1
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Alabeedi FMA. Alteration of reactive oxygen species master transcription factor Nrf2 in keratinocytes exposed to monoclonal pathogenic antibody AK23 against desmoglein-3 in pemphigus vulgaris. Autoimmunity 2024; 57:2377138. [PMID: 39037929 DOI: 10.1080/08916934.2024.2377138] [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: 05/01/2024] [Accepted: 07/02/2024] [Indexed: 07/24/2024]
Abstract
Keratinocytes in mucosal and skin tissues maintain tissue integrity via desmosomes and desmoglein-3 (Dsg3). Pemphigus Vulgaris (PV) is a life-threatening autoimmune blistering disease characterized by autoantibodies against Dsg3, disrupting desmosomes. Nuclear factor erythroid 2-related factor 2 (Nrf2) regulates oxidative stress responses crucial for skin tissue protection. Although the pathogenesis of PV is known, the detailed molecular events remain unclear. This study investigates changes in Nrf2 expression in keratinocytes following pathogenic anti-Dsg3 antibody AK23 exposure, using dose- and time-dependent studies employing immunofluorescence analysis. N/TERT keratinocytes were cultured in keratinocytes serum-free medium and treated with AK23 at varying doses (5 µg/mL,40µg/mL,75µg/mL) and durations (2, 6, 24 h). Immunofluorescence staining was performed to assess the expression of Nrf2 and Dsg3. All fluorescent images were analyzed using ImageJ software. A dose-dependent increase in Dsg3 was noted following AK23 treatment, while Nrf2 expression and subcellular localization varied. Time-course analyses showed decreased Nrf2 at 24 h and increased Dsg3 levels. Early time-point (2 and 6 h) variations were evident in Nrf2 levels. This study highlights the impact of AK23 on Nrf2 expression, potentially disrupting Nrf2-mediated cytoprotection and implicating oxidative stress (ROS generation) in PV pathogenesis. Further investigation is necessary to validate the findings.
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2
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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3
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Donnelly O, Mesquita S, Archer J, Ali SM, Bartonicek Z, Lugli EB, Webster BL. Refining the Schistosoma haematobium recombinase polymerase amplification (Sh-RPA) assay: moving towards point-of-care use in endemic settings. Parasit Vectors 2024; 17:321. [PMID: 39068490 PMCID: PMC11283713 DOI: 10.1186/s13071-024-06380-9] [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: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Urogenital schistosomiasis is caused by the parasitic trematode Schistosoma haematobium. Sensitive and specific point-of-care diagnostics are needed for elimination of this disease. Recombinase polymerase amplification (RPA) assays meet these criteria, and an assay to diagnose S. haematobium has been developed (Sh-RPA). However, false-positive results can occur, and optimisation of reaction conditions to mitigate these is needed. Ease of use and compatibility of DNA extraction methods must also be considered. METHODS Using synthetic DNA, S. haematobium genomic DNA (gDNA), and urine samples from clinical cases, Sh-RPA reactions incorporating different betaine concentrations (0 M, 1 M, 2.5 M, 12.5 M) and the sample-to-water ratios were tested to determine effects on assay specificity and sensitivity. In addition, five commercial DNA extraction kits suitable for use in resource-limited settings were used to obtain gDNA from single S. haematobium eggs and evaluated in terms of DNA quality, quantity, and compatibility with the Sh-RPA assay. All samples were also evaluated by quantitative polymerase chain reaction (qPCR) to confirm DNA acquisition. RESULTS The analytical sensitivity of the Sh-RPA with all betaine concentrations was ≥ 10 copies of the synthetic Dra1 standard and 0.1 pg of S. haematobium gDNA. The addition of betaine improved Sh-RPA assay specificity in all reaction conditions, and the addition of 2.5 M of betaine together with the maximal possible sample volume of 12.7 µl proved to be the optimum reaction conditions. DNA was successfully isolated from a single S. haematobium egg using all five commercial DNA extraction kits, but the Sh-RPA performance of these kits varied, with one proving to be incompatible with RPA reactions. CONCLUSIONS The addition of 2.5 M of betaine to Sh-RPA reactions improved reaction specificity whilst having no detrimental effect on sensitivity. This increases the robustness of the assay, advancing the feasibility of using the Sh-RPA assay in resource-limited settings. The testing of commercial extraction kits proved that crude, rapid, and simple methods are sufficient for obtaining DNA from single S. haematobium eggs, and that these extracts can be used with Sh-RPA in most cases. However, the observed incompatibility of specific kits with Sh-RPA highlights the need for each stage of a molecular diagnostic platform to be robustly tested prior to implementation.
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Affiliation(s)
- Owain Donnelly
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Malaria Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Silvia Mesquita
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- René Rachou Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - John Archer
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Said M Ali
- Public Health Laboratory-Ivo de Carneri, P.O. Box 122, Chake-Chake, Pemba, United Republic of Tanzania
| | - Zikmund Bartonicek
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Elena B Lugli
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Bonnie L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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4
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Weinfurter JT, Bennett SN, Reynolds MR. A SMART method for isolating monoclonal antibodies from individual rhesus macaque memory B cells. J Immunol Methods 2024; 525:113602. [PMID: 38103783 PMCID: PMC10842827 DOI: 10.1016/j.jim.2023.113602] [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: 06/09/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Characterizing antigen-specific B cells is a critical component of vaccine and infectious disease studies in rhesus macaques (RMs). However, it is challenging to capture immunoglobulin variable (IgV) genes from individual RM B cells using 5' multiplex (MTPX) primers in nested PCR reactions. In particular, the diversity within RM IgV gene leader sequences necessitates large 5' MTPX primer sets to amplify IgV genes, decreasing PCR efficiency. To address this problem, we developed a switching mechanism at the 5' ends of the RNA transcript (SMART)-based method for amplifying IgV genes from single RM B cells to capture Ig heavy and light chain pairs. We demonstrate this technique by isolating simian immunodeficiency virus (SIV) envelope-specific antibodies from single-sorted RM memory B cells. This approach has several advantages over existing methods for cloning antibodies from RMs. First, optimized PCR conditions and SMART 5' and 3' rapid amplification of cDNA ends (RACE) reactions generate full-length cDNAs from individual B cells. Second, it appends synthetic primer binding sites to the 5' and 3' ends of cDNA during synthesis, allowing for PCR amplification of low-abundance antibody templates. Third, the nested PCR primer mixes are simplified by employing universal 5' primers, eliminating the need for complex 5' MTPX primer sets. We anticipate this method will enhance the isolation of antibodies from individual RM B cells, supporting the genetic and functional characterization of antigen-specific B cells.
