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Tepper O, Appella DH, Zheng H, Dzikowski R, Yavin E. A Biotinylated cpFIT-PNA Platform for the Facile Detection of Drug Resistance to Artemisinin in Plasmodium falciparum. ACS Sens 2024; 9:1458-1464. [PMID: 38446423 DOI: 10.1021/acssensors.3c02553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The evolution of drug resistance to many antimalarial drugs in the lethal strain of malaria (Plasmodium falciparum) has been a great concern over the past 50 years. Among these drugs, artemisinin has become less effective for treating malaria. Indeed, several P. falciparum variants have become resistant to this drug, as elucidated by specific mutations in the pfK13 gene. This study presents the development of a diagnostic kit for the detection of a common point mutation in the pfK13 gene of P. falciparum, namely, the C580Y point mutation. FIT-PNAs (forced-intercalation peptide nucleic acid) are DNA mimics that serve as RNA sensors that fluoresce upon hybridization to their complementary RNA. Herein, FIT-PNAs were designed to sense the C580Y single nucleotide polymorphism (SNP) and were conjugated to biotin in order to bind these molecules to streptavidin-coated plates. Initial studies with synthetic RNA were conducted to optimize the sensing system. In addition, cyclopentane-modified PNA monomers (cpPNAs) were introduced to improve FIT-PNA sensing. Lastly, total RNA was isolated from red blood cells infected with P. falciparum (WT strain - NF54-WT or mutant strain - NF54-C580Y). Streptavidin plates loaded with either FIT-PNA or cpFIT-PNA were incubated with the total RNA. A significant difference in fluorescence for mutant vs WT total RNA was found only for the cpFIT-PNA probe. In summary, this study paves the way for a simple diagnostic kit for monitoring artemisinin drug resistance that may be easily adapted to malaria endemic regions.
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Affiliation(s)
- Odelia Tepper
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 9112102, Israel
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The institute for Medical Research Israel - Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 9112102, Israel
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2
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Prajapati GK, Kumar A, Wany A, Pandey DM. Molecular Beacon Probe (MBP)-Based Real-Time PCR. Methods Mol Biol 2023; 2638:273-287. [PMID: 36781649 DOI: 10.1007/978-1-0716-3024-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,R & D Biologics Division, Promea Therapeutics Pvt Ltd, Sultanpur, Hyderabad, India
| | - Ashutosh Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Aakanksha Wany
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
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Revealing transient events of molecular recognition via super-localization imaging of single-particle motion. Sci Rep 2019; 9:4870. [PMID: 30890738 PMCID: PMC6424965 DOI: 10.1038/s41598-019-41239-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/03/2019] [Indexed: 11/09/2022] Open
Abstract
Molecular recognition plays an important role in biological systems and relates to a wide range of applications in disease diagnostics and therapeutics. Studies based on steady state or ensemble analysis may mask critical dynamic information of single recognition events. Here we report a study of monitoring the transient molecular recognition via single particle motion. We utilized a super-localization imaging methodology, to comprehensively evaluate the rotational Brownian motion of a single nanoparticle in spatial-temporal-frequential domain, with a spatial accuracy ~20 nm and a temporal resolution of ~10 ms. The transient moment of molecular encountering was captured and different binding modes were discriminated. We observed that the transient recognition events were not static states of on or off, but stochastically undergoes dynamical transformation between different binding modes. This study improves our understanding about the dynamic nature of molecular recognition events beyond the ensemble characterization via binding constant.
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4
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Qi X, Xia L, Li Y, Wang T, Zhang X, Chen J, Zhang L, Fu Y. The Fabrication of 2D Cu-Based MOF Nanosheets for DNA Detection. Aust J Chem 2019. [DOI: 10.1071/ch19312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Cu-based metal–organic framework (MOF) analogues, copper 1,4-benzenedicarboxylate (CuBDC), copper 2,6-naphthalenedicarboxylate (Cu(2,6-NDC)), and copper 1,4-naphthalenedicarboxylate (Cu(1,4-NDC)) MOF nanosheets, are prepared as biosensor nanoplatforms for DNA detection by a spray method. With the ultrathin 2D structure, the fabricated MOF nanosheets exhibited better detection of target DNA, in particular when compared with the corresponding 3D MOF bulky crystals, when used as a DNA biosensor platform. The Cu(1,4-NDC) nanosheets display a distinct sensitivity with a detection limit of 0.3nM and linear range of 0–20nM, and selectivity for the target DNA or target DNA mixture. The feasible biosensor nanoplatform composed of 2D MOF nanosheets broadens the application scope of MOF nanosheets.
