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Meng J, Guo Q, Zhai X, Yang S, Wang S, Wang P, Ji D. A phosphamide nucleotide analog: a substrate for polymerase synthesis of DNA. Org Biomol Chem 2024; 22:2963-2967. [PMID: 38529657 DOI: 10.1039/d4ob00089g] [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: 03/27/2024]
Abstract
A type of modified nucleotide, deoxynucleotide γ-amidotriphosphates (dNTPγNH2s), exhibited around five times higher stability than dNTPs. These phosphamide nucleotides can be utilized by several DNA polymerases, and the amplification of a 10 kb DNA fragment through the polymerase chain reaction (PCR) can be accomplished even under conditions of high temperature, extended storage, or repeated freeze-thaw cycles. However, the control PCR with standard dNTPs was unsuccessful. These results indicate that dNTPγNH2s have the potential to substitute dNTPs in PCR.
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Affiliation(s)
- Jiong Meng
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Qiaqia Guo
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Xiaona Zhai
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Song Yang
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Shuai Wang
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Pengcheng Wang
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
| | - Debin Ji
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China.
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2
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Paasch A, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method. Sci Rep 2024; 14:7988. [PMID: 38580715 PMCID: PMC10997766 DOI: 10.1038/s41598-024-58733-0] [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: 08/15/2023] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Peter L Chang
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Amber Paasch
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA.
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3
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Panicker LR, Kummari S, Keerthanaa MR, Rao Bommi J, Koteshwara Reddy K, Yugender Goud K. Trends and challenges in electroanalytical biosensing methodologies for infectious viral diseases. Bioelectrochemistry 2024; 156:108594. [PMID: 37984310 DOI: 10.1016/j.bioelechem.2023.108594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Viral pandemic diseases have disruptive global consequences leading to millions of deaths and a severe impact on the global economy. Inadequate preventative protocols have led to an overwhelming demand for intensive care leading to uncontrollable burdens and even breakdown of healthcare sectors across many countries. The rapid detection of viral disease helps in the understanding of the relevant intricacies, helping to tackle infection with improved guidelines. Portable biosensor devices offer promising solutions by facilitating on-site detection of viral pathogens. This review summarizes the latest innovative strategies reported using electroanalytical methods for the screening of viral antigens. The structural components of viruses and their categories are presented followed by the various recognition elements and transduction techniques involved in biosensors. Core sections focus on biosensors reported for viral genomic detection(DNA and RNA) and antigenic capsid protein. Strategies for addressing the challenges of electroanalytical biosensing of viral components are also presented. The advantages, and disadvantages of biorecognition elements and nanozymes for the detection of viral disease are highlighted. Such technical insights will help researchers working in chemistry, and biochemistry as well as clinicians working in medical diagnostics.
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Affiliation(s)
- Lakshmi R Panicker
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | - Shekher Kummari
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | - M R Keerthanaa
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | | | - K Koteshwara Reddy
- School of Material Science and Engineering, Purdue University, West Lafayette, IN, 47907, USA.
| | - K Yugender Goud
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India.
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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Verma C, Dubey S, Bose R, Alfantazi A, Ebenso EE, Rhee KY. Zwitterions and betaines as highly soluble materials for sustainable corrosion protection: Interfacial chemistry and bonding with metal surfaces. Adv Colloid Interface Sci 2024; 324:103091. [PMID: 38281394 DOI: 10.1016/j.cis.2024.103091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/04/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
The primary requirements for interfacial adsorption and corrosion inhibition are solubility and the existence of polar functional groups, particularly charges. Traditional organic inhibitors have a solubility issue due to the hydrophobic moieties they incorporate. Most documented organic inhibitors have aromatic rings, hydrocarbon chains, and a few functional groups. The excellent solubility and high efficacy of zwitterions and betaines make them the perfect replacements for insoluble corrosion inhibitors. Zwitterions and betaines are more easily soluble because of interactions between their positive and negative charges (-COO-, -PO3-, -NH3, -NHR2, -NH2R, -SO3- etc.) and the polar solvents. The positive and negative charges also aid these molecules' physical and chemical adsorption at the metal-electrolyte interfaces. They develop a corrosion-inhibiting layer through their adsorption. After becoming adsorbed at the metal-electrolyte interface, they act as mixed-type inhibitors, slowing both cathodic and anodic processes. They usually adsorb according to the Langmuir adsorption isotherm. In this article, the corrosion inhibition potential of zwitterions and betaines in the aqueous phase, as well as their mode of action, are reviewed. This article details the advantages and disadvantages of utilizing zwitterions and betaines for sustainable corrosion protection.
