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Han J, Lv X, Zhang Y, Wang J, Fan D, Dong S. Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits. Anal Chem 2023; 95:16725-16732. [PMID: 37906527 DOI: 10.1021/acs.analchem.3c03793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Intelligent Wearable Engineering Research Center of Qingdao, Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Han J, Ding Y, Lv X, Zhang Y, Fan D. Integration of G-Quadruplex and Pyrene as a Simple and Efficient Ratiometric Fluorescent Platform That Programmed by Contrary Logic Pair for Highly Sensitive and Selective Coralyne (COR) Detection. BIOSENSORS 2023; 13:bios13040489. [PMID: 37185564 PMCID: PMC10136222 DOI: 10.3390/bios13040489] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
The effective and accurate detection of the anticancer drug coralyne (COR) is highly significant for drug quality control, medication safety and good health. Although various COR sensors have been reported in recent years, previous ones can only exhibit single-signal output (turn ON or turn OFF) with poor reliability and anti-interference ability. Therefore, exploring novel platform with dual-signal response for COR detection is urgently needed. Herein, we reported the first ratiometric fluorescent platform for highly sensitive and selective COR detection by integrating G-quadruplex (G4) and Pyrene (Py) as signal probes and harnessing A-COR-A interaction. In the absence of COR, the platform shows a low fluorescence signal of PPIX (F642) and a high one of Py monomer (F383). With the addition of COR, two delicately designed poly-A ssDNAs will hybridize with each other via A-COR-A coordination to form complete G4, yielding the increased fluorescence signal of PPIX and the decreased one of Py due to the formation of Py excimer. Based on the above mechanism, we constructed a simple and efficient sensor that could realize the ratiometric fluorescent detection of COR with high sensitivity and selectivity. A linear relationship between F642/F383 and COR's concentration is obtained in the range from 1 nM to 8 μM. And the limit of detection of COR could reach to as low as 0.63 nM without any amplification, which is much lower than that of most COR sensors reported so far. Notably, the logical analysis of COR can be carried out under the control of a "YES-NOT" contrary logic pair, enabling the smart dual-channel response with an adequate S/N ratio and improved reliability and anti-interference ability. Moreover, this system also presents satisfactory performance in fetal bovine serum (FBS) samples.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yaru Ding
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Han J, Wang J, Wang J, Fan D, Dong S. Recent advancements in coralyne (COR)-based biosensors: Basic principles, various strategies and future perspectives. Biosens Bioelectron 2022; 210:114343. [PMID: 35561578 DOI: 10.1016/j.bios.2022.114343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/02/2022]
Abstract
As a kind of protoberberine alkaloid heterocyclic analogues, coralyne (COR) has been reported to exhibit superior antileukemic ability and used as anticancer drug agent. While, the severe hazards and side effects caused by unreasonable use have made its accurate detection more and more important. Although scientists have explored various methods to sense COR and other related targets, a systematical review which could not only elaborate recent developments and analyze current challenges of COR-based biosensors, but also present future perspective has not been reported and is urgently needed. In this review, we attempt to summarize latest advancements in COR-based biosensors in recent decade. Firstly, the operating principles, advantages and disadvantages of various strategies for COR detection (colorimetric, fluorescent, electrochemical and other ones) are comprehensively demonstrated and reviewed. Secondly, COR-assisted biosensors for detection of different non-COR targets (heparin, toxins, nucleic acids and other small molecules) are further discussed. Finally, we analyze current challenges and also suggest potential perspectives for this area.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Juan Wang
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao, Shandong, 266071, China
| | - Jun Wang
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China.
