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Bardales AC, Smirnov V, Taylor K, Kolpashchikov DM. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing. Chembiochem 2024; 25:e202400080. [PMID: 38385968 DOI: 10.1002/cbic.202400080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.
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Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Viktor Smirnov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, 9 Lomonosova Str., St. Petersburg, Russian Federation
| | - Katherine Taylor
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
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2
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Nedorezova DD, Rubel MS, Rubel AA. Multicomponent DNAzyme Nanomachines: Structure, Applications, and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S249-S261. [PMID: 38621754 DOI: 10.1134/s0006297924140141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 04/17/2024]
Abstract
Nucleic acids (NAs) are important components of living organisms responsible for the storage and transmission of hereditary information. They form complex structures that can self-assemble and bind to various biological molecules. DNAzymes are NAs capable of performing simple chemical reactions, which makes them potentially useful elements for creating DNA nanomachines with required functions. This review focuses on multicomponent DNA-based nanomachines, in particular on DNAzymes as their main functional elements, as well as on the structure of DNAzyme nanomachines and their application in the diagnostics and treatment of diseases. The article also discusses the advantages and disadvantages of DNAzyme-based nanomachines and prospects for their future applications. The review provides information about new technologies and the possibilities of using NAs in medicine.
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Murray A, Ojeda J, El Merhebi O, Calvo-Marzal P, Gerasimova Y, Chumbimuni-Torres K. Cost-Effective Modular Biosensor for SARS-CoV-2 and Influenza A Detection. BIOSENSORS 2023; 13:874. [PMID: 37754108 PMCID: PMC10526333 DOI: 10.3390/bios13090874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
A modular, multi-purpose, and cost-effective electrochemical biosensor based on a five-stranded four-way junction (5S-4WJ) system was developed for SARS-CoV-2 (genes S and N) and Influenza A virus (gene M) detection. The 5S-4WJ structure consists of an electrode-immobilized universal stem-loop (USL) strand, two auxiliary DNA strands, and a universal methylene blue redox strand (UMeB). This design allows for the detection of specific nucleic acid sequences using square wave voltammetry (SWV). The sequence-specific auxiliary DNA strands (m and f) ensure selectivity of the biosensor for target recognition utilizing the same USL and UMeB components. An important feature of this biosensor is the ability to reuse the USL-modified electrodes to detect the same or alternative targets in new samples. This is accomplished by a simple procedure involving rinsing the electrodes with water to disrupt the 5S-4WJ structure and subsequent re-hybridization of the USL strand with the appropriate set of strands for a new analysis. The biosensor exhibited minimal loss in signal after rehybridization, demonstrating its potential as a viable multiplex assay for both current and future pathogens, with a low limit of quantification (LOQ) of as low as 17 pM.
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Affiliation(s)
| | | | | | | | | | - Karin Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA; (A.M.); (J.O.); (O.E.M.); (P.C.-M.); (Y.G.)
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4
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Péter B, Farkas E, Kurunczi S, Szittner Z, Bősze S, Ramsden JJ, Szekacs I, Horvath R. Review of Label-Free Monitoring of Bacteria: From Challenging Practical Applications to Basic Research Perspectives. BIOSENSORS 2022; 12:bios12040188. [PMID: 35448248 PMCID: PMC9026780 DOI: 10.3390/bios12040188] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/10/2023]
Abstract
Novel biosensors already provide a fast way to detect the adhesion of whole bacteria (or parts of them), biofilm formation, and the effect of antibiotics. Moreover, the detection sensitivities of recent sensor technologies are large enough to investigate molecular-scale biological processes. Usually, these measurements can be performed in real time without using labeling. Despite these excellent capabilities summarized in the present work, the application of novel, label-free sensor technologies in basic biological research is still rare; the literature is dominated by heuristic work, mostly monitoring the presence and amount of a given analyte. The aims of this review are (i) to give an overview of the present status of label-free biosensors in bacteria monitoring, and (ii) to summarize potential novel directions with biological relevancies to initiate future development. Optical, mechanical, and electrical sensing technologies are all discussed with their detailed capabilities in bacteria monitoring. In order to review potential future applications of the outlined techniques in bacteria research, we summarize the most important kinetic processes relevant to the adhesion and survival of bacterial cells. These processes are potential targets of kinetic investigations employing modern label-free technologies in order to reveal new fundamental aspects. Resistance to antibacterials and to other antimicrobial agents, the most important biological mechanisms in bacterial adhesion and strategies to control adhesion, as well as bacteria-mammalian host cell interactions are all discussed with key relevancies to the future development and applications of biosensors.