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Affiliation(s)
- Chandrabhan Verma
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
| | - Shikha Dubey
- Department of Chemistry, School of Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar 246174, Garhwal, India
| | - Ranjith Bose
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Akram Alfantazi
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Eno E Ebenso
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1710, South Africa
| | - Kyong Yop Rhee
- Department of Mechanical Engineering, College of Engineering, Kyung Hee University, Yongin 445-701, South Korea.
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6
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Semashko TA, Fisunov GY, Tsoy EA, Kharrasov DR, Chudinov IK, Evsyutina DV, Shevelev GY, Govorun VM. Modern Approaches to de novo Synthesis of Extended DNA Fragments: Assembly of a Wide Repertoire of Sequences. Acta Naturae 2024; 16:77-85. [PMID: 38738632 PMCID: PMC11062099 DOI: 10.32607/actanaturae.27362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/28/2024] [Indexed: 05/14/2024] Open
Abstract
The standardization of DNA fragment assembly methods for many tasks of synthetic biology is crucial. This is necessary for synthesizing a wider repertoire of sequences, as well as for further automation and miniaturization of such reactions. In this work, we proposed conditions for the assembly of DNA fragments from chemically synthesized oligonucleotides and we identified the errors occurring in the sequence under these conditions. Additionally, we proposed conditions for further combining synthetic fragments into larger DNA fragments. We showed that the optimized conditions are suitable for the assembly of a wide range of sequences.
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Affiliation(s)
- T. A. Semashko
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435 Russian Federation
| | - G. Y. Fisunov
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435 Russian Federation
| | - E. A. Tsoy
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435 Russian Federation
| | - D. R. Kharrasov
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
| | - I. K. Chudinov
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
| | - D. V. Evsyutina
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435 Russian Federation
| | - G. Y. Shevelev
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090 Russian Federation
| | - V. M. Govorun
- Research Institute for Systems Biology and Medicine, Moscow, 117246 Russian Federation
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7
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Devika PP, Alex S, Soni KB, Sindura KP, Ayisha R, Manju RV. Nano-PCR for the early detection of tomato leaf curl virus. 3 Biotech 2024; 14:5. [PMID: 38074290 PMCID: PMC10700262 DOI: 10.1007/s13205-023-03842-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 11/02/2023] [Indexed: 01/19/2024] Open
Abstract
Nano-PCR is a potential tool for the early detection of plant viruses. In the current study, different concentrations of silver nanoparticles (20 nm) and magnesium oxide nanoparticles (50 nm) were included in the PCR mixture to improve the sensitivity of PCR for the detection of tomato leaf curl virus. The inclusion of nanoparticles in single or combination in PCR mixture has resulted in improvement of PCR sensitivity. Four-fold improvement was exhibited by the inclusion of 3 ng/µL silver nanoparticles, whereas the combination of silver and magnesium oxide nanoparticles (3 ng/µL and 200 ng/µL, respectively), resulted in a 4.5-fold improvement. The inclusion of 200 ng/µL of magnesium oxide nanoparticles in the PCR mixture exhibited a 7.6-fold increase in PCR sensitivity. Replacement of magnesium chloride with a combination of silver and magnesium oxide nanoparticles (3 ng/µL and 275 ng/µL, respectively) resulted in a 12-fold increase. A 13-fold improvement in PCR sensitivity was observed by the replacement of magnesium chloride in PCR buffer with 275 ng/µL of magnesium oxide nanoparticles. This could also produce detectable amplicon in PCR with a minimum of 25 cycles, resulting in a 26.5% reduction in the duration of PCR. This is the first report on the use of magnesium oxide nanoparticles in PCR for the early detection and better management of tomato leaf curl virus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03842-2.