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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Kumar P, Cabaj MK, Pazio A, Dominiak PM. Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions. IUCRJ 2018; 5:449-469. [PMID: 30002846 PMCID: PMC6038959 DOI: 10.1107/s2052252518006346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
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Affiliation(s)
- Prashant Kumar
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Malgorzata Katarzyna Cabaj
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Aleksandra Pazio
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
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Chatterjee S, Suresh Kumar G. Small molecule induced poly(A) single strand to self-structure conformational switching: evidence for the prominent role of H-bonding interactions. MOLECULAR BIOSYSTEMS 2018; 13:1000-1009. [PMID: 28405661 DOI: 10.1039/c7mb00031f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
All messenger RNAs (mRNAs) have a polyadenylic acid tail that is added during post transcriptional RNA processing. Investigation of the structure-function and interactions of polyadenylic acid is an important area to target for cancer and related diseases. Jatrorrhizine and coptisine are two important isoquinoline alkaloids that are structurally very similar, differing only in the substituents on the isoquinoline chromophore. Here we demonstrate that these alkaloids differentially induce a self-structure in single stranded poly(A) using absorbance, thermal melting and differential scanning calorimetry experiments. Jatrorrhizine was found to be more effective than coptisine in binding to poly(A) from spectroscopy and calorimetry data. Molecular modeling results suggested the involvement of more H-bonds in the complexation of the former with poly(A). It appears that the presence of substituents on the alkaloid that can form H-bonding interactions with the adenine nucleotides may play a critical role in the binding and structural rearrangement of poly(A) into the self-structure. The atomic force microscopy data directly visualized the poly(A) self-structured network. We propose a plausible mechanism of the small molecule induced self-structure formation in poly(A). The results presented here may help in the design of effective poly(A) targeted molecules for therapeutic use.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
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Haque L, Bhuiya S, Das S. Self-structure assembly in single stranded polyriboadenylic acid by benzophenanthridine alkaloid: Spectroscopic and calorimetric exploration. Int J Biol Macromol 2018; 106:1130-1138. [DOI: 10.1016/j.ijbiomac.2017.08.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
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Shao C, Liang J, He S, Luan T, Yu J, Zhao H, Xu J, Tian L. pH-Responsive Graphene Oxide-DNA Nanosystem for Live Cell Imaging and Detection. Anal Chem 2017; 89:5445-5452. [PMID: 28417633 DOI: 10.1021/acs.analchem.7b00369] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The interaction between graphene oxide (GO) and DNA is very sensitive to the environment. For example, under acidic conditions, the affinity of GO for DNA is enhanced, weakening the capability of GO to distinguish DNAs with different conformations. This effect has impeded the development of sensitive pH biosensors based on GO-DNA nanosystems. In this work, we systematically studied the affinity between GO and i-motif forming oligonucleotides (IFOs) at different pH values and developed a herring sperm DNA (HSD) treatment method. Using this method, HSD occupies the surface of GO, compromising the attractive force of GO that is significantly enhanced under acidic conditions. As a result, the ability of GO to distinguish between "open" and "closed" IFOs is successfully generalized to a wider pH range. Finally, a pH-sensitive GO-IFO nanosystem was fabricated that showed excellent sensing ability both in vitro and for intracellular pH detection. Because the interaction between GO and DNA is the basis for constructing GO-DNA biosensors, the strategy developed in this work shows great potential to be applied in a variety of other GO-DNA sensing systems.
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Affiliation(s)
- Chen Shao
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Jia Liang
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Sihui He
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Tianqi Luan
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Haoran Zhao
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Jingyuan Xu
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology , 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P.R. China
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Huang Z, Liu B, Liu J. Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:11986-11992. [PMID: 27771956 DOI: 10.1021/acs.langmuir.6b03253] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA-functionalized gold nanoparticles (AuNPs) have been extensively used in sensing, drug delivery, and materials science. A key step is to attach DNA to AuNPs, forming a stable and functional conjugate. Although the traditional salt-aging method takes a full day or longer, a recent low-pH method allows DNA conjugation in a few minutes. The effect of low pH was attributed to the protonation of adenine (A) and cytosine (C), resulting in an overall lower negative charge density on DNA. In this work, the effect of DNA conformation at low pH is studied. Using circular dichroism (CD) spectroscopy, the parallel poly-A duplex (A-motif) is detected when a poly-A segment is linked to a random DNA, a design typically used for DNA conjugation. A DNA staining dye, thiazole orange, is identified for detecting such A-motifs. The A-motif structure is ideal for DNA conjugation because it exposes the thiol group to directly react with the gold surface while minimizing nonspecific DNA base adsorption. For nonthiolated DNA, the optimal procedure is to incubate DNA and AuNPs followed by lowering the pH. The i-motif formed by poly-C DNA at low pH is less favorable to the conjugation reaction because of its unique way of folding. The stability of poly-A and poly-G DNA at low pH is examined. An excellent stability of poly-A DNA is confirmed, but poly-G has lower stability. This study provides new fundamental insights into a practically useful technique of conjugating DNA to AuNPs.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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Narayanaswamy N, Nair RR, Suseela YV, Saini DK, Govindaraju T. A molecular beacon-based DNA switch for reversible pH sensing in vesicles and live cells. Chem Commun (Camb) 2016; 52:8741-4. [DOI: 10.1039/c6cc02705a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The DNA switch based on a molecular beacon (closed state) to A-motif (open state) structural transformation is developed as an efficient and reversible pH sensor in synthetic vesicles and live cells.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Raji R. Nair
- Department of Molecular Reproduction
- Development and Genetics
- Indian Institute of Science
- Bengaluru 560012
- India
| | - Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction
- Development and Genetics
- Indian Institute of Science
- Bengaluru 560012
- India
| | - T. Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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Hung SY, Tseng WL. A polyadenosine-coralyne complex as a novel fluorescent probe for the sensitive and selective detection of heparin in plasma. Biosens Bioelectron 2014; 57:186-91. [PMID: 24583690 DOI: 10.1016/j.bios.2014.02.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/27/2014] [Accepted: 02/05/2014] [Indexed: 11/28/2022]
Abstract
This study presents the development of a simple, label-free, sensitive, and selective detection system for heparin based on the use of a complex of 20-repeat adenosine (A20) and coralyne. Coralyne emits relatively weak fluorescence in an aqueous solution. In the presence of A20, coralyne molecules complexed with A20 through A2-coralyne-A2 coordination. An increase in the fluorescence of coralyne was observed because coralyne remained separate from water in the hydrophobic environment of the folded A20. The presence of heparin and the formation of the coralyne-heparin complex caused coralyne to be removed from the A20-corlayne complex. Because heparin promoted coralyne dimerization, the fluorescence of coralyne decreased as a function of the concentration of added heparin. This detection method is effective because the electrostatic attraction between heparin and coralyne is substantially stronger than the coordination between A20 and coralyne in a 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer at pH 7.0. Under optimal conditions (5 μM coralyne, 1 μM poly A20, and 10mM HEPES), this probe exhibited high selectivity (>90-fold) toward heparin over hyaluronic acid and chondroitin sulfate. The probe׳s detection limit for heparin was determined to be 4 nM (75 ng/mL) at a signal-to-noise ratio of 3. This study validates the practicality of using the A20-corlayne complex to determine the concentration of heparin in plasma.