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5
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A Label-free and Functional Fluorescent Oligonucleotide Probe Based on a G-Quadruplex Molecular Beacon for the Detection of Kanamycin. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7366-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Optical DNA Biosensor Based on Square-Planar Ethyl Piperidine Substituted Nickel(II) Salphen Complex for Dengue Virus Detection. SENSORS 2018; 18:s18041173. [PMID: 29649118 PMCID: PMC5948868 DOI: 10.3390/s18041173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 11/26/2022]
Abstract
A sensitive and selective optical DNA biosensor was developed for dengue virus detection based on novel square-planar piperidine side chain-functionalized N,N′-bis-4-(hydroxysalicylidene)-phenylenediamine-nickel(II), which was able to intercalate via nucleobase stacking within DNA and be functionalized as an optical DNA hybridization marker. 3-Aminopropyltriethoxysilane (APTS)-modified porous silica nanospheres (PSiNs), was synthesized with a facile mini-emulsion method to act as a high capacity DNA carrier matrix. The Schiff base salphen complexes-labelled probe to target nucleic acid on the PSiNs renders a colour change of the DNA biosensor to a yellow background colour, which could be quantified via a reflectance transduction method. The reflectometric DNA biosensor demonstrated a wide linear response range to target DNA over the concentration range of 1.0 × 10−16–1.0 × 10−10 M (R2 = 0.9879) with an ultralow limit of detection (LOD) at 0.2 aM. The optical DNA biosensor response was stable and maintainable at 92.8% of its initial response for up to seven days of storage duration with a response time of 90 min. The reflectance DNA biosensor obtained promising recovery values of close to 100% for the detection of spiked synthetic dengue virus serotypes 2 (DENV-2) DNA concentration in non-invasive human samples, indicating the high accuracy of the proposed DNA analytical method for early diagnosis of all potential infectious diseases or pathological genotypes.
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7
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Ariffin EY, Lee YH, Futra D, Tan LL, Karim NHA, Ibrahim NNN, Ahmad A. An ultrasensitive hollow-silica-based biosensor for pathogenic Escherichia coli DNA detection. Anal Bioanal Chem 2018; 410:2363-2375. [PMID: 29504083 DOI: 10.1007/s00216-018-0893-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/31/2017] [Accepted: 01/16/2018] [Indexed: 10/17/2022]
Abstract
A novel electrochemical DNA biosensor for ultrasensitive and selective quantitation of Escherichia coli DNA based on aminated hollow silica spheres (HSiSs) has been successfully developed. The HSiSs were synthesized with facile sonication and heating techniques. The HSiSs have an inner and an outer surface for DNA immobilization sites after they have been functionalized with 3-aminopropyltriethoxysilane. From field emission scanning electron microscopy images, the presence of pores was confirmed in the functionalized HSiSs. Furthermore, Brunauer-Emmett-Teller (BET) analysis indicated that the HSiSs have four times more surface area than silica spheres that have no pores. These aminated HSiSs were deposited onto a screen-printed carbon paste electrode containing a layer of gold nanoparticles (AuNPs) to form a AuNP/HSiS hybrid sensor membrane matrix. Aminated DNA probes were grafted onto the AuNP/HSiS-modified screen-printed electrode via imine covalent bonds with use of glutaraldehyde cross-linker. The DNA hybridization reaction was studied by differential pulse voltammetry using an anthraquinone redox intercalator as the electroactive DNA hybridization label. The DNA biosensor demonstrated a linear response over a wide target sequence concentration range of 1.0×10-12-1.0×10-2 μM, with a low detection limit of 8.17×10-14 μM (R2 = 0.99). The improved performance of the DNA biosensor appeared to be due to the hollow structure and rough surface morphology of the hollow silica particles, which greatly increased the total binding surface area for high DNA loading capacity. The HSiSs also facilitated molecule diffusion through the silica hollow structure, and substantially improved the overall DNA hybridization assay. Graphical abstract Step-by-step DNA biosensor fabrication based on aminated hollow silica spheres.