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Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
- Correspondence: (B.P.); (R.H.)
| | - Eniko Farkas
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
| | - Sandor Kurunczi
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
| | - Zoltán Szittner
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, 1120 Budapest, Hungary;
- National Public Health Center, 1097 Budapest, Hungary
| | - Jeremy J. Ramsden
- Clore Laboratory, Department of Biomedical Research, University of Buckingham, Buckingham MK18 1AD, UK;
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
| | - Robert Horvath
- Nanobiosensorics Laboratory, Centre for Energy Research, Institute of Technical Physics and Materials Science, 1121 Budapest, Hungary; (E.F.); (S.K.); (Z.S.); (I.S.)
- Correspondence: (B.P.); (R.H.)
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Identification of multiple single-nucleotide variants for clinical evaluation of Helicobacter pylori drug resistance. Talanta 2022; 243:123367. [DOI: 10.1016/j.talanta.2022.123367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
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Klimek R, Donlin-Asp PG, Polisseni C, Hanff V, Schuman EM, Heckel A. Visible light-activatable Q-dye molecular beacons for long-term mRNA monitoring in neurons. Chem Commun (Camb) 2021; 57:12683-12686. [PMID: 34780585 DOI: 10.1039/d1cc05664f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present a new class of Q-dye molecular beacons (MBs) that can be locally activated with visible light in hippocampal neurons. Our novel architecture increases the available monitoring time for neuronal mRNA from several minutes to 14 hours, since a lower light-sampling rate is required for tracking.
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Affiliation(s)
- Robin Klimek
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
| | - Paul G Donlin-Asp
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Claudio Polisseni
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Vanessa Hanff
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
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Liu X, Bu S, Wei H, Wang Z, Yu S, Li Z, Hao Z, He X, Wan J. Visual assay of Escherichia coli O157:H7 based on an isothermal strand displacement and hybrid chain reaction amplification strategy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3379-3385. [PMID: 34235517 DOI: 10.1039/d1ay00644d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here, we describe a simple, sensitive, and enzyme-free method for visual point-of-care detection of 16S rRNA of Escherichia coli O157:H7 based on an isothermal strand displacement-hybrid chain reaction (ISD-HCR) and lateral flow strip (LFS). In this study, the secondary structure of 16S rRNA of E. coli O157:H7 was unwound by two helper oligonucleotides to expose the single-strand-specific nucleic acid sequence. The free specific sequence promoted the toehold-mediated strand displacement reaction to output a large number of FITC-labeled single-stranded DNA probes (capture probe [CP]). The 3'-end sequence of the reporter probe propagated a chain reaction of hybridization events between the two hairpin probes modified with biotin to form long nicked DNA polymers with multiple biotins (RP-HCR complexes); the free CP and RP-HCR complexes then form CP/RP-HCR complexes. The biotin-labeled double-stranded DNA CP/RP-HCR polymers then introduced numerous streptavidin (SA)-labeled gold nanoparticles (AuNPs) on the LFS. The accumulation of AuNPs produced a characteristic red band, which enabled visual detection of changes in the signal of 16S rRNA of E. coli O157:H7. The current approach could detect E. coli O157:H7 at concentrations as low as 102 CFU mL-1 without instrumentation. This approach thus provides a simple, sensitive, and low-cost tool for point-of-care detection of pathogenic bacteria, especially in resource-limited countries.
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Affiliation(s)
- Xiu Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130022, China.
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Bidar N, Amini M, Oroojalian F, Baradaran B, Hosseini SS, Shahbazi MA, Hashemzaei M, Mokhtarzadeh A, Hamblin MR, de la Guardia M. Molecular beacon strategies for sensing purpose. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116143] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Dhar BC, Reed AJ, Mitra S, Rodriguez Sanchez P, Nedorezova DD, Connelly RP, Rohde KH, Gerasimova YV. Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens Bioelectron 2020; 165:112385. [PMID: 32729510 DOI: 10.1016/j.bios.2020.112385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/01/2023]
Abstract
A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.
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Affiliation(s)
- Bidhan C Dhar
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Adam J Reed
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Suvra Mitra
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | | | - Daria D Nedorezova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA.
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10
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Qu G, Sun X, Ying N, Bu S, Li Z, Hao Z, Wu H, Wan J. 16S rRNA-functionalized multi-HCR concatemers in a signal amplification nanostructure for visual detection of Salmonella. Biotechnol Appl Biochem 2020; 68:560-567. [PMID: 32472699 DOI: 10.1002/bab.1962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/16/2020] [Indexed: 01/15/2023]
Abstract
To prevent foodborne diseases and minimize their impacts, it is extremely important to develop a cost-effective and efficient bacterial detection assay for diagnostics, particularly in resource-poor settings. In this study, 16S rRNA from foodborne Salmonella was coupled with multiple HCR (hybridization chain reaction) concatemers and functionalized in a signal structure for lateral flow nucleic acid biosensor (LFNAB) detection. The 16S rRNA was incubated with two specific capture probes and multiple helper probes carrying the same initiator, to unwind its secondary structure and form an "initiators-on-a-string" complex. Through use of the initiators, each target 16S rRNA yielded multiple HCR concatemers tethered to numerous biotins, and numerous streptavidin-labeled gold nanoparticles were introduced on the LFNAB. The limit of detection was 53.65 CFU/mL for Salmonella. Notably, this method has high specificity and applicability for the detection of Salmonella in food and water samples.