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Affiliation(s)
- Jason T Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America
| | - Sarah N Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America
| | - Matthew R Reynolds
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, United States of America.
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5
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Knox A, Zerna G, Beddoe T. Current and Future Advances in the Detection and Surveillance of Biosecurity-Relevant Equine Bacterial Diseases Using Loop-Mediated Isothermal Amplification (LAMP). Animals (Basel) 2023; 13:2663. [PMID: 37627456 PMCID: PMC10451754 DOI: 10.3390/ani13162663] [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: 06/28/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Horses play an important role throughout the world, whether for work, culture, or leisure, providing an ever-growing significant contribution to the economy. The increase in importation and movement of horses, both nationally and internationally, has inevitably allowed for the global equine industry to grow. Subsequently, however, the potential for transmission of fatal equine bacterial diseases has also escalated, and devasting outbreaks continue to occur. To prevent such events, disease surveillance and diagnosis must be heightened throughout the industry. Current common, or "gold-standard" techniques, have shown to be inadequate at times, thus requiring newer technology to impede outbreaks. Loop-mediated isothermal amplification (LAMP) has proven to be a reliable, rapid, and accessible tool in both diagnostics and surveillance. This review will discuss equine bacterial diseases of biosecurity relevance and their current diagnostic approaches, as well as their respective LAMP assay developments. Additionally, we will provide insight regarding newer technology and advancements associated with this technique and their potential use for the outlined diseases.
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Affiliation(s)
| | | | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3082, Australia; (A.K.); (G.Z.)
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6
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Vajpayee K, Dash HR, Parekh PB, Shukla RK. PCR inhibitors and facilitators - Their role in forensic DNA analysis. Forensic Sci Int 2023; 349:111773. [PMID: 37399774 DOI: 10.1016/j.forsciint.2023.111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.
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Affiliation(s)
- Kamayani Vajpayee
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Hirak Ranjan Dash
- National Forensic Science University, New Delhi Campus, New Delhi, India
| | - Prakshal B Parekh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Ritesh K Shukla
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India.
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7
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Weinfurter JT, Bennett SN, Reynolds M. A SMART method for efficiently isolating monoclonal antibodies from individual rhesus macaque memory B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543510. [PMID: 37333083 PMCID: PMC10274751 DOI: 10.1101/2023.06.02.543510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Characterizing antigen-specific B cells is a critical component of vaccine and infectious disease studies in rhesus macaques (RMs). However, it is challenging to capture immunoglobulin variable (IgV) genes from individual RM B cells using 5' multiplex (MTPX) primers in nested PCR reactions. In particular, the diversity within RM IgV gene leader sequences necessitates the use of large 5' MTPX primer sets to amplify IgV genes, decreasing PCR efficiency. To address this problem, we developed a switching mechanism at the 5' ends of the RNA transcript (SMART)-based method for amplifying IgV genes from single RM B cells, providing unbiased capture of Ig heavy and light chain pairs for cloning antibodies. We demonstrate this technique by isolating simian immunodeficiency virus (SIV) envelope-specific antibodies from single-sorted RM memory B cells. This approach has several advantages over existing methods for PCR cloning antibodies from RMs. First, optimized PCR conditions and SMART 5' and 3' rapid amplification of cDNA ends (RACE) reactions generate full-length cDNAs from individual B cells. Second, it appends synthetic primer binding sites to the 5' and 3' ends of cDNA during synthesis, allowing for PCR amplification of low-abundance antibody templates. Third, universal 5' primers are employed to amplify the IgV genes from cDNA, simplifying the primer mixes in the nested PCR reactions and improving the recovery of matched heavy and light chain pairs. We anticipate this method will enhance the isolation of antibodies from individual RM B cells, supporting the genetic and functional characterization of antigen-specific B cells.
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Affiliation(s)
- Jason T. Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
| | - Sarah N. Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
| | - Matthew Reynolds
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Wisconsin, Madison WI
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8
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Effect of storage temperature and duration on direct PCR amplification of various feather types and DBS matrices. Gene 2023; 854:147116. [PMID: 36526120 DOI: 10.1016/j.gene.2022.147116] [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: 10/20/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The use of direct PCR has been pioneered over the last decade for DNA analysis of biological specimens of distinct origins. The information on how longer these specimens can be stored and amplified by direct PCR is however scanty. Such a piece of information could expedite research and diagnostic studies without compromising the reliability of results. The current study was therefore designed to analyze the effect of storage temperature and duration on direct PCR amplification of biological specimens having either low quantity or high quantity of DNA. Whole blood, dried blood spots (DBS), and feathers from chicken were stored for five years at three different temperatures, viz. room temperature (∼25 °C), 4 °C, and -20 °C. These samples were subjected to crude DNA extraction by diluting them in PBS buffer and heating at 98 °C after 1 day, 7 days, 15 days, 1 month, 3 months, 6 months, 1 year, 3 years and 5 years of storage. The crude DNA was PCR-amplified with the use of DNA sexing primers as well as DNA barcoding primers. Incubation at 98 °C for 10 min of any type of sample in PBS buffer was sufficient for crude DNA extraction. There was irrelevant impact of feather type, DBS matrix nature and storage temperature on amplification success over the period of analysis. It was possible to successfully accomplish the amplification of 96 samples with the use of routine PCR reagents within 3.5-6.0 hrs. In short, economical and fast genetic analysis of commonly used avian samples is feasible after their storage for longer time at room temperature.
