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Adil O, Eddington SB, Gagnon KT, Shamsi MH. Microprobes for Label-Free Detection of Short Tandem Repeats: An Insight into Alleviating Secondary Structure Effects. Anal Chem 2023; 95:13528-13536. [PMID: 37651633 DOI: 10.1021/acs.analchem.3c01886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Overgrowth of short tandem repeat sequences in our genes can cause various neurodegenerative disorders. Such repeat sequences are ideal targets for the label-free electrochemical detection of such potential expansions. However, their length- and sequence-dependent secondary structures may interfere with the interfacial charge transfer of a detection platform, making them complex targets. In addition, the gene contains sporadic repeats that may result in false-positive signals. Therefore, it is necessary to design a platform capable of mitigating these effects and ultimately enhancing the specificity of tandem repeats. Here, we analyzed three different backbones of nucleic acid microprobes [DNA, peptide nucleic acid, and lock-nucleic acid (LNA)] to detect in vitro transcribed RNA carrying CAG repeats, which are associated with Huntington's disease, based on the charge-transfer resistance of the interface. We found that the LNA microprobe can distinguish lengths down to the attomolar concentration level and alleviate the effect of secondary structures and sporadic repeats in the sequence, thus distinguishing the "tandem repeats" specifically. Additionally, the control experiments conducted with and without Mg2+ demonstrated the LNA microprobe to perform better in the presence of the divalent cation. The results suggest that the LNA-based platform may eventually lead to the development of a reliable and straightforward biosensor for genetic neurodegenerative disorders.
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Affiliation(s)
- Omair Adil
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| | - Seth B Eddington
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Keith T Gagnon
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
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2
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Chang Y, Wang Y, Zhang J, Xing Y, Li G, Deng D, Liu L. Overview on the Design of Magnetically Assisted Electrochemical Biosensors. BIOSENSORS 2022; 12:bios12110954. [PMID: 36354462 PMCID: PMC9687741 DOI: 10.3390/bios12110954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 06/12/2023]
Abstract
Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.
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Affiliation(s)
| | | | | | | | | | | | - Lin Liu
- Correspondence: (D.D.); (L.L.)
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3
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Asefifeyzabadi N, Durocher G, Tshilenge KT, Alam T, Ellerby LM, Shamsi MH. PNA microprobe for label-free detection of expanded trinucleotide repeats. RSC Adv 2022; 12:7757-7761. [PMID: 35424746 PMCID: PMC8982460 DOI: 10.1039/d2ra00230b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 11/28/2022] Open
Abstract
We present a PNA microprobe sensing platform to detect trinucleotide repeat mutation by electrochemical impedance spectroscopy. The microprobe platform discriminated Huntington's disease-associated CAG repeats in cell-derived total RNA with S/N 1 : 3. This sensitive, label-free, and PCR-free detection strategy may be employed in the future to develop biosensing platforms for the detection of a plethora of repeat expansion disorders.
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Affiliation(s)
- Narges Asefifeyzabadi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
| | - Grace Durocher
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
| | | | - Tanimul Alam
- The Buck Institute for Research on Aging 8001 Redwood Blvd Novato CA 94945 USA
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging 8001 Redwood Blvd Novato CA 94945 USA
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
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4
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Liu Q, Tong Y, Wang K. Genome-wide detection of short tandem repeat expansions by long-read sequencing. BMC Bioinformatics 2020; 21:542. [PMID: 33371889 PMCID: PMC7768641 DOI: 10.1186/s12859-020-03876-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR), or "microsatellite", is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific repeat expansions may be associated with human diseases. Long-read sequencing coupled with bioinformatics tools enables the estimation of repeat counts for STRs. However, with the exception of a few well-known disease-relevant STRs, normal ranges of repeat counts for most STRs in human populations are not well known, preventing the prioritization of STRs that may be associated with human diseases. RESULTS In this study, we extend a computational tool RepeatHMM to infer normal ranges of 432,604 STRs using 21 long-read sequencing datasets on human genomes, and build a genomic-scale database called RepeatHMM-DB with normal repeat ranges for these STRs. Evaluation on 13 well-known repeats show that the inferred repeat ranges provide good estimation to repeat ranges reported in literature from population-scale studies. This database, together with a repeat expansion estimation tool such as RepeatHMM, enables genomic-scale scanning of repeat regions in newly sequenced genomes to identify disease-relevant repeat expansions. As a case study of using RepeatHMM-DB, we evaluate the CAG repeats of ATXN3 for 20 patients with spinocerebellar ataxia type 3 (SCA3) and 5 unaffected individuals, and correctly classify each individual. CONCLUSIONS In summary, RepeatHMM-DB can facilitate prioritization and identification of disease-relevant STRs from whole-genome long-read sequencing data on patients with undiagnosed diseases. RepeatHMM-DB is incorporated into RepeatHMM and is available at https://github.com/WGLab/RepeatHMM .