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Affiliation(s)
- Guijuan Qu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiuwei Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Na Ying
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- East China Sea Fisheries Research Institute, China Academy of Fishery Science, Shanghai, China
| | - Shengjun Bu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Zhongyi Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Zhuo Hao
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Haibo Wu
- College of Food Engineering, Beibu Gulf University, Qinzhou, Guangxi Province, China
| | - Jiayu Wan
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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11
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MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures. ELECTROANAL 2020. [DOI: 10.1002/elan.201900690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Gnaim R, Sheviryov J, Golberg A, Ames G, Oziel M, González CA. Label-Free cDNA Detection Based on Radiofrequency Scattering Parameters: A New Approach for an Inexpensive Gene Sensor. J Med Device 2020. [DOI: 10.1115/1.4045909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Abstract
A new gene detection technique that is fast, inexpensive, and easy-to-use is urgently needed in hospitals, clinics, and laboratories without access to expensive equipments. The lack of a practical, minimally invasive, and economical method constitutes the main impediment to the promotion of genetic medicine in developing countries. Radiofrequency scattering parameters are an inexpensive gene sensor potentially capable of noninvasively identifying biological materials. They represent a quantitative value for the electromagnetic reflection/transmission characteristics of certain molecular markers in a given frequency domain. The S21 parameter is the difference between the signal received and that transmitted. The aim of this study is to evaluate the S21 transmittance parameters (magnitude and phase) as an indirect impedance measurement for detecting the label-free complementary deoxyribonucleic acid (cDNA) amplification of the 16S ribosomal subunit gene. S21 values showed differences associated with distinct cDNA concentrations. Hence, this technique could possibly facilitate the design of an inexpensive, label-free, and easy-to-use gene sensor.
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Affiliation(s)
- Rima Gnaim
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; The Triangle Regional Research and Development Center, Kfar Qari' 30075, Israel; Porter School, Tel Aviv University, Room 214, Ramat Aviv 69978, Israel
| | - Julia Sheviryov
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Porter School, Room 214, Ramat Aviv 69978, Israel
| | - Alexander Golberg
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Porter School, Room 215, Ramat Aviv 69978, Israel
| | - Gerardo Ames
- Centro de Investigación en Instrumentación e Imagenología Médica (Ci3M), Universidad Autónoma Metropolitana—Iztapalapa, CDMX 09340, Mexico; Centro de Investigación en Instrumentación e Imagenología Médica (Ci3M), Avenue San Rafael Atlixco 186, Leyes de Reforma 1ra Secc 09340, México
| | - Moshe Oziel
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - César A. González
- Instituto Politécnico Nacional-Escuela Superior de Medicina, CDMX 11340, México; Plan de San Luis esq. Díaz Mirón, Col. Casco de Santo Tomas, CDMX 11300, México
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13
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Connelly RP, Verduzco C, Farnell S, Yishay T, Gerasimova YV. Toward a Rational Approach to Design Split G-Quadruplex Probes. ACS Chem Biol 2019; 14:2701-2712. [PMID: 31599573 DOI: 10.1021/acschembio.9b00634] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hybridization probes have become an indispensable tool for nucleic acid analysis. Systematic efforts in probe optimization resulted in their improved binding affinity, turn-on ratios, and ability to discriminate single nucleotide substitutions (SNSs). The use of split (or multicomponent) probes is a promising strategy to improve probe selectivity and enable an analysis of folded analytes. Here, we developed criteria for the rational design of a split G-quadruplex (G4) peroxidase-like deoxyribozyme (sPDz) probe that provides a visual output signal. The sPDz probe consists of two DNA strands that hybridize to the abutting positions of a DNA/RNA target and form a G4 structure catalyzing, in the presence of a hemin cofactor, H2O2-mediated oxidation of organic compounds into their colored oxidation products. We have demonstrated that probe design becomes complicated in the case of target sequences containing clusters (two or more) of cytosine residues and developed strategies to overcome the challenges to achieving high signal-to-noise and excellent SNS discrimination. Specifically, to improve selectivity, a conformational constraint that stabilizes the probe's dissociated state is beneficial. If the signal intensity is compromised, introduction of flexible non-nucleotide linkers between the G4-forming and target-recognizing elements of the probe helps to decrease the steric hindrance for G4 PDz formation observed as a signal increase. Varying the modes of G4 core splitting is another instrument for the optimal sPDz design. The suggested algorithm was successfully utilized for the design of the sPDz probe interrogating a fragment of the Influenza A virus genome (subtype H1N1), which can be of practical use for flu diagnostics and surveillance.