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9
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Pereira H, Silva PC, Johansson B. Bacteria and Yeast Colony PCR. Methods Mol Biol 2023; 2967:209-221. [PMID: 37608114 DOI: 10.1007/978-1-0716-3358-8_17] [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
The bacteria Escherichia coli and the yeast Saccharomyces cerevisiae are currently the two most important organisms in synthetic biology. E. coli is almost always used for fundamental DNA manipulation, while yeast is the simplest host system for studying eukaryotic gene expression and performing large-scale DNA assembly. Yeast expression studies may also require altering the chromosomal DNA by homologous recombination. All these studies require the verification of the expected DNA sequence, and the fastest method of screening is colony PCR, which is direct PCR of DNA in cells without prior DNA purification. Colony PCR is hampered by the difficulty of releasing DNA into the PCR mix and by the presence of PCR inhibitors. We hereby present one protocol for E. coli and two protocols for S. cerevisiae differing in efficiency and complexity as well as an overview of past and possible future developments of efficient S. cerevisiae colony PCR protocols.
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Affiliation(s)
- Humberto Pereira
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Paulo César Silva
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Björn Johansson
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal.
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10
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Batool SM, Muralidharan K, Hsia T, Falotico S, Gamblin AS, Rosenfeld YB, Khanna SK, Balaj L, Carter BS. Highly sensitive EGFRvIII detection in circulating extracellular vesicle RNA of glioma patients. Clin Cancer Res 2022; 28:4070-4082. [PMID: 35849415 DOI: 10.1158/1078-0432.ccr-22-0444] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/01/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Liquid biopsy offers an attractive platform for non-invasive tumor diagnosis, prognostication and prediction of glioblastoma clinical outcomes. Prior studies report that 30-50% of GBM lesions characterized by EGFR amplification also harbor the EGFRvIII mutation. EXPERIMENTAL DESIGN A novel digital droplet PCR (ddPCR) assay for high GC content amplicons was developed and optimized for sensitive detection of EGFRvIII in tumor tissue and circulating extracellular vesicle RNA (EV RNA) isolated from the plasma of glioma patients. RESULTS Our optimized qPCR assay detected EGFRvIII mRNA in 81% (95% CI, 68% - 94%) of EGFR amplified glioma tumor tissue, indicating a higher than previously reported prevalence of EGFRvIII in glioma. Using the optimized ddPCR assay in discovery and blinded validation cohorts, we detected EGFRvIII mutation in 73% (95% CI, 64% - 82%) of patients with a specificity of 98% (95% CI, 87% - 100%), compared with qPCR tumor tissue analysis. Additionally, upon longitudinal monitoring in 4 patients, we report detection of EGFRvIII in the plasma of patients with different clinical outcomes, rising with tumor progression, and decreasing in response to treatment. CONCLUSION This study demonstrates the feasibility of detecting EGFRvIII mutation in plasma using a highly sensitive and specific ddPCR assay. We also show a higher than previously reported EGFRvIII prevalence in glioma tumor tissue. Several features of the assay are favorable for clinical implementation for detection and monitoring of EGFRvIII positive tumors.
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Affiliation(s)
| | | | - Tiffaney Hsia
- Massachusetts General Hospital, Boston, MA, United States
| | | | | | | | | | - Leonora Balaj
- Massachusetts General Hospital, Boston, United States
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11
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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12
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Girish PS, Kumari A, Gireesh‐Babu P, Karabasanavar NS, Raja B, Ramakrishna C, Barbuddhe SB. Alkaline lysis‐loop mediated isothermal amplification assay for rapid and on‐site authentication of buffalo (
Bubalus bubalis
) meat. J Food Saf 2021. [DOI: 10.1111/jfs.12955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Patil S. Girish
- ICAR – National Research Centre on Meat Hyderabad Telangana State India
| | - Aparana Kumari
- ICAR – National Research Centre on Meat Hyderabad Telangana State India
| | | | - Nagappa S. Karabasanavar
- Department of Veterinary Public Health & Epidemiology Veterinary College, Karnataka Veterinary Animal and Fisheries Sciences University Hassan Karnataka India
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13
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Rosas-Rodríguez JA, Valenzuela-Soto EM. The glycine betaine role in neurodegenerative, cardiovascular, hepatic, and renal diseases: Insights into disease and dysfunction networks. Life Sci 2021; 285:119943. [PMID: 34516992 DOI: 10.1016/j.lfs.2021.119943] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/27/2021] [Accepted: 09/04/2021] [Indexed: 12/15/2022]
Abstract
Glycine betaine (N, N, N-trimethyl amine) is an osmolyte accumulated in cells that is key for cell volume and turgor regulation, is the principal methyl donor in the methionine cycle and is a DNA and proteins stabilizer. In humans, glycine betaine is synthesized from choline and can be obtained from some foods. Glycine betaine (GB) roles are illustrated in chemical, metabolic, agriculture, and clinical medical studies due to its chemical and physiological properties. Several studies have extensively described GB role and accumulation related to specific pathologies, focusing mainly on analyzing its positive and negative role in these pathologies. However, it is necessary to explain the relationship between glycine betaine and different pathologies concerning its role as an antioxidant, ability to methylate DNA, interact with transcription factors and cell receptors, and participate in the control of homocysteine concentration in liver, kidney and brain. This review summarizes the most important findings and integrates GB role in neurodegenerative, cardiovascular, hepatic, and renal diseases. Furthermore, we discuss GB impact on other dysfunctions as inflammation, oxidative stress, and glucose metabolism, to understand their cross-talks and provide reliable data to establish a base for further investigations.
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Affiliation(s)
- Jesús A Rosas-Rodríguez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Sur, Navojoa, Sonora, Mexico
| | - Elisa M Valenzuela-Soto
- Centro de Investigación en Alimentación y Desarrollo A.C., Hermosillo 83304, Sonora, Mexico.