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yao Tong
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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5
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Asefifeyzabadi N, Alkhaldi R, Qamar AZ, Pater AA, Patwardhan M, Gagnon KT, Talapatra S, Shamsi MH. Label-free Electrochemical Detection of CGG Repeats on Inkjet Printable 2D Layers of MoS 2. ACS APPLIED MATERIALS & INTERFACES 2020; 12:52156-52165. [PMID: 33151065 DOI: 10.1021/acsami.0c14912] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Flexible and ultrasensitive biosensing platforms capable of detecting a large number of trinucleotide repeats (TNRs) are crucial for future technology development needed to combat a variety of genetic disorders. For example, trinucleotide CGG repeat expansions in the FMR1 gene can cause Fragile X syndrome (FXS) and Fragile X-associated tremor/ataxia syndrome (FXTAS). Current state-of-the-art technologies to detect repeat sequences are expensive, while relying on complicated procedures, and prone to false negatives. We reasoned that two-dimensional (2D) molybdenum sulfide (MoS2) surfaces may be useful for label-free electrochemical detection of CGG repeats due to its high affinity for guanine bases. Here, we developed a low-cost and sensitive wax-on-plastic electrochemical sensor using 2D MoS2 ink for the detection of CGG repeats. The ink containing few-layered MoS2 nanosheets was prepared and characterized using optical, electrical, electrochemical, and electron microscopic methods. The devices were characterized by electron microscopic and electrochemical methods. Repetitive CGG DNA was adsorbed on a MoS2 surface in a high cationic strength environment and the electrocatalytic current of the CGG/MoS2 interface was recorded using a soluble Fe(CN)6-3/-4 redox probe by differential pulse voltammetry (DPV). The dynamic range for the detection of prehybridized duplexes ranged from 1 aM to 100 nM with a 3.0 aM limit of detection. A detection range of 100 fM to 1 nM was recorded for surface hybridization events. Using this method, we were able to observe selectivity of MoS2 for CGG repeats and distinguish nonpathogenic from disease-associated repeat lengths. The detection of CGG repeat sequences on inkjet printable 2D MoS2 surfaces is a forward step toward developing chip-based rapid and label-free sensors for the detection of repeat expansion sequences.
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Affiliation(s)
- Narges Asefifeyzabadi
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Rana Alkhaldi
- Department of Physics, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Ahmad Z Qamar
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Meera Patwardhan
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan 62901, United States
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Saikat Talapatra
- Department of Physics, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Mohtashim H Shamsi
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
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6
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Yang Z, Hu Q, Qin L, Zhu S, Qiu L, Su Y, Jin J. RNase H amplified RNA probe and graphene oxide system for highly sensitive detection of (CAG)n DNA repeat sequences. NANOTECHNOLOGY 2019; 30:465502. [PMID: 31426052 DOI: 10.1088/1361-6528/ab3c8b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Huntington's disease is a chronic progressive neurodegeneration which is caused by CAG repeat sequences expanding in the huntingtin gene. There is currently no disease-modifying treatment for the disease, and its progression can only be slowed down before the onset of symptoms. A novel fluorescent platform which contains an RNA probe and graphene oxide for detection of the biomarker of Huntington's disease, CAG repeat sequences, was constructed in this investigation. In addition, RNase H was employed in the fluorescent system to enhance the sensitivity of the detection capability. The fluorescent signal was increased through the cyclic amplified reaction, which results from RNase H, specifically digestion of the RNA strand in the complement of the RNA-DNA duplex. The designed measurement method can detect CAG repeat sequences with a detection limit of 108 pM (R2 = 0.968) under which we optimized assay conditions. Furthermore, the detection limit is approximately 18 times lower than the traditional DNA and graphene oxide detection method without assistance of RNase H. Additionally, the probing platform also shows stronger ability to discriminate between the fluorescence of the target sequence and that of other non-target sequences. The results of our studies demonstrate that the RNase H amplified RNA probe and graphene oxide system exhibited excellent sensitivity and selectivity to the target of CAG repeats sequences.
