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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies for the preparation of non-amplified and amplified genomic dengue gene samples for electrochemical DNA biosensing applications. RSC Adv 2021; 12:1-10. [PMID: 35424522 PMCID: PMC8978653 DOI: 10.1039/d1ra06753b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
The application of electrochemical DNA biosensors in real genomic sample detection is challenging due to the existence of complex structures and low genomic concentrations, resulting in inconsistent and low current signals. This work highlights strategies for the treatment of non-amplified and amplified genomic dengue virus gene samples based on real samples before they can be used directly in our DNA electrochemical sensing system, using methylene blue (MB) as a redox indicator. The main steps in this study for preparing non-amplified cDNA were cDNA conversion, heat denaturation, and sonication. To prepare amplified cDNA dengue virus genomic samples using an RT-PCR approach, we optimized a few parameters, such as the annealing temperature, sonication time, and reverse to forward (R/F) primer concentration ratio. We discovered that the generated methylene blue (MB) signals during the electrochemical sensing of non-amplified and amplified samples differ due to the different MB binding affinities based on the sequence length and base composition. The findings show that our developed electrochemical DNA biosensor successfully discriminates MB current signals in the presence and absence of the target genomic dengue virus, indicating that both samples were successfully treated. This work also provides interesting information about the critical factors in the preparation of genomic gene samples for developing miniaturized PCR-based electrochemical sensing applications in the future. We also discuss the limitations and provide suggestions related to using redox-indicator-based electrochemical biosensors to detect real genomic nucleic acid genes.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Cordeiro TAR, de Resende MAC, Moraes SCDS, Franco DL, Pereira AC, Ferreira LF. Electrochemical biosensors for neglected tropical diseases: A review. Talanta 2021; 234:122617. [PMID: 34364426 DOI: 10.1016/j.talanta.2021.122617] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 12/26/2022]
Abstract
A group of infectious and parasitic diseases with prevalence in tropical and subtropical regions of the planet, especially in places with difficult access, internal conflicts, poverty, and low visibility from the government and health agencies are classified as neglected tropical diseases. While some well-intentioned isolated groups are making the difference on a global scale, the number of new cases and deaths is still alarming. The development and employment of low-cost, miniaturized, and easy-to-use devices as biosensors could be the key to fast diagnosis in such areas leading to a better treatment to further eradication of such diseases. Therefore, this review contains useful information regarding the development of such devices in the past ten years (2010-2020). Guided by the updated list from the World Health Organization, the work evaluated the new trends in the biosensor field applied to the early detection of neglected tropical diseases, the efficiencies of the devices compared to the traditional techniques, and the applicability on-site for local distribution. So, we focus on Malaria, Chagas, Leishmaniasis, Dengue, Zika, Chikungunya, Schistosomiasis, Leprosy, Human African trypanosomiasis (sleeping sickness), Lymphatic filariasis, and Rabies. Few papers were found concerning such diseases and there is no available commercial device in the market. The works contain information regarding the development of point-of-care devices, but there are only at proof of concepts stage so far. Details of electrode modification and construction of electrochemical biosensors were summarized in Tables. The demand for the eradication of neglected tropical diseases is increasing. The use of biosensors is pivotal for the cause, but appliable devices are scarce. The information present in this review can be useful for further development of biosensors in the hope of helping the world combat these deadly diseases.
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Affiliation(s)
- Taís Aparecida Reis Cordeiro
- Institute of Science and Technology, Laboratory of Electrochemistry and Applied Nanotechnology, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Brazil
| | | | - Simone Cristina Dos Santos Moraes
- Group of Electrochemistry Applied to Polymers and Sensors - Multidisciplinary Group of Research, Science and Technology - Laboratory of Electroanalytic Applied to Biotechnology and Food Engineering - Institute of Chemistry, Federal University of Uberlândia, Patos de Minas, Brazil
| | - Diego Leoni Franco
- Group of Electrochemistry Applied to Polymers and Sensors - Multidisciplinary Group of Research, Science and Technology - Laboratory of Electroanalytic Applied to Biotechnology and Food Engineering - Institute of Chemistry, Federal University of Uberlândia, Patos de Minas, Brazil.
| | - Arnaldo César Pereira
- Department of Natural Sciences, Federal University of São João Del-Rei, São João Del-Rei, Brazil.
| | - Lucas Franco Ferreira
- Institute of Science and Technology, Laboratory of Electrochemistry and Applied Nanotechnology, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Brazil.
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Yoo E, Choe D, Shin J, Cho S, Cho BK. Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage. Comput Struct Biotechnol J 2021; 19:2468-2476. [PMID: 34025937 PMCID: PMC8113751 DOI: 10.1016/j.csbj.2021.04.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
The market for using and storing digital data is growing, with DNA synthesis emerging as an efficient way to store massive amounts of data. Storing information in DNA mainly consists of two steps: data writing and reading. The writing step requires encoding data in DNA, building one nucleotide at a time as a form of single-stranded DNA (ssDNA). Once the data needs to be read, the target DNA is selectively retrieved and sequenced, which will also be in the form of an ssDNA. Recently, enzyme-based DNA synthesis is emerging as a new method to be a breakthrough on behalf of decades-old chemical synthesis. A few enzymatic methods have been presented for data memory, including the use of terminal deoxynucleotidyl transferase. Besides, enzyme-based amplification or denaturation of the target strand into ssDNA provides selective access to the desired dataset. In this review, we summarize diverse enzymatic methods for either synthesizing ssDNA or retrieving the data-containing DNA.