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Affiliation(s)
- Eda Yuhana Ariffin
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Yook Heng Lee
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor Darul Ehsan, Malaysia. .,Southeast Asia Disaster Prevention Research Initiative, Institute for Environment and Development, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
| | - Dedi Futra
- Department of Chemistry Education, Faculty of Education, Universitas Riau, Pekan Baru, Riau, 28131, Indonesia
| | - Ling Ling Tan
- Southeast Asia Disaster Prevention Research Initiative, Institute for Environment and Development, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nurul Huda Abd Karim
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nik Nuraznida Nik Ibrahim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Asmat Ahmad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
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Ogura Y, Onishi A, Nishimura T, Tanida J. Optically controlled release of DNA based on nonradiative relaxation process of quenchers. BIOMEDICAL OPTICS EXPRESS 2016; 7:2142-53. [PMID: 27375933 PMCID: PMC4918571 DOI: 10.1364/boe.7.002142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/27/2016] [Accepted: 05/03/2016] [Indexed: 06/02/2023]
Abstract
Optically controlled release of a DNA strand based on a nonradiative relaxation process of black hole quenchers (BHQs), which are a sort of dark quenchers, is presented. BHQs act as efficient energy sources because they relax completely via a nonradiative process, i.e., without fluorescent emission-based energy losses. A DNA strand is modified with BHQs and the release of its complementary strand is controlled by excitation of the BHQs. Experimental results showed that up to 50% of the target strands were released, and these strands were capable of inducing subsequent reactions. The controlled release was localized on a substrate within an area of no more than 5 micrometers in diameter.
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Affiliation(s)
- Yusuke Ogura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Atsushi Onishi
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Takahiro Nishimura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Jun Tanida
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
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9
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Cao Q, Teng Y, Yang X, Wang J, Wang E. A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors. Biosens Bioelectron 2015; 74:318-21. [DOI: 10.1016/j.bios.2015.06.044] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 01/21/2023]
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10
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Qiu L, Shen Z, Wu ZS, Shen GL, Yu R. Discovery of the unique self-assembly behavior of terminal suckers-contained dsDNA onto GNP and novel "light-up" colorimetric assay of nucleic acids. Biosens Bioelectron 2014; 64:292-9. [PMID: 25240129 DOI: 10.1016/j.bios.2014.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/30/2014] [Accepted: 09/04/2014] [Indexed: 11/17/2022]
Abstract
Noble metal nanoparticles are currently of great interest because of their unique optical properties and potential applications in disease diagnostics and cancer treatment. In the present work, a discovery was reported that dsDNA with terminal thiols at its two ends could lie easily flat onto the gold nanoparticle (GNP) surface rather than cross linked different GNPs, indicating an unique self-assembly behavior of newly-designed molecules on GNPs. This could intensively stabilize gold nanoparticles against aggregation even at a high salt concentration. On the basis of this discovery, a novel light-up colorimetric sensing strategy was developed for the detection of p53 gene by combining with the cyclical nucleic acid strand-displacement polymerization (CNDP). For the described colorimetric system, GNPs require no any surface functionalization, and target recognition reaction and CNDP amplification could be conducted under the optimized conditions to achieve a high efficiency. The high detection sensitivity and desirable selectivity are achieved, and the potential practical application was demonstrated. Besides, this sensing system can function in a wide range of salts, making it a suitable platform to cooperate with many biological processes.
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Affiliation(s)
- Liping Qiu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Zhifa Shen
- Shenzhen Kivita Innovative Drug Discovery Institute, Southern District of Science and Technology Park, Nan Shan, Shenzhen 518000, People's Republic of China
| | - Zai-Sheng Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China; Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People's Republic of China.
| | - Guo-Li Shen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Ruqin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China.
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11
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Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products. Talanta 2014; 129:398-403. [PMID: 25127611 DOI: 10.1016/j.talanta.2014.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
Abstract
This study presents a novel dual hairpin-like molecular beacon (MB) for the selective and sensitive detection of melamine (MA) based on the conjugation of MA and thymine. In this protocol, the coordination between coralyne and adenosine (A) leaded a dual hairpin-like MB and the fluorophore-quencher pair is close proximity resulting in the fluorescence quenching. With the addition of MA, it conjugated with thymine in the loop part of dual hairpin-like MB by triple H-bonds, triggering the dissociation of the dual hairpin-like MB. The resulting spatial separation of the fluorophore from quencher induced the enhancement in fluorescence emission. Under the optimized conditions, the sensor exhibited a wide linear range of 8×10(-9)-1.6×10(-5) M (R(2)=0.9969) towards MA, with a low detection limit of 5 nM, approximately 4000 times lower than the Drug Administration and the US Food estimated MA safety limit. The real milk samples were also investigated with a satisfying result.