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Affiliation(s)
- Szu-Ying Hung
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan; Center for Nanoscience and Nanotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan.
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12
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Tanaka A, Choi J, Kim SK, Majima T. Interaction of G-quadruplex with RecA protein studied in bulk phase and at the single-molecule level. J Phys Chem B 2013; 117:6711-7. [PMID: 23662701 DOI: 10.1021/jp4036277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As in the human genome there are numerous repeat DNA sequences to adopt into non-B DNA structures such as hairpin, triplex, Z-DNA, G-quadruplex, and so on, an understanding of the interaction between DNA repair proteins and a non-B DNA forming sequence is very important. In this regard, the interaction between RecA protein and human telomeric 5'-TAGGG-(TTAGGG)3-TT-3' sequence and the G-quadruplex formed from this sequence has been investigated in bulk phase and at the single-molecule level. The RecA@ssDNA filament, which is formed by the interaction between RecA protein and a G-rich sequence, was dissociated by the addition of K(+) ions, and the dissociated G-rich sequence was quickly folded to a G-quadruplex structure, indicating that the G-quadruplex structure is more favorable than the RecA@ssDNA filament in the presence of K(+) ions. In addition, we demonstrate that the conformation of the G-quadruplex, which is heterogeneous in the absence of RecA, converged to the specific G-quadruplex with one double-chain-reversal loop upon association of RecA protein.
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Affiliation(s)
- Atsushi Tanaka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Choi J, Majima T. Reversible conformational switching of i-motif DNA studied by fluorescence spectroscopy. Photochem Photobiol 2013; 89:513-22. [PMID: 23311444 DOI: 10.1111/php.12042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/04/2013] [Indexed: 12/19/2022]
Abstract
Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology.
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Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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14
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Kumar V, Kesavan V. Acyclic butyl nucleic acid (BuNA): a novel scaffold for A-switch. RSC Adv 2013. [DOI: 10.1039/c3ra41255e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Su X, Xiao X, Zhang C, Zhao M. Nucleic acid fluorescent probes for biological sensing. APPLIED SPECTROSCOPY 2012; 66:1249-1262. [PMID: 23146180 DOI: 10.1366/12-06803] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
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Abstract
The physicochemical properties of small molecules as well as macromolecules are modulated by solution pH, and DNA is no exception. Special sequences of DNA can adopt unusual conformations e.g., triplex, i-motif and A-motif, depending on solution pH. The specific range of pH for these unusual structures is dictated by the pKa of protonation of the relevant nucleobase involved in the resultant non-canonical base pairing that is required to stabilise the structure. The biological significance of these pH-dependent structures is not yet clear. However, these non-B-DNA structures have been used to design different devices to direct chemical reactions, generate mechanical force, sense pH, etc. The performance of these devices can be monitored by a photonic signal. They are autonomous and their ‘waste free’ operation cycles makes them highly processive. Applications of these devices help to increase understanding of the structural polymorphism of the motifs themselves. The design of these devices has continuously evolved to improve their performance efficiency in different contexts. In some examples, these devices have been shown to perform inside complex living systems with similar efficiencies, to report on the chemical environment there. The robust performance of these devices opens up exciting possibilities for pH-sensitive DNA devices in the study of various pH-regulated biological events.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
| | - Yamuna Krishnan*
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
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Saha S, Chakraborty K, Krishnan Y. Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation. Chem Commun (Camb) 2012; 48:2513-5. [PMID: 22278189 DOI: 10.1039/c2cc16347k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A colorimetric pH sensor has been developed based on GNP aggregation mediated by A-motif formation under acidic conditions. The pH response of the sensor can be tuned in the range of pH 2-5.5 by changing the length and the sequence of the A-motif forming poly dA tracts.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, India
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