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Affiliation(s)
- Ryan P. Connelly
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Charles Verduzco
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Serena Farnell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Tamar Yishay
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Yulia V. Gerasimova
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
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14
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Wang L, Wen Y, Yang X, Xu L, Liang W, Zhu Y, Wang L, Li Y, Li Y, Ding M, Ren S, Yang Z, Lv M, Zhang J, Ma K, Liu G. Ultrasensitive Electrochemical DNA Biosensor Based on a Label-Free Assembling Strategy Using a Triblock polyA DNA Probe. Anal Chem 2019; 91:16002-16009. [PMID: 31746200 DOI: 10.1021/acs.analchem.9b04757] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiblock DNA probe attracted a large amount of scientific attention, for the development of multitarget biosensor and improved specificity/sensitivity. However, the development of multiblock DNA probes highly relied on the chemical synthesis of organic linkers or nanomaterials, which limited their practicability and biological compatibility. In this work, we developed a label-free assembling strategy using a triblock DNA capture probe, which connects two DNA probes with its intrinsic polyA fragment (probe-PolyA-probe, PAP). The middle polyA segment has a high affinity to the gold electrode surface, leading to excellent reproducibility, stability, and regeneration of our biosensor. Two flanking capture probes were tandemly co-assembled on the electrode surface with consistent spatial relationship and exactly the same amount. When combined with the target DNA, the hybridization stability was improved, because of the strong base stacking effect of two capture probes. The sensitivity of our biosensor was proved to be 10 fM, with a wide analysis range between 10 fM to 1 nM. Our PAP-based biosensor showed excellent specificity when facing mismatched DNA sequences. Even single nucleotide polymorphisms can be distinguished by each probe. The excellent practicability of our biosensor was demonstrated by analyzing genomic DNA both with and without PCR amplification.
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Affiliation(s)
- Lele Wang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Xue Yang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Li Xu
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Wen Liang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Ying Zhu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Yan Li
- Division of Chemical Metrology and Analytical Science , National Institute of Metrology of China , Beijing 102200 , People's Republic of China
| | - Yuan Li
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Min Ding
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Shuzhen Ren
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Zhenzhou Yang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Min Lv
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Jichao Zhang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Kang Ma
- Division of Chemical Metrology and Analytical Science , National Institute of Metrology of China , Beijing 102200 , People's Republic of China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
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15
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Nedorezova DD, Fakhardo AF, Molden TA, Kolpashchikov DM. Deoxyribozyme‐Based DNA Machines for Cancer Therapy. Chembiochem 2019; 21:607-611. [DOI: 10.1002/cbic.201900525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Anna F. Fakhardo
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Tatiana A. Molden
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
| | - Dmitry M. Kolpashchikov
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical SciencesUniversity of Central Florida Orlando FL 32816 USA
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16
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Lynch CA, Foguel MV, Reed AJ, Balcarcel AM, Calvo-Marzal P, Gerasimova YV, Chumbimuni-Torres KY. Selective Determination of Isothermally Amplified Zika Virus RNA Using a Universal DNA-Hairpin Probe in Less than 1 Hour. Anal Chem 2019; 91:13458-13464. [DOI: 10.1021/acs.analchem.9b02455] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Charles A. Lynch
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
- Rose Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, Indiana 47803, United States
| | - Marcos V. Foguel
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Adam J. Reed
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Angelica M. Balcarcel
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Percy Calvo-Marzal
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Yulia V. Gerasimova
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Karin Y. Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
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17
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Wu F, Lin Q, Wang L, Zou Y, Chen M, Xia Y, Lan J, Chen J. A DNA electrochemical biosensor based on triplex DNA-templated Ag/Pt nanoclusters for the detection of single-nucleotide variant. Talanta 2019; 207:120257. [PMID: 31594620 DOI: 10.1016/j.talanta.2019.120257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 01/24/2023]
Abstract
A label-free electrochemical biosensor based on the triplex DNA-templated Ag/Pt bimetallic nanoclusters (triplex-Ag/PtNCs) and locked nucleic acid (LNA) modified X-shaped DNA probe was developed for the detection of single-nucleotide variant (SNV) related to β-thalassemia. Firstly, using triplex DNA as template, a site-specific and homogeneous Ag/PtNCs was prepared, which can effectively catalyze the 3,3,5,5-tetramethylbenzidine-H2O2 system and thus be employed as a signal reporter in the field of electrochemical biosensor. Secondly, the LNA modified X-shaped probes were assembled on gold electrode surface, which can only be dissociated in the presence of target, leading to the hybridization with triplex-Ag/PtNCs and significant increase of current signal. In this way, the detection limit for SNV of β-thalassemia was 0.8 fM with variant allele frequency (VAF) as low as 0.0001%.