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7
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Liu Y, Ge Z, Chen M, He H, Zhang X, Wang S. Ratiometric electrochemical biosensor based on Exo III-Assisted recycling amplification for the detection of CAG trinucleotide repeats. Biosens Bioelectron 2019; 142:111537. [DOI: 10.1016/j.bios.2019.111537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/11/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
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8
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Taki M, Rohilla KJ, Barton M, Funneman M, Benzabeh N, Naphade S, Ellerby LM, Gagnon KT, Shamsi MH. Novel probes for label-free detection of neurodegenerative GGGGCC repeats associated with amyotrophic lateral sclerosis. Anal Bioanal Chem 2019; 411:6995-7003. [PMID: 31435686 PMCID: PMC7433021 DOI: 10.1007/s00216-019-02075-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 01/28/2023]
Abstract
DNA repeat expansion sequences cause a myriad of neurological diseases when they expand beyond a critical threshold. Previous electrochemical approaches focused on the detection of trinucleotide repeats (CAG, CGG, and GAA) and relied on labeling of the probe and/or target strands or enzyme-linked assays. However, detection of expanded GC-rich sequences is challenging because they are prone to forming secondary structures such as cruciforms and quadruplexes. Here, we present label-free detection of hexanucleotide GGGGCC repeat sequences, which cause the leading genetic form of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The approach relies on capturing targets by surface-bound oligonucleotide probes with a different number of complementary repeats, which proportionately translates the length of the target strands into charge transfer resistance (RCT) signal measured by electrochemical impedance spectroscopy. The probe carrying three tandem repeats transduces the number of repeats into RCT with a 3× higher calibration sensitivity and detection limit. Chronocoulometric measurements show a decrease in surface density with increasing repeat length, which is opposite of the impedance trend. This implies that the length of the target itself can contribute to amplification of the impedance signal independent of the surface density. Moreover, the probe can distinguish between a control and patient sequences while remaining insensitive to non-specific Huntington's disease (CAG) repeats in the presence of a complementary target. This label-free strategy might be applied to detect the length of other neurodegenerative repeat sequences using short probes with a few complementary repeats. Graphical abstract Short oligomeric probes with multiple complementary repeats detect long neurodegenerative targets with high sensitivity and transduce into higher impedance signal.
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Affiliation(s)
- Motahareh Taki
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Kushal J Rohilla
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Maria Barton
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Madison Funneman
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Najiyah Benzabeh
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Swati Naphade
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Keith T Gagnon
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Mohtashim H Shamsi
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA.
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9
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Plucnara M, Eksin E, Erdem A, Fojta M. Electrochemical Detection of SNP in Human Mitochondrial DNA Using Cyclic Primer Extension with Biotinylated Nucletides and Enzymatic Labeling at Disposable Pencil Graphite Electrodes. ELECTROANAL 2018. [DOI: 10.1002/elan.201800314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Medard Plucnara
- Institute of Biophysics Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135 612 65 Brno Czech Republic
| | - Ece Eksin
- Ege University, Faculty of Pharmacy Analytical Chemistry Department 35100 Bornova, Izmir Turkey
- Ege University, Graduate School of Natural and Applied Science Biotechnology Department 35100 Bornova, Izmir Turkey
| | - Arzum Erdem
- Ege University, Faculty of Pharmacy Analytical Chemistry Department 35100 Bornova, Izmir Turkey
- Ege University, Graduate School of Natural and Applied Science Biotechnology Department 35100 Bornova, Izmir Turkey
| | - Miroslav Fojta
- Institute of Biophysics Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135 612 65 Brno Czech Republic
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10
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Paleček E, Heyrovský M, Dorčák V. J. Heyrovský's Oscillographic Polarography. Roots of Present Chronopotentiometric Analysis of Biomacromolecules. ELECTROANAL 2018. [DOI: 10.1002/elan.201800109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Emil Paleček
- Institute of Biophysics of the CAS; Královopolská 135 612 65 Brno Czech Republic
| | - Michael Heyrovský
- J. Heyrovský Institute of Physical Chemistry of the CAS; Dolejškova 2155/3 182 23 Prague 8 Czech Republic
| | - Vlastimil Dorčák
- Institute of Biophysics of the CAS; Královopolská 135 612 65 Brno Czech Republic
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11
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Liu Y, Li J, Chang G, Zhu R, He H, Zhang X, Wang S. A novel electrochemical method based on screen-printed electrodes and magnetic beads for detection of trinucleotide repeat sequence d(CAG)n. NEW J CHEM 2018. [DOI: 10.1039/c8nj00443a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The combination of SPCE and magnetic beads simplifies the experimental procedure, which is useful for early diagnosis of trinucleotide repeat diseases.