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14
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Wang T, Ji H, Yu Y, Wang X, Cheng Y, Li Z, Chen J, Guo L, Xu J, Gao C. Development of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Phytopythium vexans. Front Microbiol 2021; 12:720485. [PMID: 34552572 PMCID: PMC8450588 DOI: 10.3389/fmicb.2021.720485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Brown root rot caused by Phytopythium vexans is a new destructive root disease on many plants such as Gingko, Citrus, kiwifruit, and ramie. The establishment of loop-mediated isothermal amplification (LAMP) technology for detecting P. vexans can help monitor and control brown root rot quickly, efficiently, and accurately. LAMP technology is known for its simplicity, sensitivity, and speed; and it does not require any specialized equipment – a water bath or a thermoblock is sufficient for isothermal amplifications. LAMP products can be visualized by using hydroxy naphthol blue (HNB) dye or agarose gel electrophoresis. In this study, by searching and comparing the internal transcribed spacer (ITS) sequences of P. vexans and the related species in oomycete genera Pythium, Phytopythium, and Phytophthora, we designed specific primers targeting the ITS gene region of P. vexans. Using HNB dye, we established a LAMP technique for rapid detection of P. vexans by visible color change. In addition, we optimized the protocol to enhance both sensitivity and specificity for P. vexans detection. Under the optimized condition, our protocol based on LAMP technology could detect as low as 24 copies of the P. vexans genomic DNA, which is ∼100 times more sensitive than conventional PCR. This method can successfully detect P. vexans using cell suspensions from P. vexans – infected ramie root tissues.
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Affiliation(s)
- Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Haojun Ji
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yongting Yu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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15
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Low stutter ratio by SuperFi polymerase. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Lan L, Huang J, Liu M, Yin Y, Wei C, Cai Q, Meng X. Polymerization and isomerization cyclic amplification for nucleic acid detection with attomolar sensitivity. Chem Sci 2021; 12:4509-4518. [PMID: 34163716 PMCID: PMC8179492 DOI: 10.1039/d0sc05457g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
DNA amplification is one of the most valuable tools for the clinical diagnosis of nucleic acid-related diseases, but current techniques for DNA amplification are based on intermolecular polymerization reactions, resulting in the risk of errors in the intermolecular reaction pattern. In this article, we introduce the concept of intramolecular polymerization and isomerization cyclic amplification (PICA), which extends a short DNA strand to a long strand containing periodic repeats of a sequence through cyclic alternating polymerization and isomerization. To the best of our knowledge, this is the first time that a real ssDNA self-extension method without any additional auxiliary oligonucleotides has been reported. By interfacing PICA with external molecular elements, it can be programmed to respond to different targets. Herein, we designed two distinct types of amplified nucleic acid detection platforms that can be implemented with PICA, including cyclic reverse transcription (CRT) and cyclic replication (CR). We experimentally demonstrate the mechanisms of CRT-PICA and CR-PICA using mammalian miRNA and virus DNA. The results showed that this proposed detection platform has excellent sensitivity, selectivity, and reliability. The detection level could reach the aM level, that is, several copies of target molecules can be detected if a small volume is taken into account.
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Affiliation(s)
- Lin Lan
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Mengtan Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Can Wei
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Qinyun Cai
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
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Assal N, Lin M. PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis. J Microbiol Methods 2020; 181:106121. [PMID: 33316290 DOI: 10.1016/j.mimet.2020.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Amplification of high GC content genes by PCR is a major challenge during the creation of recombinant GC-rich DNA constructs. This may be due to the difficulty in DNA denaturation or the possibility of forming secondary structures from DNA templates. Tools have been described to address the technical problems associated with the amplification of shorter sequences (<1000 bp). However, obstacles of synthesizing larger-sized GC-rich sequences by PCR continue to exist. This study aims to investigate the amplification of long and high GC content genes by PCR from the Mycobacterium bovis, a genome with GC content >60%, in comparison to amplifying a gene from the Listeria monocytogenes genome, a genome with a 37.8% GC content. Three PCR protocols were designed and experimented at various conditions with two M. bovis genes, Mb0129, a large gene of 1794 bp with 77.5% GC content, mpb83, a smaller gene of 663 bp in length with moderate GC content of 63%, together with LMHCC_RS00060, a large L. monocytogenes gene of 1617 bp with a lower GC content of 41.5%. The result demonstrated the superiority of the 2-step PCR protocol over other protocols in PCR amplification of Mb0129 when specific high fidelity DNA polymerases were used in the presence of an enhancer. The study highlighted the importance of manipulating the cycling conditions to perform the annealing and extension steps at higher temperatures while adjusting the ramp speed at a lower speed for a successful PCR amplification of a large GC-rich DNA template. A final PCR protocol was developed and enabled the amplification of 51 GC-rich targets. This can be a valuable tool for the amplification of long GC-rich DNA sequences for various downstream applications.
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Affiliation(s)
- Nadia Assal
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Min Lin
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
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Edgü G, Freund LJ, Hartje S, Tacke E, Hofferbert HR, Twyman RM, Noll GA, Muth J, Prüfer D. Fast, Precise, and Reliable Multiplex Detection of Potato Viruses by Loop-Mediated Isothermal Amplification. Int J Mol Sci 2020; 21:ijms21228741. [PMID: 33228234 PMCID: PMC7699554 DOI: 10.3390/ijms21228741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/04/2022] Open
Abstract
Potato is an important staple food crop in both developed and developing countries. However, potato plants are susceptible to several economically important viruses that reduce yields by up to 50% and affect tuber quality. One of the major threats is corky ringspot, which is a tuber necrosis caused by tobacco rattle virus (TRV). The appearance of corky ringspot symptoms on tubers prior to commercialization results in ≈ 45% of the tubers being downgraded in quality and value, while ≈ 55% are declared unsaleable. To improve current disease management practices, we have developed simple diagnostic methods for the reliable detection of TRV without RNA purification, involving minimalized sample handling (mini), subsequent improved colorimetric loop-mediated isothermal amplification (LAMP), and final verification by lateral-flow dipstick (LFD) analysis. Having optimized the mini-LAMP-LFD approach for the sensitive and specific detection of TRV, we confirmed the reliability and robustness of this approach by the simultaneous detection of TRV and other harmful viruses in duplex LAMP reactions. Therefore, our new approach offers breeders, producers, and farmers an inexpensive and efficient new platform for disease management in potato breeding and cultivation.