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Affiliation(s)
- Fang Wu
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Qian Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Liangliang Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yulian Zou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Mei Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jianming Lan
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China.
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18
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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19
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Wang Q, Wen Y, Li Y, Liang W, Li W, Li Y, Wu J, Zhu H, Zhao K, Zhang J, Jia N, Deng W, Liu G. Ultrasensitive Electrochemical Biosensor of Bacterial 16S rRNA Gene Based on polyA DNA Probes. Anal Chem 2019; 91:9277-9283. [PMID: 31198030 DOI: 10.1021/acs.analchem.9b02175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Traditional microbiology analysis is usually hindered by the long time-cost and lack of portability in many urgent situations. In this work, we developed a novel electrochemical DNA biosensor (E-biosensor) for sensitive analysis of the 16S rRNA gene of five bacteria, using a consecutive adenine (polyA) probe. The polyA probe consists of a polyA tail and a recognition part. The polyA tail can combine onto the gold surface with improved controllability of the surface density, by conveniently changing the length of polyA. The recognition part of the capture probe together with two biotin-labeled reporter probes hybridize with the target DNA and form a stable DNA-tetramer sandwich structure, and then avidin-HRP enzyme was added to produce a redox current signal for the following electrochemical detection. Finally, we realized sensitive quantification of artificial target DNA with a limit of detection (LOD) of 10 fM, and excellent selectivity and reusability were also demonstrated. Importantly, the detection capability was equally good when facing bacterial genomic DNA, due to the base-stacking force of our multireporter-probe system, which can help to break the second structure and stabilize the probe-target complexes. Our biosensor was constructed on a 16-channel electrode chip without any polymerase chain reaction (PCR) process needed, which took a significant step toward a portable bacteria biosensor.
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Affiliation(s)
- Qian Wang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China.,Department of Chemistry, College of Chemistry and Materials Science , Shanghai Normal University , 100 Guilin Road , Shanghai 200234 , P. R. China
| | - Yanli Wen
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Yan Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Wen Liang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Wen Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Yuan Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Jiahuan Wu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Huichen Zhu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Keke Zhao
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Jun Zhang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Nengqin Jia
- Department of Chemistry, College of Chemistry and Materials Science , Shanghai Normal University , 100 Guilin Road , Shanghai 200234 , P. R. China
| | - Wangping Deng
- Chinese Center for Disease Control and Prevention , National Institute of Parasitic Diseases , 207 Rui Jin Er Road , Shanghai 200025 , P. R. China
| | - Gang Liu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
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20
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Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
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Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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21
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A universal and label-free impedimetric biosensing platform for discrimination of single nucleotide substitutions in long nucleic acid strands. Biosens Bioelectron 2018. [PMID: 29524915 DOI: 10.1016/j.bios.2018.02.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report a label-free universal biosensing platform for highly selective detection of long nucleic acid strands. The sensor consists of an electrode-immobilized universal stem-loop (USL) probe and two adaptor strands that form a 4J structure in the presence of a specific DNA/RNA analyte. The sensor was characterized by electrochemical impedance spectroscopy (EIS) using K3[Fe(CN)6]/K4[Fe(CN)6] redox couple in solution. An increase in charge transfer resistance (RCT) was observed upon 4J structure formation, the value of which depends on the analyte length. Cyclic voltammetry (CV) was used to further characterize the sensor and monitor the electrochemical reaction in conjunction with thickness measurements of the mixed DNA monolayer obtained using spectroscopic ellipsometry. In addition, the electron transfer was calculated at the electrode/electrolyte interface using a rotating disk electrode. Limits of detection in the femtomolar range were achieved for nucleic acid targets of different lengths (22 nt, 60 nt, 200 nt). The sensor produced only a background signal in the presence of single base mismatched analytes, even in hundred times excess in concentration. This label-free and highly selective biosensing platform is versatile and can be used for universal detection of nucleic acids of varied lengths which could revolutionize point of care diagnostics for applications such as bacterial or cancer screening.