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12
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Xiao Z, Guo X, Ling L. Sequence-specific recognition of double-stranded DNA with molecular beacon with the aid of Ag+ under neutral pH environment. Chem Commun (Camb) 2013; 49:3573-5. [DOI: 10.1039/c3cc40333e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Wu CS, Peng L, You M, Han D, Chen T, Williams KR, Yang CJ, Tan W. Engineering molecular beacons for intracellular imaging. INTERNATIONAL JOURNAL OF MOLECULAR IMAGING 2012; 2012:501579. [PMID: 23209893 PMCID: PMC3502855 DOI: 10.1155/2012/501579] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/21/2012] [Indexed: 12/25/2022]
Abstract
Molecular beacons (MBs) represent a class of nucleic acid probes with unique DNA hairpin structures that specifically target complementary DNA or RNA. The inherent "OFF" to "ON" signal transduction mechanism of MBs makes them promising molecular probes for real-time imaging of DNA/RNA in living cells. However, conventional MBs have been challenged with such issues as false-positive signals and poor biostability in complex cellular matrices. This paper describes the novel engineering steps used to improve the fluorescence signal and reduce to background fluorescence, as well as the incorporation of unnatural nucleotide bases to increase the resistance of MBs to nuclease degradation for application in such fields as chemical analysis, biotechnology, and clinical medicine. The applications of these de novo MBs for single-cell imaging will be also discussed.
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Affiliation(s)
- Cuichen Sam Wu
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Lu Peng
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Mingxu You
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Da Han
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Tao Chen
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Kathryn R. Williams
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemical Biology, Key Laboratory of Analytical Science, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface and Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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15
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Kabeláč M, Kroutil O, Předota M, Lankaš F, Šíp M. Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study. Phys Chem Chem Phys 2012; 14:4217-29. [PMID: 22354557 DOI: 10.1039/c2cp23540d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.
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Affiliation(s)
- M Kabeláč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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16
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Gu Y, Lai MT. The potential application of a poly(3,4-ethylenedioxythiopene) modified platinum DNA biosensor in mutation analysis. Biosens Bioelectron 2012; 31:124-9. [DOI: 10.1016/j.bios.2011.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/03/2011] [Accepted: 10/03/2011] [Indexed: 11/15/2022]
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17
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Xiao W, Huang J. Immobilization of oligonucleotides onto zirconia-modified filter paper and specific molecular recognition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12284-12288. [PMID: 21905718 DOI: 10.1021/la203150f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A morphologically complex cellulosic substance (e.g., commercial filter paper) was employed as a substrate for DNA immobilization and successive recognition. A uniform ultrathin zirconia gel film was first deposited on each cellulose nanofiber in bulk filter paper by a facile sol-gel process. Relying on the large surface area of filter paper and the strong affinity of zirconia for the phosphate group, terminal-phosphate probe DNA was abundantly immobilized on the zirconia-modified filter paper so as to convert the composite to a biofunctional material for the sensitive and repetitive recognition of the corresponding complementary target DNA on the nanomolar level. By contrast, in spite of the viability of the immobilization of the probe DNA and the recognition of target DNA on the quartz plate, the amount of captured probe DNA or recognized target DNA on such a flat substrate was much less than that captured or recognized on filter paper, resulting in a relatively insensitive recognition event. Moreover, control experiments on bare filter paper (without a zirconia nanocoating) suggested that the zirconia gel film was essential to probe DNA immobilization and subsequent target DNA recognition.
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Affiliation(s)
- Wei Xiao
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
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18
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19
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Carrasquilla C, Li Y, Brennan JD. Surface immobilization of structure-switching DNA aptamers on macroporous sol-gel-derived films for solid-phase biosensing applications. Anal Chem 2011; 83:957-65. [PMID: 21214191 DOI: 10.1021/ac102679r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-switching signaling aptamers (ss-aptamers) are single-stranded DNA molecules that are generated through in vitro selection and have the ability to switch between a duplex composed of a quencher-labeled DNA strand (QDNA) hybridized adjacent to a fluorophore label on the aptamer, and an aptamer-target complex wherein the QDNA strand is released, generating a fluorescence signal. While such species have recently emerged as promising biological recognition and signaling elements, very little has been done to evaluate their potential for solid-phase assays. In this study, we demonstrate that high surface area, sol-gel-derived macroporous silica films are suitable platforms for high-density affinity-based immobilization of functional ss-aptamer molecules, allowing for binding of both large and small target analytes with robust signal development. These films are formed using a poly(ethylene glycol) (PEG)-doped sodium silicate material, and we show that it is possible to control the pore size distribution and surface area of the silica film by varying the amount of PEG. Materials with the highest surface area are shown to be able to immobilize up to 6-fold more ss-aptamer than planar glass surfaces, providing greater detection sensitivity and somewhat improved detection limits as compared to immobilization on conventional glass. The solid-phase assay is performed using two different structure-switching signaling aptamers with high selectivity for adenosine 5'-triphosphate and platelet-derived growth factor, respectively, demonstrating that this immobilization scheme should be suitable for a variety of target ligands.