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Affiliation(s)
- Eojin Yoo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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4
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Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:molecules25153386. [PMID: 32722650 PMCID: PMC7435391 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
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Nehdi A, Samman N, Aguilar-Sánchez V, Farah A, Yurdusev E, Boudjelal M, Perreault J. Novel Strategies to Optimize the Amplification of Single-Stranded DNA. Front Bioeng Biotechnol 2020; 8:401. [PMID: 32432100 PMCID: PMC7214742 DOI: 10.3389/fbioe.2020.00401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/08/2020] [Indexed: 11/13/2022] Open
Abstract
The generation of single stranded DNA plays a key role in in vitro selection of DNA aptamers and in other molecular techniques such as DNA sequencing and microarrays. Here we describe three novel methodologies for ssDNA production and amplification. Furthermore, we describe some previously unnoticed aspects of random DNA amplification. Our results showed that in asymmetric PCR the addition of a high melting temperature reverse primer blocked at its 3' end by a dideoxy nucleotide drives the reaction further toward ssDNA production. We demonstrated also that incorporation of internally inverted nucleotide/(s) in one primer can be used as a new method of polymerization termination. Using such modified primer, the PCR product includes two complementary DNA strands having different lengths and separable from one another by denaturing gel electrophoresis. In addition, we showed that nicking enzymes can be used to cleave the undesirable strand allowing the isolation of the target ssDNA strand.
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Affiliation(s)
- Atef Nehdi
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,Department of Life Sciences, Faculty of Sciences of Gabes, University of Gabes, Gabes, Tunisia.,Medical Research Core Facility and Platforms, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Nosaibah Samman
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,Medical Research Core Facility and Platforms, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Azer Farah
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Emre Yurdusev
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Mohamed Boudjelal
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,Medical Research Core Facility and Platforms, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Heiat M, Ranjbar R, Latifi AM, Rasaee MJ, Farnoosh G. Essential strategies to optimize asymmetric PCR conditions as a reliable method to generate large amount of ssDNA aptamers. Biotechnol Appl Biochem 2017; 64:541-548. [PMID: 27222205 DOI: 10.1002/bab.1507] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/20/2016] [Indexed: 12/19/2022]
Abstract
Asymmetric PCR, a simple method to generate single-stranded DNA (ssDNA) aptamers in systematic evaluation of ligand by exponential enrichments rounds, is coupled with limitations. We investigated the essential strategies for optimization of conditions to perform a high-quality asymmetric PCR. Final concentrations of primers and template, the number of PCR cycles, and annealing temperature were selected as optimizing variables. The qualities of visualized PCR products were analyzed by ImageJ software. The highest proportion of interested DNA than unwanted products was considered as optimum conditions. Results revealed that the best values for primers ratio, final template concentration, annealing temperature, and PCR cycles were, respectively, 30:1, 1 ng/μL, 55 °C, and 20 cycles for the first and 50:1, 2 ng/μL, 59 °C, and 20 cycles for other rounds. No significant difference was found between optimized asymmetric PCR results in the rounds of two to eight (P > 0.05). The ssDNA quality in round 10 was significantly better than other rounds (P < 0.05). Generally, the ssDNA product with less dimers, double-stranded DNA (dsDNA), and smear are preferable. The dsDNA contamination is the worst, because it can act as antidote and inhibits aptameric performance. Therefore, to choose the best conditions, the lower amount of dsDNA is more important than other unwanted products.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Expanding the MDx toolbox for filarial diagnosis and surveillance. Trends Parasitol 2015; 31:391-400. [DOI: 10.1016/j.pt.2015.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022]
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Tabarzad M, Kazemi B, Vahidi H, Aboofazeli R, Shahhosseini S, Nafissi-Varcheh N. Challenges to design and develop of DNA aptamers for protein targets. I. Optimization of asymmetric PCR for generation of a single stranded DNA library. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2014; 13:133-41. [PMID: 24711839 PMCID: PMC3977063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Aptamers, or single stranded oligonucleotides, are produced by systematic evolution of ligands by exponential enrichment, abbreviated as SELEX. In the amplification and regeneration step of SELEX technique, dsDNA is conversed to ssDNA. Asymmetric PCR is one of the methods used for the generation of ssDNA. The purpose of this study was to design a random DNA library for selection of aptamers with high affinity for protein targets and develop an efficient asymmetric PCR amplification. Thus, the influence of factors including annealing temperature, number of amplification cycles, primer ratio, Mg(2+) concentration and the presence of a PCR enhancer on the amplification of the desired product were evaluated. Results obtained by agarose gel electrophoresis showed that the annealing temperature of 64 °C, Mg(2+) concentration of 0.25 mM, reverse to forward primer ratio of 15:1, amplification cycle of 25 and the presence L-ectoin as a PCR enhancer with the concentration of 0.4 M were the optimal conditions. Our results supported that the yield of this type of ssDNA production is sufficient for combinatorial screening of aptamers.
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Affiliation(s)
- Maryam Tabarzad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Student᾽s Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. ,Biotechnology Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Aboofazeli
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soraya Shahhosseini
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran .
| | - Nastaran Nafissi-Varcheh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Corresponding author:
E-mail:
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