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22
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Kamar O, Sun SC, Lin CH, Chung WY, Lee MS, Liao YC, Kolpashchikov DM, Chuang MC. A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids. Chem Commun (Camb) 2017; 53:10592-10595. [PMID: 28900642 PMCID: PMC5645154 DOI: 10.1039/c7cc05576e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Highly selective probes hybridize only to fully complementary DNA or RNA sequences and, therefore, often fail to recognize mutated viral genomes. Here we designed a probe that possesses two seemingly incompatible properties: it tolerates some point mutations in genome, while it remains selective towards others. An OR deoxyribozyme logic gate was designed to fluorescently report the sequences of enterovirus 71 (EV71) covering ∼90% of all known EV71 strains. Importantly, sequences of closely related coxsackieviruses that differed by single nucleotides were reliably differentiated in 7 out of 8 cases.
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Affiliation(s)
- Ola Kamar
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA.
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23
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Campbell EA, Peterson E, Kolpashchikov DM. Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles. Chemphyschem 2017; 18:1730-1734. [PMID: 28234410 DOI: 10.1002/cphc.201700109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 02/02/2023]
Abstract
DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions.
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Affiliation(s)
- Eleanor A Campbell
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Evan Peterson
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine and National Center for Forensic Science, University of Central Florida, Orlando, FL, 32816, USA)An invited contribution to a Special Issue on Molecular Logic
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24
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Stancescu M, Fedotova TA, Hooyberghs J, Balaeff A, Kolpashchikov DM. Nonequilibrium Hybridization Enables Discrimination of a Point Mutation within 5-40 °C. J Am Chem Soc 2016; 138:13465-13468. [PMID: 27681667 PMCID: PMC5645261 DOI: 10.1021/jacs.6b05628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Detection of point mutations and single nucleotide polymorphisms in DNA and RNA has a growing importance in biology, biotechnology, and medicine. For the application at hand, hybridization assays are often used. Traditionally, they differentiate point mutations only at elevated temperatures (>40 °C) and in narrow intervals (ΔT = 1-10 °C). The current study demonstrates that a specially designed multistranded DNA probe can differentiate point mutations in the range of 5-40 °C. This unprecedentedly broad ambient-temperature range is enabled by a controlled combination of (i) nonequilibrium hybridization conditions and (ii) a mismatch-induced increase of equilibration time in respect to that of a fully matched complex, which we dub "kinetic inversion".
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Affiliation(s)
- Maria Stancescu
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Tatiana A. Fedotova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Boeretang 200, Mol B-2400, Belgium
- Theoretical Physics, Hasselt University, Campus Diepenbeek, Agoralaan - Building D, Diepenbeek B-3590, Belgium
| | - Alexander Balaeff
- NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, Florida 32826, United States
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
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25
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Gerasimova YV, Kolpashchikov DM. Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Gerasimova YV, Kolpashchikov DM. Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits. Angew Chem Int Ed Engl 2016; 55:10244-7. [DOI: 10.1002/anie.201603265] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/05/2016] [Indexed: 11/06/2022]
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27
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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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28
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Gerasimova YV, Yakovchuk P, Dedkova LM, Hecht SM, Kolpashchikov DM. Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors. RNA (NEW YORK, N.Y.) 2015; 21:1834-43. [PMID: 26289345 PMCID: PMC4574759 DOI: 10.1261/rna.052613.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/13/2015] [Indexed: 05/06/2023]
Abstract
Mutations in ribosomal RNA (rRNA) have traditionally been detected by the primer extension assay, which is a tedious and multistage procedure. Here, we describe a simple and straightforward fluorescence assay based on binary deoxyribozyme (BiDz) sensors. The assay uses two short DNA oligonucleotides that hybridize specifically to adjacent fragments of rRNA, one of which contains a mutation site. This hybridization results in the formation of a deoxyribozyme catalytic core that produces the fluorescent signal and amplifies it due to multiple rounds of catalytic action. This assay enables us to expedite semi-quantification of mutant rRNA content in cell cultures starting from whole cells, which provides information useful for optimization of culture preparation prior to ribosome isolation. The method requires less than a microliter of a standard Escherichia coli cell culture and decreases analysis time from several days (for primer extension assay) to 1.5 h with hands-on time of ∼10 min. It is sensitive to single-nucleotide mutations. The new assay simplifies the preliminary analysis of RNA samples and cells in molecular biology and cloning experiments and is promising in other applications where fast detection/quantification of specific RNA is required.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, USA
| | - Petro Yakovchuk
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Larisa M Dedkova
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, USA National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, USA Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, USA
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29
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Brown CW, Lakin MR, Fabry-Wood A, Horwitz EK, Baker NA, Stefanovic D, Graves SW. A unified sensor architecture for isothermal detection of double-stranded DNA, oligonucleotides, and small molecules. Chembiochem 2015; 16:725-30. [PMID: 25663617 PMCID: PMC4422402 DOI: 10.1002/cbic.201402615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 12/29/2022]
Abstract
Pathogen detection is an important problem in many areas of medicine and agriculture, which can involve genomic or transcriptomic signatures or small-molecule metabolites. We report a unified, DNA-based sensor architecture capable of isothermal detection of double-stranded DNA targets, single-stranded oligonucleotides, and small molecules. Each sensor contains independent target detection and reporter modules, enabling rapid design. We detected gene variants on plasmids by using a straightforward isothermal denaturation protocol. The sensors were highly specific, even with a randomized DNA background. We achieved a limit of detection of ∼15 pM for single-stranded targets and ∼5 nM for targets on denatured plasmids. By incorporating a blocked aptamer sequence, we also detected small molecules using the same sensor architecture. This work provides a starting point for multiplexed detection of multi-strain pathogens, and disease states caused by genetic variants (e.g., sickle cell anemia).
