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Foguel MV, Zamora V, Ojeda J, Reed M, Bennett A, Calvo-Marzal P, Gerasimova YV, Kolpashchikov D, Chumbimuni-Torres KY. DNA nanotechnology for nucleic acid analysis: sensing of nucleic acids with DNA junction-probes. Analyst 2024; 149:968-974. [PMID: 38197474 PMCID: PMC11439508 DOI: 10.1039/d3an01707a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
DNA nanotechnology deals with the design of non-naturally occurring DNA nanostructures that can be used in biotechnology, medicine, and diagnostics. In this study, we introduced a nucleic acid five-way junction (5WJ) structure for direct electrochemical analysis of full-length biological RNAs. To the best of our knowledge, this is the first report on the interrogation of such long nucleic acid sequences by hybridization probes attached to a solid support. A hairpin-shaped electrode-bound oligonucleotide hybridizes with three adaptor strands, one of which is labeled with methylene blue (MB). The four strands are combined into a 5WJ structure only in the presence of specific DNA or RNA analytes. Upon interrogation of a full-size 16S rRNA in the total RNA sample, the electrode-bound MB-labeled 5WJ association produces a higher signal-to-noise ratio than electrochemical nucleic acid biosensors of alternative design. This advantage was attributed to the favorable geometry on the 5WJ nanostructure formed on the electrode's surface. The 5WJ biosensor is a cost-efficient alternative to the traditional electrochemical biosensors for the analysis of nucleic acids due to the universal nature of both the electrode-bound and MB-labeled DNA components.
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Affiliation(s)
- Marcos V Foguel
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Victor Zamora
- Escuela Professional de Quimica, Facultad de Ciencias, Universidad Nacional Ingenieria, Av. Tupac 210, Lima, Peru
| | - Julio Ojeda
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Mark Reed
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Alexander Bennett
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Percy Calvo-Marzal
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Yulia V Gerasimova
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
| | - Dmitry Kolpashchikov
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
- Burnett School of Biomedical Science, university of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA
| | - Karin Y Chumbimuni-Torres
- Department of Chemistry. University of Central Florida, 4000 Central Florida Boulevard, Orlando, Fl 32816, USA.
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2
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Khajouei S, Ravan H, Ebrahimi A. Developing a colorimetric nucleic acid-responsive DNA hydrogel using DNA proximity circuit and catalytic hairpin assembly. Anal Chim Acta 2020; 1137:1-10. [PMID: 33153592 DOI: 10.1016/j.aca.2020.08.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 12/13/2022]
Abstract
The development of powerful techniques for sensitive detection of nucleic acids has attracted much attention for fabricating accurate biosensors in various fields, such as genomics, clinical diagnostics, and forensic sciences. Up to now, different systems have been introduced, the majority of which are expensive, time-consuming, and relatively low selectivity/limit of detection. These limitations caught our attention to fabricate a nucleic acid responsive system by combining three layers of signal amplification strategy, namely a split proximity circuit (SPC), a catalytic hairpin assembly (CHA), and a DNA hydrogel. Herein, by SPC operation, two initiators and a target strand were assembled and activated the CHA reaction in the presence of three 5'-cytosine (C)-rich hairpins. Then, produced C-rich embedded three-way junction structures could form i-motif structures under acidic environment followed by a transition from sol to gel state. To acquire a quantitative and colorimetric measurement, gold nanoparticles (GNPs) were used that encapsulated and sediment by the gel formation. The resulting platform detected the target with a limit of detection of 1 pM and considerable selectivity.