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Affiliation(s)
- P. P. Devika
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Swapna Alex
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. B. Soni
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. P. Sindura
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R. Ayisha
- Department of Plant Pathology, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur, Kerala 680656 India
| | - R. V. Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
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Wang X, Yang S, Lu J, Xie G, Wu D. Screening and application of purine degrading Limosilactobacillus fermentum LF-1 from Huangjiu fermentation broth. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7921-7931. [PMID: 37490358 DOI: 10.1002/jsfa.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND As the important building blocks of nucleic acids, purines are alkaloids and responsible for hyperuricemia and gout. The purine content in Huangjiu is higher, and mainly exists in the form of free bases, which is easier to be absorbed by human body. However, the currently available reports on purine in Huangjiu mainly focus on detection methods and content survey. No studies on the regulation of the purine content in Huangjiu have been reported. RESULTS Eighty-four strains, with the degradation capacity of purine, were screened from the fermentation broth of Huangjiu. In detail, the isolated lactic acid bacteria (LAB) strain 75 # showed the strongest degradation ability of guanosine, inosine and four purines, which reduce their levels by 83.4% (guanosine), 97.4% (inosine), 95.1% (adenine), 95.0% (guanine), 94.9% (hypoxanthine) and 65.9% (xanthine), respectively. Subsequently, the LAB strain 75# was identified to be Limosilactobacillus fermentum by 16S rRNA gene sequencing, which was named as Limosilactobacillus fermentum LF-1 and applied to the fermentation of Huangjiu in the laboratory. Compared with the fermentation broth of Huangjiu without adding L. fermentum LF-1, the content of purine compounds in the fermentation broth inoculated with L. fermentum LF-1 was reduced by 64.7%. In addition, the fermented Huangjiu had richer flavor compounds, and the physicochemical indices were in accordance with the national standard of Chinese Huangjiu. CONCLUSION The screened strain L. fermentum LF-1 may be a promising probiotic for the development of a novel that can efficiently degrade purine in Huangjiu. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xianglin Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shaojie Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guangfa Xie
- Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, China
- Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
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Elias M, Guan X, Hudson D, Bose R, Kwak J, Petrounia I, Touah K, Mansour S, Yue P, Errasti G, Delacroix T, Ghosh A, Chakrabarti R. Evolution of Organic Solvent-Resistant DNA Polymerases. ACS Synth Biol 2023; 12:3170-3188. [PMID: 37611245 DOI: 10.1021/acssynbio.2c00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The introduction of thermostable polymerases revolutionized the polymerase chain reaction (PCR) and biotechnology. However, many GC-rich genes cannot be PCR-amplified with high efficiency in water, irrespective of temperature. Although polar organic cosolvents can enhance nucleic acid polymerization and amplification by destabilizing duplex DNA and secondary structures, nature has not selected for the evolution of solvent-tolerant polymerase enzymes. Here, we used ultrahigh-throughput droplet-based selection and deep sequencing along with computational free-energy and binding affinity calculations to evolve Taq polymerase to generate enzymes that are both stable and highly active in the presence of organic cosolvents, resulting in up to 10% solvent resistance and over 100-fold increase in stability at 97.5 °C in the presence of 1,4-butanediol, as well as tolerance to up to 10 times higher concentrations of the potent cosolvents sulfolane and 2-pyrrolidone. Using these polymerases, we successfully amplified a broad spectrum of GC-rich templates containing regions with over 90% GC content, including templates recalcitrant to amplification with existing polymerases, even in the presence of cosolvents. We also demonstrated dramatically reduced GC bias in the amplification of genes with widely varying GC content in quantitative polymerase chain reaction (qPCR). By expanding the scope of solvent systems compatible with nucleic acid polymerization, these organic solvent-resistant polymerases enable a dramatic reduction of sequence bias not achievable through thermal resistance alone, with significant implications for a wide range of applications including sequencing and synthetic biology in mixed aqueous-organic media.