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Affiliation(s)
- Carl W. Brown
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
| | - Matthew R. Lakin
- Department of Computer Science University of New Mexico, Albuquerque, NM 87131, USA
| | - Aurora Fabry-Wood
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
| | - Eli K. Horwitz
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
| | - Nicholas A. Baker
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
| | - Darko Stefanovic
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
- Department of Computer Science University of New Mexico, Albuquerque, NM 87131, USA
| | - Steven W. Graves
- Center for Biomedical Engineering University of New Mexico, Albuquerque, NM 87131, USA
- Department of Chemical and Biological Engineering University of New Mexico, Albuquerque, NM 87131, USA
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30
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Ahmed A, Rushworth JV, Hirst NA, Millner PA. Biosensors for whole-cell bacterial detection. Clin Microbiol Rev 2014; 27:631-46. [PMID: 24982325 PMCID: PMC4135896 DOI: 10.1128/cmr.00120-13] [Citation(s) in RCA: 339] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bacterial pathogens are important targets for detection and identification in medicine, food safety, public health, and security. Bacterial infection is a common cause of morbidity and mortality worldwide. In spite of the availability of antibiotics, these infections are often misdiagnosed or there is an unacceptable delay in diagnosis. Current methods of bacterial detection rely upon laboratory-based techniques such as cell culture, microscopic analysis, and biochemical assays. These procedures are time-consuming and costly and require specialist equipment and trained users. Portable stand-alone biosensors can facilitate rapid detection and diagnosis at the point of care. Biosensors will be particularly useful where a clear diagnosis informs treatment, in critical illness (e.g., meningitis) or to prevent further disease spread (e.g., in case of food-borne pathogens or sexually transmitted diseases). Detection of bacteria is also becoming increasingly important in antibioterrorism measures (e.g., anthrax detection). In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing. There is a particular focus on electrochemical biosensors, especially impedance-based systems, as these present key advantages in terms of ease of miniaturization, lack of reagents, sensitivity, and low cost.
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Affiliation(s)
- Asif Ahmed
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Jo V Rushworth
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Natalie A Hirst
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul A Millner
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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31
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Bengtson HN, Kolpashchikov DM. A differential fluorescent receptor for nucleic acid analysis. Chembiochem 2014; 15:228-31. [PMID: 24339354 PMCID: PMC4066444 DOI: 10.1002/cbic.201300657] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Indexed: 01/28/2023]
Abstract
Differential receptors use an array of sensors to recognize analytes. Each sensor in the array can recognize not one, but several analytes with different rates, so a single analyte triggers a response of several sensors in the array. The receptor thus produces a pattern of signals that is unique for each analyte, thereby enabling identification of a specific analyte by producing a "fingerprint" pattern. We applied this approach for the analysis of DNA sequences of Mycobacterium tuberculosis strains that differ by single nucleotide substitutions in the 81-bp hot-spot region that imparts rifampin resistance. The technology takes advantage of the new multicomponent, selfassembling sensor, which produces a fluorescent signal in the presence of specific DNA sequences. A differential fluorescent receptor (DFR) contained an array of three such sensors and differentiated at least eight DNA sequences. The approach requires only one molecular-beacon-like fluorescent reporter, which can be used by all three sensors. The DFR developed in this study represents a cost-efficient alternative to molecular diagnostic technologies that use fluorescent hybridization probes.