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Affiliation(s)
- Güven Edgü
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Lena Julie Freund
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Hans-Reinhard Hofferbert
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Richard M. Twyman
- Twyman Research Management Ltd., P.O. Box 493, Scarborough YO11 9FJ, UK;
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
- Correspondence: ; Tel.: +49-251-8322302
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Rupnik K, Tanifuji K, Rettberg L, Ribbe MW, Hu Y, Hales BJ. Electron Paramagnetic Resonance and Magnetic Circular Dichroism Spectra of the Nitrogenase M Cluster Precursor Suggest Sulfur Migration upon Oxidation: A Proposal for Substrate and Inhibitor Binding. Chembiochem 2020; 21:1767-1772. [PMID: 31881119 PMCID: PMC7481019 DOI: 10.1002/cbic.201900681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 02/01/2023]
Abstract
The active site of the nitrogen-fixing enzyme Mo-nitrogenase is the M cluster ([MoFe7 S9 C⋅R-homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical-SAM enzyme, is instrumental in the assembly of the L cluster ([Fe8 S9 C]), a precursor and all-iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe8 S8 C]), which lacks the final ninth sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled LOx and [L*]Ox . This study shows that both LOx and [L*]Ox have nearly identical EPR and MCD spectra, thus suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from LOx following oxidation, thereby rendering the cluster identical to [L*]Ox . It is proposed that a similar migration could occur to the M cluster upon oxidation, and that this is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding.
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Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Brian J Hales
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
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Naveen KP, Bhat AI. Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays for the detection of two novel viruses infecting ginger. J Virol Methods 2020; 282:113884. [PMID: 32442456 DOI: 10.1016/j.jviromet.2020.113884] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022]
Abstract
Our recent studies have shown the association of two novel viruses namely, ginger chlorotic fleck-associated virus 1 (GCFaV-1) and ginger chlorotic fleck-associated virus 2 (GCFaV-2) with chlorotic fleck disease of ginger. As ginger is propagated through vegetative means, the development of diagnostics would aid in the identification of virus-free plants. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays were developed and validated for the quick detection of GCFaV-1 and GCFaV-2. The detection limits of viruses by these assays, when compared with conventional and real-time RT-PCR, showed that RT-LAMP was up to 1000 times more sensitive than conventional RT-PCR and one-hundredth that of real-time RT-PCR for both the viruses. The detection limit of RT-RPA for GCFaV-1 was up to 100 times more than that of RT-PCR and one-thousandth that of real-time RT-PCR. On the other hand, for detecting GCFaV-2, RT-RPA was found up to 1000 times more sensitive than conventional RT-PCR and one hundredth that of real-time RT-PCR. Based on the cost-effectiveness and duration, RT-LAMP and RT-RPA assays can be suggested for the rapid detection of both viruses.
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Affiliation(s)
- K P Naveen
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India
| | - A I Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India.
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Song J, Hegge JW, Mauk MG, Chen J, Till JE, Bhagwat N, Azink LT, Peng J, Sen M, Mays J, Carpenter EL, van der Oost J, Bau HH. Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics. Nucleic Acids Res 2020; 48:e19. [PMID: 31828328 PMCID: PMC7038991 DOI: 10.1093/nar/gkz1165] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Detection of disease-associated, cell-free nucleic acids in body fluids enables early diagnostics, genotyping and personalized therapy, but is challenged by the low concentrations of clinically significant nucleic acids and their sequence homology with abundant wild-type nucleic acids. We describe a novel approach, dubbed NAVIGATER, for increasing the fractions of Nucleic Acids of clinical interest Via DNA-Guided Argonaute from Thermus thermophilus (TtAgo). TtAgo cleaves specifically guide-complementary DNA and RNA with single nucleotide precision, greatly increasing the fractions of rare alleles and, enhancing the sensitivity of downstream detection methods such as ddPCR, sequencing, and clamped enzymatic amplification. We demonstrated 60-fold enrichment of the cancer biomarker KRAS G12D and ∼100-fold increased sensitivity of Peptide Nucleic Acid (PNA) and Xenonucleic Acid (XNA) clamp PCR, enabling detection of low-frequency (<0.01%) mutant alleles (∼1 copy) in blood samples of pancreatic cancer patients. NAVIGATER surpasses Cas9-based assays (e.g. DASH, Depletion of Abundant Sequences by Hybridization), identifying more mutation-positive samples when combined with XNA-PCR. Moreover, TtAgo does not require targets to contain any specific protospacer-adjacent motifs (PAM); is a multi-turnover enzyme; cleaves ssDNA, dsDNA and RNA targets in a single assay; and operates at elevated temperatures, providing high selectivity and compatibility with polymerases.
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Jorrit W Hegge
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Junman Chen
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Jacob E Till
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neha Bhagwat
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lotte T Azink
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Moen Sen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jazmine Mays
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erica L Carpenter
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
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24
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Varona M, Eitzmann DR, Pagariya D, Anand RK, Anderson JL. Solid-Phase Microextraction Enables Isolation of BRAF V600E Circulating Tumor DNA from Human Plasma for Detection with a Molecular Beacon Loop-Mediated Isothermal Amplification Assay. Anal Chem 2020; 92:3346-3353. [PMID: 31950824 PMCID: PMC7155775 DOI: 10.1021/acs.analchem.9b05323] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker that can provide a wealth of information regarding the genetic makeup of cancer as well as provide a guide for monitoring treatment. Methods for rapid and accurate profiling of ctDNA are highly desirable in order to obtain the necessary information from this biomarker. However, isolation of ctDNA and its subsequent analysis remains a challenge due to the dependence on expensive and specialized equipment. In order to enable widespread implementation of ctDNA analysis, there is a need for low-cost and highly accurate methods that can be performed by nonexpert users. In this study, an assay is developed that exploits the high specificity of molecular beacon (MB) probes with the speed and simplicity of loop-mediated isothermal amplification (LAMP) for the detection of the BRAF V600E single-nucleotide polymorphism (SNP). Furthermore, solid-phase microextraction (SPME) is applied for the successful isolation of clinically relevant concentrations (73.26 fM) of ctDNA from human plasma. In addition, the individual effects of plasma salts and protein on the extraction of ctDNA with SPME are explored. The performed work expands the use of MB-LAMP for SNP detection as well as demonstrates SPME as a sample preparation tool for nucleic acid analysis in plasma.
