [PMID: 38167920 PMCID: PMC11142916 DOI: 10.1038/s41589-023-01504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion ('DNA sliding') initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8-15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.
Collapse
Affiliation(s)
- Martin Göse
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Emma E Magill
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex Hughes-Games
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Steven J Shaw
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Tara Rawson
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Zsofia Nagy
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, UK.
| |
Collapse
|
2
|
Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
| |
Collapse
|
3
|
Integration of logic gates to CRISPR/Cas12a system for rapid and sensitive detection of pathogenic bacterial genes. Anal Chim Acta 2020; 1125:162-168. [DOI: 10.1016/j.aca.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022]
|
4
|
Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT. Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress. J Mol Biol 2020; 432:324-342. [DOI: 10.1016/j.jmb.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 11/25/2022]
|
5
|
Ma L, Cao X, Wang H, Lu K, Wang Y, Tu C, Dai Y, Meng Y, Li Y, Yu P, Man S, Diao A. Discovery of Myricetin as a Potent Inhibitor of Human Flap Endonuclease 1, Which Potentially Can Be Used as Sensitizing Agent against HT-29 Human Colon Cancer Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1656-1665. [PMID: 30694659 DOI: 10.1021/acs.jafc.8b05447] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Human flap endonuclease 1 (hFEN1) is instrumental in DNA replication and repair. It is able to cleave the 5' single-stranded protrusion (also known as 5' flap) resulting from strand displacement reactions. In light of its crucial functions, hFEN1 is now deemed as a nontrivial target in the DNA damage response system for anticancer drug development. Herein, we report that myricetin and some natural flavonoids are able to inhibit hFEN1. Structure-activity relationship, inhibitory mechanisms, molecular docking, and cancer cell-based assays have been performed. Our original findings expand the activity of flavonoids and may pave the way for flavonoid-assisted targeted cancer therapy.
Collapse
Affiliation(s)
- Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Xiuqi Cao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Haiyue Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Kui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Ying Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Chunhao Tu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yujie Dai
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yuanyuan Meng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yuyin Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Peng Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Aipo Diao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| |
Collapse
|
6
|
Ma L, Sun N, Meng Y, Tu C, Cao X, Wei Y, Chu L, Diao A. Harnessing the affinity of magnetic nanoparticles toward dye-labeled DNA and developing it as an universal aptasensor revealed by lipopolysaccharide detection. Anal Chim Acta 2018; 1036:107-114. [PMID: 30253820 DOI: 10.1016/j.aca.2018.06.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 12/20/2022]
Abstract
In current study, we have found that several magnetic nanoparticles (MNPs) are able to absorb DNA molecules, and surface engineering would be beneficial to tune such interaction. We then have focused on the assembly of polyethylenimine (PEI) coated MNPs (PEI-MNPs) with ssDNA (single-stranded DNA) and found this assembly is mediated by two forces, namely the electrostatic interactions of surface charges of MNPs and the phosphate backbones of DNA; as well as the coordination of exterior iron ions (especially Fe3+) of MNPs and DNA phosphate backbones. The fluorescence of dye-labeled DNA is significantly quenched when being complexed with PEI-MNPs, which is proved to be caused by static quenching. This PEI-MNPs interact with DNA, which could be harnessed for devising a novel type of aptasensor. This has been examplified by the selective and sensitive detection of lipopolysaccharide (LPS). The LOD (limit of detection) is ∼35 ng/mL and the linear range from 50 ng/mL to 10 μg/mL. Compared with widely used graphene oxide (GO)‒ssDNA aptamer sensors, we also have demonstrated that the PEI-MNPs based sensor is able to better avoid non-specific DNA displacement by interfering proteins, generating more satisfactory signal-to-background ratio. Our proposed sensor could be a supplement to classic GO‒DNA sensors. In summary, our work provides fundamental understanding of MNPs‒DNA interactions and also paves the way for developing novel MNPs based sensing approaches, which would contribute to nano‒bio interface and DNA-assisted bio-analysis, DNA-coordinated nano-materials and DNA-directed assembly.
Collapse
Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yuanyuan Meng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Chunhao Tu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiuqi Cao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yongchang Wei
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Liqiang Chu
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China.
| |
Collapse
|
7
|
Ma L, Sun N, Tu C, Zhang Q, Diao A. Design of an aptamer – based fluorescence displacement biosensor for selective and sensitive detection of kanamycin in aqueous samples. RSC Adv 2017. [DOI: 10.1039/c7ra07052g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A label-free detection method for kanamycin A using an aptamer-based displacement biosensor has been developed.
Collapse
Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Chunhao Tu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Qian Zhang
- College of Chemical Engineering and Materials Science
- Tianjin University of Science & Technology
- Tianjin 300457
- China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| |
Collapse
|
8
|
Ma L, Li Y, Meng L, Deng H, Li Y, Zhang Q, Diao A. Biological fluorination from the sea: discovery of a SAM-dependent nucleophilic fluorinating enzyme from the marine-derived bacterium Streptomyces xinghaiensis NRRL B24674. RSC Adv 2016. [DOI: 10.1039/c6ra00100a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The first ever marine originated fluorinating enzyme, which promises to be useful in biotransformation and synthetic biology, is described.
Collapse
Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Yufeng Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Lingpei Meng
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Hai Deng
- Marine Biodiscovery Centre
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
| | - Yuyin Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Qiang Zhang
- Tianjin 3rd Center Hospital
- Tianjin 300170
- China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| |
Collapse
|
9
|
Ma L, Liu H, Wu G, Sun N, Meng L, Li Y, Liu Z, Diao A. A dual-channel detection of mercuric ions using a label free G-quadruplex-based DNAzyme molecule. Analyst 2016; 141:3997-4000. [DOI: 10.1039/c6an00795c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have constructed a ‘turn-off’ and label free bio-sensor using a DNAzyme molecule.
Collapse
Affiliation(s)
- Long Ma
- Biomolecular Sciences Research Complex
- EaStCHEM School of Chemistry
- University of St Andrews
- Fife KY16 9ST
- UK
| | - Haiyan Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Guanrong Wu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Lingpei Meng
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Yuyin Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Zhenxing Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| |
Collapse
|
10
|
Ma L, Wu G, Li Y, Qin P, Meng L, Liu H, Li Y, Diao A. A reversible metal ion fueled DNA three-way junction molecular device for "turn-on and -off" fluorescence detection of mercury ions (II) and biothiols respectively with high selectivity and sensitivity. NANOSCALE 2015; 7:18044-18048. [PMID: 26487480 DOI: 10.1039/c5nr04688b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We constructed a reversible molecular device in the nanoscale based on a DNA three-way junction (3WJ) fueled by Hg(2+) binding and sequestration. It is highly responsive to external stimuli, which brings about optically detectable global structural changes. Such a DNA device can serve as a novel "turn-on and -off" fluorescent sensor for Hg(2+) and biothiol detection with high selectivity and sensitivity.
Collapse
Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China. and Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanrong Wu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yufeng Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Ping Qin
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Lingpei Meng
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Haiyan Liu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yuyin Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Aipo Diao
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| |
Collapse
|
11
|
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Collapse
|
12
|
Ma L, Diao A. Design of enzyme-interfaced DNA logic operations (AND, OR and INHIBIT) with an assaying application for single-base mismatch. Chem Commun (Camb) 2015; 51:10233-5. [DOI: 10.1039/c5cc02835c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We devised AND, OR and INHIBIT logic gates.
Collapse
Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| |
Collapse
|