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Affiliation(s)
- Mohammed Elias
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Xiangying Guan
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Devin Hudson
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Rahul Bose
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Joon Kwak
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Ioanna Petrounia
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Kenza Touah
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Sourour Mansour
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Peng Yue
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Gauthier Errasti
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Thomas Delacroix
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Anisha Ghosh
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- McGill University, 845 Rue Sherbrooke Ouest, Montreal, QC H3A 0G4, Canada
| | - Raj Chakrabarti
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
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10
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Ndraha N, Lin HY, Tsai SK, Hsiao HI, Lin HJ. The Rapid Detection of Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus via Polymerase Chain Reaction Combined with Magnetic Beads and Capillary Electrophoresis. Foods 2023; 12:3895. [PMID: 37959014 PMCID: PMC10649415 DOI: 10.3390/foods12213895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Food safety concerns regarding foodborne pathogen contamination have gained global attention due to its significant implications. In this study, we developed a detection system utilizing a PCR array combined with an automated magnetic bead-based system and CE technology to enable the detection of three foodborne pathogens, namely Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus. The results showed that our developed method could detect these pathogens at concentrations as low as 7.3 × 101, 6.7 × 102, and 6.9 × 102 cfu/mL, respectively, in the broth samples. In chicken samples, the limit of detection for these pathogens was 3.1 × 104, 3.5 × 103, and 3.9 × 102 cfu/g, respectively. The detection of these pathogens was accomplished without the necessity for sample enrichment, and the entire protocols, from sample preparation to amplicon analysis, were completed in approximately 3.5 h. Regarding the impact of the extraction method on detection capability, our study observed that an automated DNA extraction system based on the magnetic bead method demonstrated a 10-fold improvement or, at the very least, yielded similar results compared to the column-based method. These findings demonstrated that our developed model is effective in detecting low levels of these pathogens in the samples analyzed in this study. The PCR-CE method developed in this study may help monitor food safety in the future. It may also be extended to identify other foodborne pathogens across a wide range of food samples.
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Affiliation(s)
- Nodali Ndraha
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
| | - Hung-Yun Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
| | | | - Hsin-I Hsiao
- Department of Food Science, National Taiwan Ocean University, Keelung 202301, Taiwan;
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
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11
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Yang Z, Yang J, Yue L, Shen B, Wang J, Miao Y, Ouyang R, Hu Y. Enhancement Effects and Mechanism Studies of Two Bismuth-Based Materials Assisted by DMSO and Glycerol in GC-Rich PCR. Molecules 2023; 28:molecules28114515. [PMID: 37298991 DOI: 10.3390/molecules28114515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 06/12/2023] Open
Abstract
Polymerase chain reaction (PCR) has extensive bioanalytical applications in molecular diagnostics and genomic research studies for rapid detection and precise genomic amplification. Routine integrations for analytical workflow indicate certain limitations, including low specificity, efficiency, and sensitivity in conventional PCR, particularly towards amplifying high guanine-cytosine (GC) content. Further, there are many ways to enhance the reaction, for example, using different PCR strategies such as hot-start/touchdown PCR or adding some special modifications or additives such as organic solvents or compatible solutes, which can improve PCR yield. Due to the widespread use of bismuth-based materials in biomedicine, which have not yet been used for PCR optimization, this attracts our attention. In this study, two bismuth-based materials that are inexpensive and readily available were used to optimize GC-rich PCR. The results demonstrated that ammonium bismuth citrate and bismuth subcarbonate effectively enhanced PCR amplification of the GNAS1 promoter region (∼84% GC) and APOE (75.5% GC) gene of Homo sapiens mediated by Ex Taq DNA polymerase within the appropriate concentration range. Combining DMSO and glycerol additives was critical in obtaining the target amplicons. Thus, the solvents mixed with 3% DMSO and 5% glycerol were used in bismuth-based materials. That allowed for better dispersion of bismuth subcarbonate. As for the enhanced mechanisms, the surface interaction of PCR components, including Taq polymerase, primer, and products with bismuth-based materials, was maybe the main reason. The addition of materials can reduce the melting temperature (Tm), adsorb polymerase and modulate the amount of active polymerase in PCR, facilize the dissociation of DNA products, and enhance the specificity and efficiency of PCR. This work provided a class of candidate enhancers for PCR, deepened our understanding of the enhancement mechanisms of PCR, and also explored a new application field for bismuth-based materials.