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Affiliation(s)
- Marcelino Varona
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Derek R. Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Darshna Pagariya
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Robbyn K. Anand
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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Kumari S, Kumar RR, Mendiratta SK, Kumar D, Kumar A, Kumar D, Rana P, Jawla J. On-Site Detection of Tissues of Buffalo Origin by Loop-Mediated Isothermal Amplification (LAMP) Assay Targeting Mitochondrial Gene Sequences. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01718-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Smith LD, Willard MC, Smith JP, Cunningham BT. Development of a Linker-Mediated Immunoassay Using Chemically Transitioned Nanosensors. Anal Chem 2020; 92:3627-3635. [DOI: 10.1021/acs.analchem.9b04518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Lucas D. Smith
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Michael C. Willard
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Jordan P. Smith
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Pyshnaya IA, Lomzov AA, Pyshnyi DV. Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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García-Bernalt Diego J, Fernández-Soto P, Crego-Vicente B, Alonso-Castrillejo S, Febrer-Sendra B, Gómez-Sánchez A, Vicente B, López-Abán J, Muro A. Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test. Sci Rep 2019; 9:14744. [PMID: 31611563 PMCID: PMC6791938 DOI: 10.1038/s41598-019-51342-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
Schistosomiasis is one of the most prevalent Neglected Tropical Disease, affecting approximately 250 million people worldwide. Schistosoma mansoni is the most important species causing human intestinal schistosomiasis. Despite significant efforts in recent decades, the global disease burden of schistosomiasis remains extremely high. This could partly be attributed to the absence of accurate diagnostic tools, primarily in endemic areas. Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as a field-friendly alternative to many other complex molecular methods and it has been proposed as an ideal candidate for revolutionizing point-of-care molecular diagnostics. In a previous work, a LAMP-based method to detect S. mansoni DNA (SmMIT-LAMP) was developed by our research group for early diagnosis of active schistosomiasis in an experimental infection murine model. The SmMIT-LAMP has been further successfully evaluated in both human stool and snail samples and, recently, in human urine samples. In this study, we developed an important improvement for SmMIT-LAMP molecular assay, transforming it into a cold maintenance dry format suitable for potentially manufacturing as kit for ready-to-use for schistosomiasis diagnosis. This procedure could be applied to create dry LAMP kits for a laboratory setting and for diagnostic applications for other neglected tropical diseases.
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Affiliation(s)
- J García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - P Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
| | - B Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - S Alonso-Castrillejo
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Gómez-Sánchez
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - J López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
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Ding X, Xu Z, Yin K, Sfeir M, Liu C. Dual-Priming Isothermal Amplification (DAMP) for Highly Sensitive and Specific Molecular Detection with Ultralow Nonspecific Signals. Anal Chem 2019; 91:12852-12858. [PMID: 31525941 DOI: 10.1021/acs.analchem.9b02582] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid amplification tests have been widely used in clinical diagnostics, food safety monitoring, and molecular biology. Loop-mediated isothermal amplification (LAMP) is a prevailing nucleic acid isothermal amplification method. It has become a powerful alternative to conventional polymerase chain reaction (PCR) for pathogen detection because of its simplicity, rapidity, and high sensitivity. However, the current LAMP methods, especially LAMP with two loop primers, suffer from undesired nonspecific amplification with strong background signals due to the increasing target sites. This nonspecific amplification substantially reduced the reliability of LAMP and limited its applications in clinical diagnostics. Here, we report a "dual-priming" ("self-priming" and "pairing-priming") isothermal amplification (DAMP) assay for rapid nucleic acid detection with ultralow nonspecific signals. This method takes advantage of the "dual-priming" strand extension strategy by adding two pairing-competition primers and designing unique inner primers, enabling highly sensitive and specific molecular detection. As an application demonstration, the DAMP assay was used to detect HIV-1 DNA/RNA and Escherichia coli DNA, showing equal or better sensitivity with shorter detection time compared to conventional LAMP and PCR methods. More importantly, the DAMP assay showed ultralow background signals without false positive signals even after a 2 h incubation. Such a simple, reliable, sensitive, and specific DAMP assay can be well suited for rapid nucleic acid detection as point-of-care testing, particularly in resource-limited settings.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Zhiheng Xu
- Department of Biomedical Engineering , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Kun Yin
- Department of Biomedical Engineering , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Maroun Sfeir
- Department of Pathology and Laboratory Medicine , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Changchun Liu
- Department of Biomedical Engineering , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
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Rapid assessment of viral water quality using a novel recombinase polymerase amplification test for human adenovirus. Appl Microbiol Biotechnol 2019; 103:8115-8125. [PMID: 31435714 DOI: 10.1007/s00253-019-10077-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/28/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022]
Abstract
Sensitive and rapid methods for determining viral contamination of water are critical, since illness can be caused by low numbers of viruses and bacterial indicators do not adequately predict viral loads. We developed novel rapid assays for detecting the viral water quality indicator human adenovirus (HAdV). A simple 15-min recombinase polymerase amplification step followed by a 5-min lateral flow detection is used. Species-specific assays were developed to discriminate HAdV A, B, C and F, and combined into a multiplex test (Ad-FAC). Species-specific assays enabled detection of 10-50 copies of the HAdV plasmid. Sample testing using methods optimised for wastewater analysis indicated the Ad-FAC assay showed 100% sensitivity and 100% specificity when compared with HAdV qPCR, with a detection limit as low as 50 gene copies. This is the first study to demonstrate the use of RPA for detecting enteric viruses in water samples, to assess virological water quality. The ability to rapidly detect enteric virus contamination of water could assist in more effective management of water safety and better protection of public health.