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Affiliation(s)
- Carmen Carrasquilla
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Zerrouki C, Fourati N, Lucas R, Vergnaud J, Fougnion JM, Zerrouki R, Pernelle C. Biological investigation using a shear horizontal surface acoustic wave sensor: Small “Click generated” DNA hybridization detection. Biosens Bioelectron 2010; 26:1759-62. [DOI: 10.1016/j.bios.2010.08.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 08/05/2010] [Accepted: 08/12/2010] [Indexed: 11/28/2022]
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21
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Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang L, Song S, Fan C. A graphene-enhanced molecular beacon for homogeneous DNA detection. NANOSCALE 2010; 2:1021-6. [PMID: 20648302 DOI: 10.1039/b9nr00401g] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work, we report the design of a novel graphene-based molecular beacon (MB) that could sensitively and selectively detect specific DNA sequences. The ability of water-soluble graphene oxide (GO) to differentiated hairpin and dsDNA offered a new approach to detect DNA. We found that the background fluorescence of MB was significantly suppressed in the presence of GO, which increased the signal-to-background ratio, hence the sensitivity. Moreover, the single-mismatch differentiation ability of hairpin DNA was maintained, leading to high selectivity of this new method.
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Affiliation(s)
- Fan Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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22
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Sethi D, Gandhi RP, Kuma P, Gupta KC. Chemical strategies for immobilization of oligonucleotides. Biotechnol J 2010; 4:1513-29. [PMID: 19844919 DOI: 10.1002/biot.200900162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
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23
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Zhu Z, Yang R, You M, Zhang X, Wu Y, Tan W. Single-walled carbon nanotube as an effective quencher. Anal Bioanal Chem 2009; 396:73-83. [DOI: 10.1007/s00216-009-3192-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 09/22/2009] [Accepted: 09/24/2009] [Indexed: 12/25/2022]
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24
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Martinez K, Estevez MC, Wu Y, Phillips JA, Medley CD, Tan W. Locked nucleic acid based beacons for surface interaction studies and biosensor development. Anal Chem 2009; 81:3448-54. [PMID: 19351140 DOI: 10.1021/ac8027239] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA sensors and microarrays permit fast, simple, and real-time detection of nucleic acids through the design and use of increasingly sensitive, selective, and robust molecular probes. Specifically, molecular beacons (MBs) have been employed for this purpose; however, their potential in the development of solid-surface-based biosensors has not been fully realized. This is mainly a consequence of the beacon's poor stability because of the hairpin structure once immobilized onto a solid surface, commonly resulting in a low signal enhancement. Here, we report the design of a new MB that overcomes some of the limitations of MBs for surface immobilization. Essentially, this new design adds locked nucleic acid bases (LNAs) to the beacon structure, resulting in a LNA molecular beacon (LMB) with robust stability after surface immobilization. To test the efficacy of LMBs against that of regular molecular beacons (RMBs), the properties of selectivity, sensitivity, thermal stability, hybridization kinetics, and robustness for the detection of target sequences were compared and evaluated. A 25-fold enhancement was achieved for the LMB on surface with detection limits reaching the low nanomolar range. In addition, the LMB-based biosensor was shown to possess better stability, reproducibility, selectivity, and robustness when compared to the RMB. Therefore, as an alternative to conventional DNA and as a prospective tool for use in both DNA microarrays and biosensors, these results demonstrate the potential of the locked nucleic acid bases for nucleic acid design for surface immobilization.
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Affiliation(s)
- Karen Martinez
- Center for Research at the Bio/Nano Interface, Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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25
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
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Horejsh D, Martini F, Capobianchi MR. BeadCons: detection of nucleic acid sequences by flow cytometry. ACTA ACUST UNITED AC 2008; Chapter 13:Unit13.5. [PMID: 18770821 DOI: 10.1002/0471142956.cy1305s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Molecular beacons are single-stranded nucleic acid structures with a terminal fluorophore and a distal, terminal quencher. These molecules are typically used in real-time PCR assays, but have also been conjugated with solid matrices. This unit describes protocols related to molecular beacon-conjugated beads (BeadCons), whose specific hybridization with complementary target sequences can be resolved by cytometry. Assay sensitivity is achieved through the concentration of fluorescence signal on discrete particles. By using molecular beacons with different fluorophores and microspheres of different sizes, it is possible to construct a fluid array system with each bead corresponding to a specific target nucleic acid. Methods are presented for the design, construction, and use of BeadCons for the specific, multiplexed detection of unlabeled nucleic acids in solution. The use of bead-based detection methods will likely lead to the design of new multiplex molecular diagnostic tools.