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Affiliation(s)
- Hillary N. Bengtson
- Chemistry Department and Burnett School of Biomedical Sciences University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816 (USA)
| | - Dmitry M. Kolpashchikov
- Chemistry Department and Burnett School of Biomedical Sciences University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816 (USA)
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32
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Johnson BN, Mutharasan R. A cantilever biosensor-based assay for toxin-producing cyanobacteria Microcystis aeruginosa using 16S rRNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:12333-12341. [PMID: 24070168 DOI: 10.1021/es402925k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Monitoring of cyanotoxins in source waters is currently done through toxin-targeting assays which suffer from low sensitivity due to poor antibody avidity. We present a biosensor-based method as an alternative for detecting toxin-producing cyanobacteria M. aeruginosa via species-selective region of 16S rRNA at concentrations as low as 50 cells/mL, and over a five-log dynamic range. The cantilever biosensor was immobilized with a 27-base DNA strand that is complementary to the target variable region of 16S rRNA of M. aeruginosa. The cantilever sensor detects mass-changes through shifts in its resonant frequency. Increase in the biosensor's effective mass, caused by hybridization of target strand with the biosensor-immobilized complementary strand, showed consistent and proportional frequency shift to M. aeruginosa concentrations. The sensor hybridization response was verified in situ by two techniques: (a) presence of duplex DNA structure postdetection via fluorescence measurements, and (b) secondary hybridization of nanogold-labeled DNA strands to the captured 16S rRNA strands. The biosensor-based assay, conducted in a flow format (∼ 0.5 mL/min), is relatively short, and requires a postextraction analysis time of less than two hours. The two-step detection protocol (primary and secondary hybridization) is less prone to false negatives, and the technique as a whole can potentially provide an early warning for toxin presence in source waters.
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Affiliation(s)
- Blake N Johnson
- Department of Chemical and Biological Engineering, Drexel University , Philadelphia, Pennsylvania 19104, United States
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Kumar TS, Myznikova A, Samokhina E, Astakhova IK. Rapid genotyping using pyrene-perylene locked nucleic acid complexes. ARTIFICIAL DNA, PNA & XNA 2013; 4:58-68. [PMID: 24044052 PMCID: PMC3771999 DOI: 10.4161/adna.25903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/07/2013] [Accepted: 07/25/2013] [Indexed: 01/27/2023]
Abstract
We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene-perylene FRET pairs, e.g., in imaging and clinical diagnostics.
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Affiliation(s)
- T. Santhosh Kumar
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
- National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health; Molecular Recognition Section; Bethesda, MD USA
| | - Anna Myznikova
- Central Research Institute of Epidemiology; Moscow, Russia
| | | | - Irina Kira Astakhova
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
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Cornett EM, O’Steen MR, Kolpashchikov DM. Operating Cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLoS One 2013; 8:e55919. [PMID: 23441157 PMCID: PMC3575382 DOI: 10.1371/journal.pone.0055919] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/03/2013] [Indexed: 11/18/2022] Open
Abstract
Molecular Beacon (MB) probes have been extensively used for nucleic acid analysis because of their ability to produce fluorescent signal in solution instantly after hybridization. The indirect binding of MB probe to a target analyte offers several advantages, including: improved genotyping accuracy and the possibility to analyse folded nucleic acids. Here we report on a new design for MB-based sensor, called ‘Operating Cooperatively’ (OC), which takes advantage of indirect binding of MB probe to a target analyte. The sensor consists of two unmodified DNA strands, which hybridize to a universal MB probe and a nucleic acid analyte to form a fluorescent complex. OC sensors were designed to analyze two human SNPs and E.coli 16S rRNA. High specificity of the approach was demonstrated by the detection of true analyte in over 100 times excess amount of single base substituted analytes. Taking into account the flexibility in the design and the simplicity in optimization, we conclude that OC sensors may become versatile and efficient tools for instant DNA and RNA analysis in homogeneous solution.
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Affiliation(s)
- Evan M. Cornett
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Martin R. O’Steen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Dmitry M. Kolpashchikov
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
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Gerasimova YV, Ballantyne J, Kolpashchikov DM. Detection of SNP-containing human DNA sequences using a split sensor with a universal molecular beacon reporter. Methods Mol Biol 2013; 1039:69-80. [PMID: 24026686 DOI: 10.1007/978-1-62703-535-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Hybridization-based techniques have been extensively employed for the analysis of specific DNA/RNA sequences. Herein, we describe highly specific inexpensive smart hybridization-based sensor that takes advantage of a universal molecular beacon probe as a fluorescent reporter. The sensor has a straightforward design, and demonstrates improved selectivity and specificity of nucleic acid recognition. It is cost-efficient since it utilizes the same molecular beacon probe for the analysis of many nucleic acid sequences.
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Affiliation(s)
- Yulia V Gerasimova
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
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Kolpashchikov DM. An elegant biosensor molecular beacon probe: challenges and recent solutions. SCIENTIFICA 2012; 2012:928783. [PMID: 24278758 PMCID: PMC3820487 DOI: 10.6064/2012/928783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/10/2012] [Indexed: 05/02/2023]
Abstract
Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
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