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Affiliation(s)
- Yalan Liu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- Hubei University
- Wuhan
- P. R. China
| | - Jiao Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- Hubei University
- Wuhan
- P. R. China
| | - Gang Chang
- School of Materials Science and Engineering
- Hubei University
- Wuhan
- P. R. China
| | - Ruizhi Zhu
- Key Laboratory of Tobacco Chemistry of Yunnan Province
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
- China
| | - Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- Hubei University
- Wuhan
- P. R. China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- Hubei University
- Wuhan
- P. R. China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- Hubei University
- Wuhan
- P. R. China
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12
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Le BH, Joo HN, Hwang DW, Kim KW, Seo YJ. AuNP-CTG based probing system targeting CAG repeat DNA and RNA sequences. Bioorg Med Chem Lett 2017; 27:3772-3775. [DOI: 10.1016/j.bmcl.2017.06.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/29/2022]
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13
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Nguyen TVT, Le BH, Seo YJ. Highly fluorescence quenching graphene oxide-based oligodeoxynucleotide hairpin systems for probing CNG DNA repeat sequences. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Liu Q, Zhang P, Wang D, Gu W, Wang K. Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Med 2017; 9:65. [PMID: 28720120 PMCID: PMC5514472 DOI: 10.1186/s13073-017-0456-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/30/2017] [Indexed: 12/26/2022] Open
Abstract
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches. We concluded that long-read sequencing coupled with RepeatHMM can estimate repeat counts on microsatellites and can interrogate the “unsequenceable” genomic trinucleotide repeat disorders.
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Affiliation(s)
- Qian Liu
- Institute for Genomic Medicine, Columbia University, New York, NY, 10032, USA
| | - Peng Zhang
- Nextomics Biosciences, Wuhan, Hubei, 430000, China
| | - Depeng Wang
- Nextomics Biosciences, Wuhan, Hubei, 430000, China
| | - Weihong Gu
- China-Japan Friendship Hospital, Beijing, 100029, China
| | - Kai Wang
- Institute for Genomic Medicine, Columbia University, New York, NY, 10032, USA. .,Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA.
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15
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Das P, Reches M. Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex. NANOSCALE 2016; 8:9527-36. [PMID: 26730518 DOI: 10.1039/c5nr07714a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.
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Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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16
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Josypčuk O, Fojta M, Daňhel A, Josypčuk B. Applying Mesoporous Silica SBA-15 in Electrochemical Detection of DNA Hybridization. ELECTROANAL 2016. [DOI: 10.1002/elan.201501137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Oksana Josypčuk
- J. Heyrovský Institute of Physical Chemistry of AS CR; v.v.i. Department of Biomimetic Electrochemistry; Dolejskova 3 Prague Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of AS CR; v.v.i. Kralovopolska 135 612 65 Brno Czech Republic
| | - Aleš Daňhel
- Institute of Biophysics of AS CR; v.v.i. Kralovopolska 135 612 65 Brno Czech Republic
| | - Bohdan Josypčuk
- J. Heyrovský Institute of Physical Chemistry of AS CR; v.v.i. Department of Biomimetic Electrochemistry; Dolejskova 3 Prague Czech Republic
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17
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A new method to evaluate trinucleotide repeats length polymorphism. Talanta 2015; 143:414-418. [DOI: 10.1016/j.talanta.2015.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/03/2015] [Accepted: 05/06/2015] [Indexed: 11/19/2022]
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18
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Zhang GY, Deng SY, Cai WR, Cosnier S, Zhang XJ, Shan D. Magnetic zirconium hexacyanoferrate(II) nanoparticle as tracing tag for electrochemical DNA assay. Anal Chem 2015; 87:9093-100. [PMID: 26259126 DOI: 10.1021/acs.analchem.5b02395] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Novel multifunctional magnetic zirconium hexacyanoferrate nanoparticles (ZrHCF MNPs) were prepared, which consisted of magnetic beads (MBs) inner core and zirconium hexacyanoferrate(II) (ZrHCF) outer shell. As an artificial peroxidase, the ZrHCF MNPs exhibited remarkable electrocatalytic properties in the reduction of H2O2 at 0.2 V vs saturated calomel electrode (SCE). On the basis of the bonding interaction between Zr (IV) of the shell ZrHCF framework and phosphonate groups, the 5'-phosphorylated ssDNA probes with a consecutive stretch of guanines as a spacer could be incorporated in ZrHCF MNPs easily. Thus, DNA-grafted ZrHCF MNPs could be simply obtained by magnetic separation. The prepared nanoelectrocatalyst was further used as signal nanoprobe for the ultrasensitive electrochemical DNA assay. Under optimal conditions, the proposed biosensor presents high sensitivity for detecting target DNA with a linear range from 1.0 fM to 1.0 nM and a low detection limit of 0.43 fM. Moreover, it exhibits good performance with excellent selectivity, high stability, and acceptable fabrication reproducibility.