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Affiliation(s)
- Douglas Horejsh
- National Institute for Infectious Diseases "L. Spallazani"-IRCSS, Rome, Italy
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28
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Li X, Qian J, He S. Impact of the self-assembly of multilayer polyelectrolyte functionalized gold nanorods and its application to biosensing. NANOTECHNOLOGY 2008; 19:355501. [PMID: 21828850 DOI: 10.1088/0957-4484/19/35/355501] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Multilayered polyelectrolyte functionalized gold nanorods (GNRs) are reported for the conjugation of and sensitive detection of bio-molecules. Multilayered polyelectrolyte functionalized GNRs can significantly improve the biocompatibility of cetyltrimethylammonium bromide (CTAB) coated GNRs in a bio-environment and can diminish the toxicity induced by CTAB. Biotin, bovine serum albumin (BSA)-biotin and streptavidin are conjugated to polyelectrolyte functionalized GNRs, and the conjugates can serve as a platform for many biotin-streptavidin-based biological applications. Through the robust self-assembly effect of GNRs, biotin-conjugated GNRs are also utilized as a very sensitive probe for the detection of a small amount of streptavidin.
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Affiliation(s)
- Xin Li
- Centre for Optical and Electromagnetic Research, Zhejiang University, Zijingang Campus, Hangzhou 310058, People's Republic of China. Joint Research Center of Photonics of the Royal Institute of Technology (Sweden) and Zhejiang University, Zhejiang University, Zijingang Campus, Hangzhou 310058, People's Republic of China
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29
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Raab M, Hancock WO. Transport and detection of unlabeled nucleotide targets by microtubules functionalized with molecular beacons. Biotechnol Bioeng 2008; 99:764-73. [PMID: 17879297 DOI: 10.1002/bit.21645] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shrinking biosensors down to microscale dimensions enables increases in sensitivity and the ability to analyze minute samples such as the contents of individual cells. The goal of the present study is to create mobile microscale biosensors by attaching molecular beacons to microtubules and using kinesin molecular motors to transport these functionalized microtubules across two-dimensional surfaces. Previous work has shown that microfluidic channels can be functionalized with kinesin motors such that microtubules can be transported and directed through these channels without the need for external power or pressure-driven pumping. In this work, we show that molecular beacons can be attached to microtubules such that both the fluorescence reporting capability of the beacon and the motility of the microtubules are retained. These molecular beacon-functionalized microtubules were able to bind ssDNA target sequences, transport them across surfaces, and report their presence by an increase in fluorescence that was detected by fluorescence microscopy. This work is an important step toward creating hybrid microdevices for sensitive virus detection or analyzing mRNA profiles of individual cells.
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Affiliation(s)
- Matthew Raab
- Department of Bioengineering, 229 Hallowell Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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30
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31
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Affiliation(s)
- Audrey Sassolas
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Béatrice D. Leca-Bouvier
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Loïc J. Blum
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
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33
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Situma C, Moehring AJ, Noor MAF, Soper SA. Immobilized molecular beacons: a new strategy using UV-activated poly(methyl methacrylate) surfaces to provide large fluorescence sensitivities for reporting on molecular association events. Anal Biochem 2006; 363:35-45. [PMID: 17300739 PMCID: PMC2836515 DOI: 10.1016/j.ab.2006.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 11/21/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
We have designed appropriately prepared solid supports consisting of poly(methyl methacrylate) (PMMA) that provide enhanced performance levels for molecular beacons (MBs) that are used for recognizing and reporting on signature DNA sequences in solution. The attachment of primary amine-containing MBs to the PMMA surface was carried out by UV activating the PMMA to produce surface-confined carboxylate groups, which could then be readily coupled to the MBs using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) chemistry. The fluorescence properties of the MBs covalently attached onto this UV-activated PMMA surface were evaluated and compared with the same MBs immobilized onto glass supports. We observed improved limits of detection for the solution complement to the MBs when immobilized onto PMMA, and this was attributed to both the lower autofluorescence levels exhibited by PMMA at the detection wavelengths used and the improved quenching efficiency of the MBs when in their closed hairpin configuration when strapped to a PMMA surface as opposed to glass. As an example of the utility of the PMMA-based immobilization strategies developed for MBs, we report on the analysis of complementary DNAs specific for fruitless (fru) and Ods-site homeobox (OdsH) genes extracted from Drosophila melanogaster fruit flies. The fru gene functions in the central nervous system, where it is necessary for sex determination and male courtship behavior, whereas the OdsH gene is involved in the regulation of transcription.