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Affiliation(s)
- Zhu Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Junlei Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lihuan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bei Shen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Wang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yihong Hu
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
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12
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Shan W, Chen K, Sun J, Liu R, Xu W, Shao B. Mismatched duplexed aptamer-isothermal amplification-based nucleic acid-nanoflower for fluorescent detection of okadaic acid. Food Chem 2023; 424:136374. [PMID: 37207608 DOI: 10.1016/j.foodchem.2023.136374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
We developed a highly sensitive fluorescent assay to detect okadaic acid (OA), a prevalent aquatic toxin posing serious health risks. Our approach uses a mismatched duplexed aptamer (DA) immobilized on streptavidin-conjugated magnetic beads (SMBs) to create a DA@SMB complex. In the presence of OA, the cDNA unwinds, hybridizes with a G-rich segment pre-encoding circular template (CT), and undergoes rolling circle amplification (RCA) to produce G-quadruplexes, which are detected using the fluorescent dye thioflavine T (ThT). The method has a LOD of 3.1 × 10-3 ng/mL, a linear range of 0.1 ∼ 1.0 × 103 ng/mL, and was successfully applied to shellfish samples with spiked recoveries of 85.9% ∼ 102.2% and RSD less than 13%. Furthermore, instrumental analysis confirmed the accuracy and reliability of this rapid detection method. Overall, this work represents a significant advancement in the field of rapid aquatic toxin detection and has important implications for public health and safety.
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Affiliation(s)
- Wenchong Shan
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Keren Chen
- Department of Nutrition and Health (Institute of Nutrition and Health), China Agricultural University, Beijing 100083, PR China
| | - Jiefang Sun
- Beijing Center for Disease Prevention and Control, Beijing 100013, PR China
| | - Runqing Liu
- Beijing Center for Disease Prevention and Control, Beijing 100013, PR China
| | - Wentao Xu
- Department of Nutrition and Health (Institute of Nutrition and Health), China Agricultural University, Beijing 100083, PR China.
| | - Bing Shao
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China; Beijing Center for Disease Prevention and Control, Beijing 100013, PR China; Food Laboratory of Zhongyuan, Luohe 462300, PR China.
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13
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Zhang J, Tang L, Liu D, Zhang S, Ding X, Gao G, Deng X, Liu Z, Tian X, He W, Hu B, Huang Z. Reducing COVID-19 diagnostic errors with dNTPαSe supplementation. Analyst 2023; 148:1214-1220. [PMID: 36825426 DOI: 10.1039/d2an01698b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Timely and accurate diagnosis of COVID-19 is critical for controlling the pandemic. As the standard method to diagnose SARS-CoV-2, the real-time reverse transcription polymerase chain reaction (RT-qPCR) has good convenience. However, RT-qPCR still has a relatively high false-negative rate, particularly in the case of detecting low viral loads. In this study, using selenium-modified nucleoside triphosphates (dNTPαSe) in the RT-PCR reactions, we successfully increased the detection sensitivity and reduced the false-negative rate in COVID-19 diagnosis. By detecting positive controls, pseudovirus, and clinical samples with the commercial kits, we found that the dNTPαSe supplementation to these kits could generally offer smaller Ct values, permit the viral detection even in single-digit copies, and increase the detection specificity, sensitivity, and accuracy, thereby reducing the false-negative rate. Our experimental results demonstrated that dNTPαSe supplementation can make the commercial kits more specific, sensitive, and accurate, and this method is a convenient and efficient strategy for the disease detection and diagnosis.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064. .,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Xiaoling Ding
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Guolong Gao
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Xiaodong Deng
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Zhengying Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Xi Tian
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Wei He
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064. .,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China
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14
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531179. [PMID: 36945366 PMCID: PMC10028795 DOI: 10.1101/2023.03.05.531179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked-that is, phased-is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as 'linked-reads'). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Peter L. Chang
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093 USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
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15
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Gandhi H, Jain M, Gupta S, Singh AK, Kumar A, Sohal JS. Comparative evaluation of various in-house protocols on diagnostic performance for paratuberculosis IS900 PCR. Mol Biol Rep 2023; 50:943-947. [PMID: 36371554 DOI: 10.1007/s11033-022-07984-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/23/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Paratuberculosis is a worldwide endemic infectious disease of ruminants that results in high economic losses. Public health concerns are also being raised with human Crohn's disease. Therefore, control is becoming priority for governments. Control is largely dependent on "Test and Cull" or "Test and Segregate" policy. Hence, it is critical to assure the infection before making the decision. Commercial kits are costly especially in view of resource limited areas. Present study analyzed the performance various in house DNA isolation methods and PCR master mix combinations to optimize a protocol for confirmation of paratuberculosis bacilli shedding in feces. METHODS AND RESULTS Present study included five protocols of fecal DNA isolation (chemical, bio-chemical, physio-chemical and physical) and three reaction mixes (based on Qiagen, Genei and Thermo 2X master mixes) in nine different combinations using additives and tested their performance for IS900 PCR. Spiked fecal samples were used to select the best combination of DNA isolation method and PCR master mix (PRM). Selected combination was used to test reference (positive and negative) fecal samples and field samples. Findings revealed that combination physical method of DNA isolation and Genei based PRM (with additives; betaine DMSO and BSA) had lowest limit of detection. Sensitivity was 83% and specificity was 100% in comparison to fecal culture. High prevalence (23%) was reported for paratuberculosis on field samples. CONCLUSION Optimized protocol has acceptable sensitivity and can easily be adopted in resource-limited laboratories. High prevalence of paratuberculosis needs immediate implementation of the control strategies.