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Affiliation(s)
- Sima Khajouei
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Ali Ebrahimi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
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3
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Ang YS, Lai PS, Yung LYL. Design of Split Proximity Circuit as a Plug-and-Play Translator for Point Mutation Discrimination. Anal Chem 2020; 92:11164-11170. [PMID: 32605366 DOI: 10.1021/acs.analchem.0c01379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Point mutations are a common form of genetic variation and have been identified as important disease biomarkers. Conventional methods for analyzing point mutations, e.g., polymerase chain reaction (PCR), are based on differences in thermal stability of the DNA duplex, which require extensive optimization of the reaction condition and nontrivial design of sequence-selective primers. This motivated the design of molecular translators to convert molecular inputs into generic output sequences, which allows for the target recognition and signal generation regions to be designed independently. In this work, we propose a translator design based on the concept of split proximity circuit (SPC) to achieve both high sequence selectivity and assay robustness using a universal reaction condition, i.e., room temperature and constant ionic concentration. We discussed the design aspects of the SPC recognition regions and demonstrated its plug-and-play capability to discriminate different point mutations for both DNA (seven G6PD mutations) and RNA (let-7 microRNA family members) targets while retaining the same signal generation region. Despite its simple design and nonstringent assay condition requirements, the SPC retained good analytical performance to detect subnanomolar target concentration within a reasonable time of an hour.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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4
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Colorimetric detection of miRNA-21 by DNAzyme-coupled branched DNA constructs. Talanta 2020; 216:120913. [DOI: 10.1016/j.talanta.2020.120913] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/18/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022]
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5
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Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles. Mikrochim Acta 2020; 187:392. [PMID: 32556573 DOI: 10.1007/s00604-020-04368-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/01/2020] [Indexed: 12/16/2022]
Abstract
According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin. In the presence of target cell, chimeric aptamer binds to its ligand on cell surface and initiates 3WJ nanostructures formation. These 3WJ nanostructures interact with streptavidin-modified gold nanoparticles (AuNPs) via non-covalent biotin-streptavidin interactions and create a crossover lattice of nanoparticles. This event leads to AuNPs aggregation and red-shifting. The results were confirmed by gel electrophoresis and UV-visible spectrophotometry. The dynamic range of this assay is 25 to 107 cells with a detection limit of 10 cells which is respectively 9 and 4 times more significant than the sensitivity of AuNP-based approaches without amplification and enzyme-mediated signal amplification. Graphical abstract.
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Khajouei S, Ravan H, Ebrahimi A. DNA hydrogel-empowered biosensing. Adv Colloid Interface Sci 2020; 275:102060. [PMID: 31739981 PMCID: PMC7094116 DOI: 10.1016/j.cis.2019.102060] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 01/28/2023]
Abstract
DNA hydrogels as special members in the DNA nanotechnology have provided crucial prerequisites to create innovative gels owing to their sufficient stability, biocompatibility, biodegradability, and tunable multifunctionality. These properties have tailored DNA hydrogels for various applications in drug delivery, tissue engineering, sensors, and cancer therapy. Recently, DNA-based materials have attracted substantial consideration for the exploration of smart hydrogels, in which their properties can change in response to chemical or physical stimuli. In other words, these gels can undergo switchable gel-to-sol or sol-to-gel transitions upon application of different triggers. Moreover, various functional motifs like i-motif structures, antisense DNAs, DNAzymes, and aptamers can be inserted into the polymer network to offer a molecular recognition capability to the complex. In this manuscript, a comprehensive discussion will be endowed with the recognition capability of different kinds of DNA hydrogels and the alternation in physicochemical behaviors upon target introducing. Finally, we offer a vision into the future landscape of DNA based hydrogels in sensing applications.
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Affiliation(s)
- Sima Khajouei
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Ali Ebrahimi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
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7
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8
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Ravan H, Fozooni T, Amandadi M, Sasan H, Norouzi A. DNAzyme-embedded hyperbranched DNA dendrimers as signal amplifiers for colorimetric determination of nucleic acids. Mikrochim Acta 2018; 185:443. [DOI: 10.1007/s00604-018-2975-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/23/2018] [Indexed: 12/25/2022]
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Target-triggered three-way junction in conjugation with catalytic concatemers-functionalized nanocomposites provides a highly sensitive colorimetric method for miR-21 detection. Biosens Bioelectron 2018; 117:567-574. [PMID: 30005375 DOI: 10.1016/j.bios.2018.06.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
With the great advances in DNA nanotechnology, scientists have shown interest in developing dynamic nanostructures for theranostic applications, analyte sensing and cargo delivery. Here, we present a specific enzyme-free ultrasensitive platform based on a multilayer coupled signal amplification strategy to quantify miR-21 molecule. The biosensor was integrated based on three signal amplification gadgets, namely a translator-mediated catalytic hairpin assembly (CHA), a multilayer DNA concatemer on the surface of gold decorated magnetic nanoparticle (GMNP), and a DNAzyme-mediated catalytic signal amplification. MiR-21 mediates the release of a DNA translator from an immobilized duplex to engage in a CHA reaction using three hairpins, including a GMNP-conjugated hairpin 1 (H1), biotin-labeled hairpin 2 (H2) and a GMNP-conjugated hairpin 3 (H3) to form a three-way junction (3WJ). Meanwhile, a plenty of initiator strand 0 (S0) on GMNPs - each of which has been bifunctionalized with S0/H1 or S0/H3 - drive several multilayer peroxidase-mimicking DNAzyme concatemers in the presence of two accessory oligonucleotides; strand 1 (S1) and strand 2 (S2). Since a G-rich sequence was attached at the 5'-end of S1 strand, in the presence of hemin cofactor, an active G-quadruplex DNAzyme with peroxidase activity was formed. The concatemers on the surface of GMNPs can convert a colorless substrate to a green product. The biosensor can detect as low as 1 aM of miR-21 and provide an excellent capability to discriminate single-base mismatches. The required time for the formulation of the assay reagents is about three days and the reaction time for the detection of miR-21 takes place in less than four hours.