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Affiliation(s)
- Guang-Yao Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Sheng-Yuan Deng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Wen-Rong Cai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Serge Cosnier
- University of Grenoble Alpes-CNRS , DCM UMR 5250, F-38000 Grenoble, France
| | - Xue-Ji Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Dan Shan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
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19
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20
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Kim KT, Veedu RN, Seo YJ, Kim BH. Quencher-free molecular beacons as probes for oligonucleotides containing CAG repeat sequences. Chem Commun (Camb) 2014; 50:1561-3. [PMID: 24382518 DOI: 10.1039/c3cc48853e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have identified quencher-free molecular beacons that allow the sensitive probing of CAG repeat oligonucleotides, including mRNA fragments of trinucleotide repeat diseases, with significant increases in fluorescence intensity mediated by disruption of the stacking of their (Py)U units.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
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21
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He H, Peng X, Huang M, Chang G, Zhang X, Wang S. An electrochemical impedance sensor based on a small molecule modified Au electrode for the recognition of a trinucleotide repeat. Analyst 2014; 139:5482-7. [DOI: 10.1039/c4an00853g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A small molecule modified sensor was developed for the detection of XGG trinucleotide repeats (X = C, T) by electrochemical impedance spectroscopy.
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Affiliation(s)
- Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Hubei University
- Wuhan, PR China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
| | - Xiaoqian Peng
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Wuhan, P. R. China
| | - Min Huang
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Wuhan, P. R. China
| | - Gang Chang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Hubei University
- Wuhan, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Hubei University
- Wuhan, PR China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials
- Hubei University
- Wuhan, PR China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
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22
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Smerkova K, Dostalova S, Vaculovicova M, Kynicky J, Trnkova L, Kralik M, Adam V, Hubalek J, Provaznik I, Kizek R. Investigation of interaction between magnetic silica particles and lambda phage DNA fragment. J Pharm Biomed Anal 2013; 86:65-72. [DOI: 10.1016/j.jpba.2013.07.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/29/2013] [Indexed: 11/25/2022]
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23
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Liu P, Yang X, Sun S, Wang Q, Wang K, Huang J, Liu J, He L. Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification. Anal Chem 2013; 85:7689-95. [PMID: 23895103 DOI: 10.1021/ac4001157] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A novel, high sensitive, and specific DNA assay based on gold nanoparticle (AuNP) colorimetric detection and hybridization chain reaction (HCR) amplification has been demonstrated in this article. Two hairpin auxiliary probes were designed with single-stranded DNA (ssDNA) sticky ends which stabilize AuNPs and effectively prevent them from salt-induced aggregation. The target DNA hybridized with the hairpin auxiliary probes and triggered the formation of extended double-stranded DNA (dsDNA) polymers through HCR. As a result, the formed dsDNA polymers provide less stabilization without ssDNA sticky ends, and AuNPs undergo aggregation when salt concentration is increased. Subsequently, a pale purple-to-blue color variation is observed in the colloid solution. The system is simple in design and convenient in operation. The novel strategy eliminates the need for enzymatic reactions, separation processes, chemical modifications, and sophisticated instrumentation. The detection and discrimination process can be seen with the naked eye. The detection limit of this method is lower than or at least comparable to previous AuNP-based methods. Importantly, the protocol offers high selectivity for the determination between perfectly matched target oligonucleotides and targets with single base-pair mismatches.