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Tahara Y. Study at the Kool Lab in Stanford University —Chemical Biology of Nucleic Acid—. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuki Tahara
- New Frontiers Research Group, Frontier Research Labs, Institute for Innovation, Ajinomoto Co., Inc
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32
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Luo GC, Yi TT, Jiang B, Guo XL, Zhang GY. Betaine-assisted recombinase polymerase assay with enhanced specificity. Anal Biochem 2019; 575:36-39. [PMID: 30930198 DOI: 10.1016/j.ab.2019.03.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Recombinase polymerase amplification (RPA) is a widespread isothermal amplification method and regarded as an excellent candidate to replace polymerase chain reaction. However, the specificity of RPA is not always satisfactory when the sample contains amounts of background DNA. Herein, we report a novel RPA method named betaine-assisted RPA (B-RPA) that uses inexpensive betaine to avoid nonspecific amplification effectively. Result show that nonspecific amplification is prone to occur in RPA if the primers have not been rigorously refined, especially in detecting samples with large amounts of background DNA. This problem has been addressed by adding betaine to the RPA reactions. Our data show that the addition of 0.8 M betaine can significantly increase specificity and efficiency simultaneously. This B-RPA method is also used to detect hepatitis B virus DNA in clinical plasma samples, thereby demonstrating the clinical practicability of B-RPA.
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Affiliation(s)
- Guang-Cheng Luo
- College of Life Sciences, Sichuan University, Chengdu, China; Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Ting-Ting Yi
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Bing Jiang
- Nanbu County People's Hospital, Nanchong, Sichuan, China
| | - Xiao-Lan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Guo-Yuan Zhang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China.
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33
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Green MR, Sambrook J. Polymerase Chain Reaction (PCR) Amplification of GC-Rich Templates. Cold Spring Harb Protoc 2019; 2019:2019/2/pdb.prot095141. [PMID: 30710022 DOI: 10.1101/pdb.prot095141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The efficiency of polymerase chain reaction (PCR) amplification is influenced by the nucleotide composition and sequence of the template DNA. Problematic templates include those with long homopolymeric runs, inverted repeats, or GC-rich tracts-such as those containing >60% G + C residues-that are found in the regulatory regions of many mammalian genes. Localized regions of templates rich in GC residues tend to fold into complex secondary structures that might not melt during the annealing phase of the PCR cycle. Also, the primers used to amplify GC-rich regions often have a high capacity to form self- and cross-dimers and a strong tendency to fold into stem-loop structures that can impede the progress of the DNA polymerase along the template molecule. Predictably, amplification of full-length template DNA is inefficient, and the products of the reaction contain a high proportion of shorter molecules that result from blockage of the DNA polymerase. Altering the design of the primers and using a combination of hot start and touchdown PCR can sometimes improve the efficiency of amplification. More often, a multipronged approach is required, such as the use of enhancers in the amplification reaction, adjustment of the cycling protocol, and, if necessary, designing new sets of primers. This protocol uses a mixture of four additives-betaine, dithiothreitol (DTT), dimethyl sulfoxide (DMSO), and bovine serum albumin (BSA)-for use with Taq DNA polymerase.
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Kestemont D, Herdewijn P, Renders M. Enzymatic Synthesis of Backbone-Modified Oligonucleotides Using T4 DNA Ligase. ACTA ACUST UNITED AC 2019; 11:e62. [PMID: 30688416 DOI: 10.1002/cpch.62] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
T4 DNA ligase in high concentrations of certain crowding agents and cosolutes catalyzes the synthesis of a series of backbone-modified oligonucleotides that are difficult to obtain chemically. Backbone-modified nucleic acids are often enzymatically and chemically more stable, making them interesting as potential diagnostic or therapeutic agents, as a biosafety tool, or in nanotechnology. In this article, we describe a small-scale experiment to probe the efficiency of the ligation reaction of modified oligonucleotides in the presence of 3 M betaine and 10% PEG 8000, followed by large-scale ligation with subsequent isolation of the ligated oligonucleotide. The correct product formation can be verified using denaturing polyacrylamide gel electrophoresis and mass spectrometry. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Genoscope, Université Paris-Saclay, Évry, France
| | - Marleen Renders
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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35
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Rakowska PW, Kogut M, Czub J, Stangret J. Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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36
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Srisuwan W, Tatu T. A Simple Whole-Blood Polymerase Chain Reaction without DNA Extraction for Thalassemia Diagnosis. Hemoglobin 2018; 42:178-183. [PMID: 30282496 DOI: 10.1080/03630269.2018.1496929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Polymerase chain reaction (PCR) diagnosis of thalassemia usually relies on using genomic DNA. Preparing the genomic DNA can lead to sample-to-sample contamination. This report was aimed to establish the PCR protocol using whole-blood for detecting mutations of α- and β-globin genes causing the thalassemia syndrome. First, the PCR facilitators, betaine and bovine serum albumin (BSA), were tested, simultaneously with an adjustment of PCR thermal cycler and of whole-blood volume. Thereafter, the established whole-blood PCR was applied for detecting, in both known and unknown samples, the HBA1 Southeast Asian (- -SEA) (NG_000006.1: g.26264_45564del19301) deletion, Hb Constant Spring (Hb CS, HBA2: c.427T>C, αCSα), codon 17 (A>T) (HBB: c.52A>T), codons 41/42 (-TTCT) (HBB: c.126_129delCTTT) deletion, -28 (A>G) (HBB: c.-78A>G) and codon 26 (G>A) (Hb E or HBB: c.79G>A). It was shown that the whole-blood PCR worked successfully in 9.0% (w/v) betaine, with 1 μL of EDTA whole blood and with addition of 10 heat-cool steps (3 min. at 94 °C, followed by 3 min. at 55 °C) prior to the typical thermal cycles for the mutations. The capability of the new whole-blood PCR was similar to that of the typical DNA-based PCR. Therefore, the newly established whole-blood PCR could be performed for PCR diagnosis of thalassemia. Using this platform, sample-to-sample contamination should be eliminated.
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Affiliation(s)
- Wibhasiri Srisuwan
- a Research Center for Hematology and Health Technology, Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences , Chiang Mai University , Chiang Mai , Thailand
| | - Thanusak Tatu
- a Research Center for Hematology and Health Technology, Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences , Chiang Mai University , Chiang Mai , Thailand
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37
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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38
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Chen X, Zhang J, Wang Z, Xu X, Zhu B. Combination of Zn2+ and betaine can eliminate the effect of DNA fragments with different GC content on gene chip. Acta Biochim Biophys Sin (Shanghai) 2018; 50:826-827. [PMID: 29897387 DOI: 10.1093/abbs/gmy064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiang Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Jiaqi Zhang
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
| | - Ze Wang
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
| | - Xu Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Bin Zhu
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
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39
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Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun (Camb) 2018; 54:6408-6411. [PMID: 29872779 DOI: 10.1039/c8cc02414f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 box 1041, 3000 Leuven, Belgium.