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10
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Kikuchi N, Kolpashchikov DM. A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. Chem Commun (Camb) 2018; 53:4977-4980. [PMID: 28425510 DOI: 10.1039/c7cc01540b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA
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11
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Norouzi A, Ravan H, Mohammadi A, Hosseinzadeh E, Norouzi M, Fozooni T. Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells. Anal Chim Acta 2018. [PMID: 29534792 DOI: 10.1016/j.aca.2018.02.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals. As proof-of-concept, as low as 175 cancer cells were detected by the assay, and color change was clearly distinguished by the naked eyes. The proposed system enjoys potential applications for point-of-care cancer diagnosis, with its excellent sensitivity and selectivity.
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Affiliation(s)
- Akram Norouzi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Abbas Mohammadi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Elyas Hosseinzadeh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdieh Norouzi
- Department of Nursing, Islamic Azad University of Kerman, Kerman, Iran
| | - Tahereh Fozooni
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
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12
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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13
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Ravan H, Amandadi M, Esmaeili-Mahani S. DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids. Anal Chem 2017; 89:6021-6028. [PMID: 28459545 DOI: 10.1021/acs.analchem.7b00607] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle. After harvesting the complex, 3' overhang regions of the TRs were labeled with three distinct monolayer double-stranded (ds) DNA-gold nanoparticles (DNA-AuNPs). Upon gleaning the complex and addition of initiator oligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of a domino chain, spontaneously occurred between the confined dsDNAs on the nanoparticles' surface in the second AND gate. The output of the second gate entered into the last gate and triggered an exponential hairpin assembly to form four-way junction nanostructures. The resulting nanostructures bear split parts of DNAzyme at each end of the four arms which, in the presence of hemin, form catalytic hemin/G-quadruplex DNAzymes with peroxidase activity. The smart biosensor has exhibited a turn-on signal when all biomarkers are present in the sample. In fact, should any of the biomarkers be nonexistent, the signal remains turned-off. The biosensor can detect the biomarkers with a LOD value of 100 aM and a noticeable capability to discriminate single-nucleotide substitutions.
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Affiliation(s)
- Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Mojdeh Amandadi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Saeed Esmaeili-Mahani
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
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Mills DM, Calvo-Marzal P, Pinzon JM, Armas S, Kolpashchikov DM, Chumbimuni-Torres KY. A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences. ELECTROANAL 2017; 29:873-879. [PMID: 29371782 PMCID: PMC5777621 DOI: 10.1002/elan.201600548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/27/2016] [Indexed: 01/28/2023]
Abstract
Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode's surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode's surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets.
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Affiliation(s)
- Dawn M. Mills
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
| | - Percy Calvo-Marzal
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
| | - Jeffer M. Pinzon
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
| | - Stephanie Armas
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
| | - Dmitry M. Kolpashchikov
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, United States
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL 32816, United States
| | - Karin Y. Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States
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Isothermal RNA detection through the formation of DNA concatemers containing HRP-mimicking DNAzymes on the surface of gold nanoparticles. Biosens Bioelectron 2016; 80:67-73. [DOI: 10.1016/j.bios.2016.01.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/16/2016] [Accepted: 01/18/2016] [Indexed: 12/21/2022]
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16
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Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids. Anal Chim Acta 2016; 910:68-74. [DOI: 10.1016/j.aca.2016.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/02/2016] [Accepted: 01/07/2016] [Indexed: 12/25/2022]
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