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Affiliation(s)
- Pei Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
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24
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Balintová J, Plucnara M, Vidláková P, Pohl R, Havran L, Fojta M, Hocek M. Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases. Chemistry 2013; 19:12720-31. [DOI: 10.1002/chem.201301868] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/18/2013] [Indexed: 12/24/2022]
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25
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He H, Xia J, Peng X, Chang G, Zhang X, Wang Y, Nakatani K, Lou Z, Wang S. Facile electrochemical biosensor based on a new bifunctional probe for label-free detection of CGG trinucleotide repeat. Biosens Bioelectron 2013; 49:282-9. [PMID: 23774165 DOI: 10.1016/j.bios.2013.05.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 11/19/2022]
Abstract
We have developed a simple and label-free electrochemical assay to detect CGG trinucleotide repeat. For this purpose, a new bifunctional probe (FecNCD2) was developed, in which a recognition part (naphthyridine carbamate dimmer, NCD) was connected with an electro-active part (ferrocenyl group) using a chain of -CO-NH-CH2-CH2-. The results of circular dichroismic measurements indicated that FecNCD2 exhibited a superior performance for selective binding to CGG trinucleotide repeats compared to a previous bifunctional electrochemical probe connected with shorter linker -CH2- (FecNCD1). Then, the electrochemical properties of FecNCD2 were evaluated and were found to show a good redox response due to the ferrocene moiety. Owing to the high performances of FecNCD2, the label-free electrochemical biosensor for CGG repeats was constructed by immobilizing them onto gold disk electrode and by using FecNCD2 as an electrochemical probe in solution. Further CGG repeats in solution were confirmed to be detectable using the CGG modified biosensor in competitive experiments, i.e., by treating it in test solutions containing FecNCD2 and d(CGG)10 or others. No interference of ct-DNA on the CGG detection was also confirmed with this approach. The strategy should have significant potential for the development of versatile and low-cost biosensor for early diagnosis and treatment of neurodegenerative diseases associated with trinucleotide repeats.
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Affiliation(s)
- Hanping He
- College of Chemistry and Chemical Engineer, Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
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26
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Jacobsen M, Flechsig GU. Hybridization Detection of Osmium Tetroxide Bipyridine-Labeled DNA and RNA on Heated Gold Wire Electrodes. ELECTROANAL 2012. [DOI: 10.1002/elan.201200460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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28
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Shimron S, Wang F, Orbach R, Willner I. Amplified detection of DNA through the enzyme-free autonomous assembly of hemin/G-quadruplex DNAzyme nanowires. Anal Chem 2011; 84:1042-8. [PMID: 22242838 DOI: 10.1021/ac202643y] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An enzyme-free amplified detection platform is described using the horseradish peroxidase (HRP)-mimicking DNAzyme as an amplifying label. Two hairpin structures that include three-fourths and one-fourth of the HRP-mimicking DNAzyme in caged, inactive configurations are used as functional elements for the amplified detection of the target DNA. In the presence of the analyte DNA, one of the hairpins is opened, and this triggers the autonomous cross-opening of the two hairpins using the strand displacement principle. This leads to the formation of nanowires consisting of the HRP-mimicking DNAzyme. The resulting DNA nanowires act as catalytic labels for the colorimetric or chemiluminescent readout of the sensing processes (the term "enzyme-free" refers to a protein-free catalyst). The analytical platform allows the sensing of the analyte DNA with a detection limit corresponding to 1 × 10(-13) M. The optimized system acts as a versatile sensing platform, and by coaddition of a "helper" hairpin structure any DNA sequence may be analyzed by the system. This is exemplified with the detection of the BRCA1 oncogene with a detection limit of 1 × 10(-13) M.
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Affiliation(s)
- Simcha Shimron
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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29
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Wang F, Elbaz J, Orbach R, Magen N, Willner I. Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. J Am Chem Soc 2011; 133:17149-51. [PMID: 21954996 DOI: 10.1021/ja2076789] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic study of the amplified optical detection of DNA by Mg(2+)-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10(-9) M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg(2+)-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10(-14) M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene.
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Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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30
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García T, Revenga-Parra M, Sobrino B, Carracedo A, Alonso C, Lorenzo E, Pariente F. Electrochemical DNA base pairs quantification and endonuclease cleavage detection. Biosens Bioelectron 2011; 27:40-5. [DOI: 10.1016/j.bios.2011.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/25/2011] [Accepted: 06/07/2011] [Indexed: 10/18/2022]
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31
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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32
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Huska D, Adam V, Babula P, Trnkova L, Hubalek J, Zehnalek J, Havel L, Kizek R. Microfluidic robotic device coupled with electrochemical sensor field for handling of paramagnetic micro-particles as a tool for determination of plant mRNA. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0545-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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33
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34