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Affiliation(s)
- Harshita Gandhi
- Amity Institute of Microbial Technology, Amity University Rajasthan, Kant-Kalwar, NH11C, Delhi- Jaipur, 303 002, Jaipur, Rajasthan, India
| | - Mukta Jain
- Biogenix Inc Pvt. Ltd, Amausi Industrial Area, 226008, Nadarganj, Lucknow, UP, India
| | - Saurabh Gupta
- Department of of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, NH-2, Post- Chaumunha, 281 406, Mathura, India.
| | - Amit Kumar Singh
- Amity Institute of Microbial Technology, Amity University Rajasthan, Kant-Kalwar, NH11C, Delhi- Jaipur, 303 002, Jaipur, Rajasthan, India
| | - Amit Kumar
- Department of Immunology & Defense Mechanism, Sardar Vallabh Bhai Patel University of Agriculture & Technology (SVPUAT), 250 110, Modipurum, Meerut, India
| | - Jagdip Singh Sohal
- Centre for Vaccines and Diagnostic Research, GLA University, NH-2, 281 406, Chaumunha, Mathura, India.
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16
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Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW. Long-Range Polymerase Chain Reaction. Methods Mol Biol 2023; 2967:181-192. [PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
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Affiliation(s)
- Ping Siu Kee
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Harsheni Karunanathie
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Simran D S Maggo
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
- Department of Pathology, Center for Personalized Medicine, Children's Hospital Los Angeles, California, LA, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Eng Wee Chua
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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17
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Cao X, Mao Y, Gu Y, Ge S, Lu W, Gu Y, Li Z. Highly sensitive and simultaneous detection of ctDNAs related to non-small cell lung cancer in serum using a catalytic hairpin assembly strategy in a SERS microfluidic chip. J Mater Chem B 2022; 10:6194-6206. [PMID: 35904034 DOI: 10.1039/d2tb01024k] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circulating tumor DNA (ctDNA) is an ideal biomarker for cancer diagnosis based on liquid biopsy, so there is an urgent need for developing an efficient, rapid, and ultrasensitive detection method to meet clinical needs. In this paper, a novel surface-enhanced Raman scattering (SERS) microfluidic chip combined with a catalytic hairpin assembly (CHA) was proposed to detect two non-small cell lung cancer (NSCLC)-related ctDNA (TP53 and PIK3CA-Q546K) simultaneously. The chip consists of six channels for parallel detection. In the reaction region, the CHA reaction between HP1 of the SERS probe and HP2 of the capture substrate was triggered by ctDNAs to form HP1-HP2 duplexes. As the reaction proceeds, more and more SERS probes are captured on the substrate. The gathered reaction products continuously form a lot of hot spots, which greatly enhance the SERS signal. This reaction was completed within 5 minutes. Through this method, the detection limits of TP53 and PIK3CA-Q546K in human serum were as low as 2.26 aM and 2.34 aM, respectively. The microfluidic chip also exhibited high specificity, reproducibility and stability. The clinical feasibility of the SERS microfluidic chip was verified by analyzing the serum samples of healthy subjects and NSCLC patients. The reliability of the experimental results was verified by the qRT-PCR test. The constructed SERS-based analytical micro-platform has great potential in dynamic monitoring of cancer staging and could be used as a clinical tool for early cancer screening.
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Affiliation(s)
- Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Yu Mao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Yuexing Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Shengjie Ge
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Wenbo Lu
- Shanxi Normal University, College of Chemistry and Material Science, Linfen, 041004, P. R. China
| | - Yingyan Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Zhiyue Li
- The First Clinical College, Dalian Medical University, Dalian, 116000, P. R. China
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