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Affiliation(s)
- Catherine Situma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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34
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Park SH, Krull U. A spatially resolved nucleic acid biochip based on a gradient of density of immobilized probe oligonucleotide. Anal Chim Acta 2006. [DOI: 10.1016/j.aca.2006.01.107] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Affiliation(s)
- G Goel
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132-001, Haryana, India
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36
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Marras SAE, Tyagi S, Kramer FR. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin Chim Acta 2006; 363:48-60. [PMID: 16111667 DOI: 10.1016/j.cccn.2005.04.037] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 04/22/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. METHODS The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. CONCLUSIONS The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.
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Affiliation(s)
- Salvatore A E Marras
- Department of Molecular Genetics, Public Health Research Institute, Newark, NJ 07103, USA
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37
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Altschuh D, Oncul S, Demchenko AP. Fluorescence sensing of intermolecular interactions and development of direct molecular biosensors. J Mol Recognit 2006; 19:459-77. [PMID: 17089349 DOI: 10.1002/jmr.807] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular biosensors are devices of molecular size that are designed for sensing different analytes on the basis of biospecific recognition. They should provide two coupled functions - the recognition (specific binding) of the target and the transduction of information about the recognition event into a measurable signal. The present review highlights the achievements and prospects in design and operation of molecular biosensors for which the transduction mechanism is based on fluorescence. We focus on the general strategy of fluorescent molecular sensing, construction of sensor elements, based on natural and designed biopolymers (proteins and nucleic acids). Particular attention is given to the coupling of sensing elements with fluorescent reporter dyes and to the methods for producing efficient fluorescence responses.
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Affiliation(s)
- Danièle Altschuh
- UMR 7175 CNRS/ULP, ESBS, Parc d'Innovation, Bld S. Brant, BP 10413, 67412 Illkirch Cedex, France.
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38
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Dyadyusha L, Yin H, Jaiswal S, Brown T, Baumberg JJ, Booy FP, Melvin T. Quenching of CdSe quantum dot emission, a new approach for biosensing. Chem Commun (Camb) 2005:3201-3. [PMID: 15968371 DOI: 10.1039/b500664c] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emission of CdSe quantum dots linked to the 5'-end of a DNA sequence is efficiently quenched by hybridisation with a complementary DNA strand with a gold nanoparticle attached at the 3'-end; contact of the quantum dot and gold nanoparticle occurs.
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Affiliation(s)
- L Dyadyusha
- School of Electronics and Computer Science, University of Southampton, Highfield, UK
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39
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Horejsh D, Martini F, Poccia F, Ippolito G, Di Caro A, Capobianchi MR. A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry. Nucleic Acids Res 2005; 33:e13. [PMID: 15659574 PMCID: PMC548373 DOI: 10.1093/nar/gni015] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular beacons are dual-labelled probes that are typically used in real-time PCR assays, but have also been conjugated with solid matrices for use in microarrays or biosensors. We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. For this array system, molecular beacons were conjugated with microspheres using a biotin-streptavidin linkage. A bridged conjugation method using streptavidin increased the signal-to-noise ratio, allowing for further discrimination of target quantitation. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. Considering that routine flow cytometers are able to detect up to four fluorescent channels, this novel assay may allow for the specific multiplex detection of a nucleic acid panel in a single tube.
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Affiliation(s)
- Douglas Horejsh
- National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS Rome, Italy.
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40
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Culha M, Stokes DL, Griffin GD, Vo-Dinh T. Screening for the breast cancer gene (BRCA1) using a biochip system and molecular beacon probes immobilized on solid surfaces. JOURNAL OF BIOMEDICAL OPTICS 2004; 9:439-443. [PMID: 15189080 DOI: 10.1117/1.1691025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We describe the use of a biochip based on complementary metal oxide semiconductor (CMOS) technology for detection of specific genetic sequences using molecular beacons (MB) immobilized on solid surfaces as probes. The applicability of this miniature detection system for screening for the BRCA1 gene is evaluated using MB probes, designed especially for the BRCA1 gene. MB probes are immobilized on a zeta-probe membrane by biotin-streptavidin immobilization. Two immobilization strategies are investigated to obtain optimal assay sensitivity. The MB is immobilized by manual spotting on zeta-probe membrane surfaces with the use of a custom-made stamping system. The detection of the BRCA1 gene using an MB probe is successfully demonstrated and expands the use of the CMOS biochip for medical applications.