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Pivoňková H, Horáková P, Fojtová M, Fojta M. Direct Voltammetric Analysis of DNA Modified with Enzymatically Incorporated 7-Deazapurines. Anal Chem 2010; 82:6807-13. [DOI: 10.1021/ac100757v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Pivoňková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Petra Horáková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miloslava Fojtová
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
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35
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Yosypchuk B, Fojta M, Barek J. Preparation and Properties of Mercury Film Electrodes on Solid Amalgam Surface. ELECTROANAL 2010. [DOI: 10.1002/elan.201000032] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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36
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Surkus AE, Flechsig GU. Electrochemical Detection of DNA Melting Curves by Means of Heated Biosensors. ELECTROANAL 2009. [DOI: 10.1002/elan.200804539] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Paleček E, Trefulka M, Fojta M. End-labeling of peptide nucleic acid with osmium complex. Voltammetry at carbon and mercury electrodes. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2008.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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38
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Li X, Zhan Z, Zhang S, Chen H. Enzyme enhanced quantitative determination of multiple DNA targets based on capillary electrophoresis. J Chromatogr A 2009; 1216:2567-73. [PMID: 19171352 DOI: 10.1016/j.chroma.2009.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 01/05/2009] [Indexed: 11/15/2022]
Abstract
In the current paper, enzyme enhanced simultaneous quantitative determination of multiple DNA targets based on capillary electrophoresis (CE) was described. We used three biotin-modified DNA probes, which reacted with avidin-conjugated horseradish peroxidase (avidin-HRP) conjugate to obtain the HRP labeled probes, to hybridize with three corresponding targets. The resulting mixture containing double-strand DNA (dsDNA)-HRP, excess single-strand DNA (ssDNA)-HRP and remaining avidin-HRP was separated by capillary electrophoresis, and then the system of HRP catalyzing H(2)O(2)/o-aminophenol (OAP) reaction was adopted. The catalytic product was detected with electrochemical detection. With this protocol, the limits of quantification for the hybridization assay of 21-, 39- and 80-mer DNA fragments were of 1.2 x 10(-11), 2.4 x 10(-11) and 3.0 x 10(-11)M, respectively. The multiplex assay also provided good specificity without any cross-reaction.
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Affiliation(s)
- Xuemei Li
- Department of Chemistry, Nanjing University, Nanjing, China
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39
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Duwensee H, Jacobsen M, Flechsig GU. Electrochemical competitive hybridization assay for DNA detection using osmium tetroxide-labelled signalling strands. Analyst 2009; 134:899-903. [DOI: 10.1039/b819283a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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40
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Lucarelli F, Capponcelli S, Marrazza G, Sangiorgi L, Mascini M. Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms. Analyst 2008; 134:52-9. [PMID: 19082174 DOI: 10.1039/b806514d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.
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Affiliation(s)
- Fausto Lucarelli
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto F.no, Florence, Italy
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41
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Cathodic adsorptive stripping voltammetric detection of tRNA by labelling with osmium tetroxide. Electrochem commun 2008. [DOI: 10.1016/j.elecom.2008.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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42
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Fojta M, Billová S, Havran L, Pivoňková H, Černocká H, Horáková P, Paleček E. Osmium Tetroxide, 2,2′-Bipyridine: Electroactive Marker for Probing Accessibility of Tryptophan Residues in Proteins. Anal Chem 2008; 80:4598-605. [DOI: 10.1021/ac800527u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sabina Billová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Luděk Havran
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Pivoňková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Černocká
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Horáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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43
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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44
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Hason S, Pivonkova H, Vetterl V, Fojta M. Label-free sequence-specific DNA sensing using copper-enhanced anodic stripping of purine bases at boron-doped diamond electrodes. Anal Chem 2008; 80:2391-9. [PMID: 18321078 DOI: 10.1021/ac7019305] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stripping voltammetric determination of purine bases in the presence of copper ions at mercury, amalgam, or carbon-based electrodes has recently been utilized in analysis of DNA or synthetic oligodeoxynucleotides (ODNs). Here we report on copper-enhanced label-free anodic stripping detection of guanine and adenine bases in acid-hydrolyzed DNA at anodically oxidized boron-doped diamond electrode (AO-BDDE). The AO-BDDE was successfully applied in a three-electrode microcell in which an approximately 50 microL drop of the analyte solution can be efficiently stirred during the accumulation step by streaming of an inert gas. Accelerated mass transport due to the solution motion in the presence of copper resulted in enhancement of the guanine oxidation signal by about 2 orders of magnitude (compared to accumulation of the analyte from still solution not containing copper), allowing an easy detection of approximately 25 fmol of the ODNs. The proposed technique is shown to be suitable for a determination of purine (particularly guanine) content in DNA samples. Applications of the technique in magnetic bead-based DNA assays (such as hybridization with DNA sequences exhibiting asymmetrical distribution of purine/pyrimidine nucleotides between the complementary strands or monitoring of amplification of specific DNA fragments in a duplex polymerase chain reaction) are demonstrated.
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Affiliation(s)
- Stanislav Hason
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., KrAlovopolskA 135, CZ-612 65 Brno, Czech Republic
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Brázdilová P, Vrábel M, Pohl R, Pivonková H, Havran L, Hocek M, Fojta M. Ferrocenylethynyl derivatives of nucleoside triphosphates: synthesis, incorporation, electrochemistry, and bioanalytical applications. Chemistry 2008; 13:9527-33. [PMID: 17896337 DOI: 10.1002/chem.200701249] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modified dATP (2'-deoxyadenosine-5'-triphosphate) and dUTP (2'-deoxyuridine-5'-triphosphate) bearing ferrocene (Fc) labels linked via a conjugate acetylene spacer were prepared by single-step aqueous-phase cross-coupling reactions of 7-iodo-7-deaza-dATP or 5-iodo-dUTP with ethynylferrocene. The Fc-labeled dNTPs were good substrates for DNA polymerases and were efficiently incorporated to DNA by primer extension (PEX). Electrochemical analysis of the 2'-deoxyribonucleoside triphosphates (dNTPs) and PEX products revealed significant differences in redox potentials of the Fc label bound either to U or to 7-deazaA and between isolated dNTPs and conjugates incorporated to DNA. Prospective bioanalytical applications are outlined.
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Affiliation(s)
- Petra Brázdilová
- Institute of Biophysics, v.v.i. Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
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Ding C, Zhao F, Zhang M, Zhang S. Hybridization biosensor using 2,9-dimethyl-1,10-phenantroline cobalt as electrochemical indicator for detection of hepatitis B virus DNA. Bioelectrochemistry 2008; 72:28-33. [DOI: 10.1016/j.bioelechem.2007.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 01/16/2023]
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Enzyme-Linked Electrochemical Detection of PCR-Amplified Nucleotide Sequences Using Disposable Screen-Printed Sensors. Applications in Gene Expression Monitoring. SENSORS 2008; 8:193-210. [PMID: 27879703 PMCID: PMC3681127 DOI: 10.3390/s8010193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 01/07/2008] [Indexed: 11/17/2022]
Abstract
Electrochemical enzyme-linked techniques for sequence-specific DNA sensing are presented. These techniques are based on attachment of streptavidin-alkaline phosphatase conjugate to biotin tags tethered to DNA immobilized at the surface of disposable screen-printed carbon electrodes (SPCE), followed by production and electrochemical determination of an electroactive indicator, 1-naphthol. Via hybridization of SPCE surface-confined target DNAs with end-biotinylated probes, highly specific discrimination between complementary and non-complementary nucleotide sequences was achieved. The enzyme-linked DNA hybridization assay has been successfully applied in analysis of PCR-amplified real genomic DNA sequences, as well as in monitoring of plant tissue-specific gene expression. In addition, we present an alternative approach involving sequence-specific incorporation of biotin-labeled nucleotides into DNA by primer extension. Introduction of multiple biotin tags per probe primer resulted in considerable enhancement of the signal intensity and improvement of the specificity of detection.
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Peter J, Reske T, Flechsig GU. Comparison of DNA Hybridization at Rotating and Heated Gold Disk Electrodes. ELECTROANAL 2007. [DOI: 10.1002/elan.200703881] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Flechsig GU, Reske T. Electrochemical detection of DNA hybridization by means of osmium tetroxide complexes and protective oligonucleotides. Anal Chem 2007; 79:2125-30. [PMID: 17326604 DOI: 10.1021/ac062075c] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have utilized protective oligonucleotides to modify DNA fragments with osmium tetroxide complexes without compromising their ability to hybridize with immobilized thiol-linked probe-SAMs on gold electrodes. Due to reversible voltammetric signals of Os(VI/IV), this method allowed sensitive electrochemical hybridization detection of short (25 bases) and long (120 bases) thymine-containing DNA targets. The detection limit was 3.2 nM for the long target. We found an optimum 40 degrees C hybridization temperature for the short target. No interference by noncomplementary DNA was observed. At least 10 repetitive hybridization experiments at the same probe-SAM were possible with thermal denaturation in between. Such use of protective strands could be useful also for other types of DNA recognition and even for other DNA-modifying agents. Moreover, it is possible to produce electrochemically active oligonucleotides (targets and reporter probes) in ones own laboratory in a simple way.
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Affiliation(s)
- Gerd-Uwe Flechsig
- Department of Chemistry, University of Rostock, Dr.-Lorenz-Weg 1, D-18059 Rostock, Germany.
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Trefulka M, Ferreyra N, Ostatná V, Fojta M, Rivas G, Paleček E. Voltammetry of Osmium End-Labeled Oligodeoxynucleotides at Carbon, Mercury, and Gold Electrodes. ELECTROANAL 2007. [DOI: 10.1002/elan.200703849] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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