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Affiliation(s)
- Mustafa Culha
- Advanced Biomedical Science and Technology Group, Oak Ridge National Laboratory, Bethel Valley Road, MS-6101 P.O. Box 2008, Oak Ridge, Tennessee 37831-6101, USA
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41
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Culha M, Stokes DL, Griffin GD, Vo-Dinh T. Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection. Biosens Bioelectron 2004; 19:1007-12. [PMID: 15018955 DOI: 10.1016/j.bios.2003.09.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2003] [Revised: 09/18/2003] [Accepted: 09/23/2003] [Indexed: 10/26/2022]
Abstract
We report for the first time the application of a biochip using the molecular beacon (MB) detection scheme. The usability of this biochip novel detection system for the analysis of the breast cancer gene BRCA1 is demonstrated using molecular beacon probes. The MB is designed for the BRCA1 gene and a miniature biochip system is used for detection. The performance of the biochip-MB detection system is evaluated. The optimum conditions for the MB system for highest fluorescence detection sensitivity are investigated for the detection system. The detection of BRCA1 gene is successfully demonstrated in solution and the limit of detection (LOD) is estimated as 70 nM.
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Affiliation(s)
- Mustafa Culha
- Advanced Biomedical Science and Technology Group, Oak Ridge National Laboratory, Life Science Division, Bethel Valley Road, MS-6101, P.O. Box 2008, Oak Ridge, TN 37831-6101, USA
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42
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Geddes CD, Parfenov A, Roll D, Fang J, Lakowicz JR. Electrochemical and Laser Deposition of Silver for Use in Metal-Enhanced Fluorescence. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2003; 19:6236-6241. [PMID: 20725608 PMCID: PMC2923409 DOI: 10.1021/la020930r] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We describe two reagentless methods of silver deposition for metal-enhanced fluorescence. Silver was deposited on glass positioned between two silver electrodes with a constant current in pure water. Illumination of the glass between the electrodes resulted in localized silver deposition. Alternatively, silver was deposited on an Indium Tin Oxide cathode, with a silver electrode as the anode. Both types of deposited silver produced a 5-18-fold increase in the fluorescence intensity of a nearby fluorophore, indocyanine green (ICG). Additionally, the photostability of ICG was dramatically increased by proximity to the deposited silver. These results suggest the use of silver deposited from pure water for surface-enhanced fluorescence, with potential applications in surface assays and lab-on-a-chip-based technologies, which ideally require highly fluorescent photostable systems.
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Affiliation(s)
- Chris D Geddes
- Institute of Fluorescence and Center for Fluorescence Spectroscopy, Medical Biotechnology Center, University of Maryland Biotechnology Institute, 725 West Lombard Street, Baltimore, Maryland 21201, Department of Biochemistry and Molecular Biology, Center for Fluorescence Spectroscopy, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, Maryland 21201, Department of Chemistry, Roberts Wesleyan College, 2301 Westside Drive, Rochester, New York 14624, and Center for Biomolecular Science and Engineering (Code 6900), Naval Research Laboratory, Washington, D.C. 20375
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43
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Geddes CD, Parfenov A, Lakowicz JR. Photodeposition of silver can result in metal-enhanced fluorescence. APPLIED SPECTROSCOPY 2003; 57:526-31. [PMID: 14658678 PMCID: PMC2737405 DOI: 10.1366/000370203321666542] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chemically deposited silver particles are widely used for surface-enhanced Raman scattering (SERS) and more recently for surface-enhanced fluorescence (SEF), also known as metal-enhanced fluorescence (MEF). We now show that metallic silver deposited by laser illumination results in an approximately 7-fold increased intensity of locally bound indocyanine green. The increased intensity is accompanied by a decreased lifetime and increased photostability. These results demonstrate the possibility of photolithographic preparation of surfaces for enhanced fluorescence in microfluidics, medical diagnostics, and other applications.
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Affiliation(s)
- Chris D Geddes
- University Maryland Baltimore, Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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Wang Y, Yang J, Wu X, Li L, Sun S, Su B, Zhao Z. Progress of Spectral Probes for Nucleic Acids. ANAL LETT 2003. [DOI: 10.1081/al-120023702] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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