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40
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Rivas L, Reuterswärd P, Rasti R, Herrmann B, Mårtensson A, Alfvén T, Gantelius J, Andersson-Svahn H. A vertical flow paper-microarray assay with isothermal DNA amplification for detection of Neisseria meningitidis. Talanta 2018; 183:192-200. [DOI: 10.1016/j.talanta.2018.02.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 01/13/2023]
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41
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Becherer L, Bakheit M, Frischmann S, Stinco S, Borst N, Zengerle R, von Stetten F. Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters. Anal Chem 2018; 90:4741-4748. [PMID: 29508609 DOI: 10.1021/acs.analchem.7b05371] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A variety of real-time detection techniques for loop-mediated isothermal amplification (LAMP) based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However, these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets. The innovation features a mediator displacement probe and a universal reporter. During amplification of target DNA the mediator is displaced from the mediator displacement probe. Then it hybridizes to the reporter generating a fluorescence signal. The novel mediator displacement (MD) detection was validated against state-of-the-art molecular beacon (MB) detection by means of a HIV-1 RT-LAMP: MD surpassed MB detection by accelerated probe design (MD: 10 min, MB: 3-4 h), shorter times to positive (MD 4.1 ± 0.1 min shorter than MB, n = 36), improved signal-to-noise fluorescence ratio (MD: 5.9 ± 0.4, MB: 2.7 ± 0.4; n = 15), and showed equally good or better analytical performance parameters. The usability of one universal mediator-reporter set in different multiplex assays was successfully demonstrated for a biplex RT-LAMP of HIV-1 and HTLV-1 and a biplex LAMP of Haemophilus ducreyi and Treponema pallidum, both showing good correlation between target concentration and time to positive. Due to its simple implementation it is suggested to extend the use of the universal mediator-reporter sets to the detection of various other diagnostic panels.
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Affiliation(s)
- Lisa Becherer
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering , University of Freiburg , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany
| | | | | | - Silvina Stinco
- Max von Pettenkofer-Institute , Diagnostic Virology Department , Pettenkoferstr. 9A , 80336 Munich , Germany
| | - Nadine Borst
- Hahn-Schickard , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering , University of Freiburg , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany.,Hahn-Schickard , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany.,BIOSS - Centre for Biological Signalling Studies , University of Freiburg , Schaenzlestr. 1 , 79104 Freiburg , Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering , University of Freiburg , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany.,Hahn-Schickard , Georges-Koehler-Allee 103 , 79110 Freiburg , Germany
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42
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Jensen MA, Davis RW. Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges. Biochemistry 2018. [PMID: 29533604 DOI: 10.1021/acs.biochem.7b00937] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single-stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template-free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis.
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Affiliation(s)
- Michael A Jensen
- Stanford Genome Technology Center, Department of Biochemistry , Stanford University , Palo Alto , California 94304 , United States
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry , Stanford University , Palo Alto , California 94304 , United States.,Department of Genetics , Stanford University , Palo Alto , California 94304 , United States
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43
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Tahara YK, Auld D, Ji D, Beharry AA, Kietrys AM, Wilson DL, Jimenez M, King D, Nguyen Z, Kool ET. Potent and Selective Inhibitors of 8-Oxoguanine DNA Glycosylase. J Am Chem Soc 2018; 140:2105-2114. [PMID: 29376367 PMCID: PMC5823510 DOI: 10.1021/jacs.7b09316] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The activity of DNA repair enzyme 8-oxoguanine DNA glycosylase (OGG1), which excises oxidized base 8-oxoguanine (8-OG) from DNA, is closely linked to mutagenesis, genotoxicity, cancer, and inflammation. To test the roles of OGG1-mediated repair in these pathways, we have undertaken the development of noncovalent small-molecule inhibitors of the enzyme. Screening of a PubChem-annotated library using a recently developed fluorogenic 8-OG excision assay resulted in multiple validated hit structures, including selected lead hit tetrahydroquinoline 1 (IC50 = 1.7 μM). Optimization of the tetrahydroquinoline scaffold over five regions of the structure ultimately yielded amidobiphenyl compound 41 (SU0268; IC50 = 0.059 μM). SU0268 was confirmed by surface plasmon resonance studies to bind the enzyme both in the absence and in the presence of DNA. The compound SU0268 was shown to be selective for inhibiting OGG1 over multiple repair enzymes, including other base excision repair enzymes, and displayed no toxicity in two human cell lines at 10 μM. Finally, experiments confirm the ability of SU0268 to inhibit OGG1 in HeLa cells, resulting in an increase in accumulation of 8-OG in DNA. The results suggest the compound SU0268 as a potentially useful tool in studies of the role of OGG1 in multiple disease-related pathways.
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Affiliation(s)
- Yu-ki Tahara
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Douglas Auld
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Andrew A. Beharry
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Anna M. Kietrys
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Marta Jimenez
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel King
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zachary Nguyen
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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44
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Ma YD, Luo K, Chang WH, Lee GB. A microfluidic chip capable of generating and trapping emulsion droplets for digital loop-mediated isothermal amplification analysis. LAB ON A CHIP 2018; 18:296-303. [PMID: 29188245 DOI: 10.1039/c7lc01004d] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that rapidly amplifies specific DNA molecules at high yield. In this study, a microfluidic droplet array chip was designed to execute the digital LAMP process. The novel device was capable of 1) creating emulsion droplets, 2) sorting them into a 30 × 8 droplet array, and 3) executing LAMP across the 240 trapped and separated droplets (with a volume of 0.22 nL) after only 40 min of reaction at 56 °C. Nucleic acids were accurately quantified across a dynamic range of 50 to 2.5 × 103 DNA copies per μL, and the limit of detection was a single DNA molecule. This is the first time that an arrayed emulsion droplet microfluidic device has been used for digital LAMP analysis. When compared to microwell digital nucleic acid amplification assays, this droplet array-based digital LAMP assay eliminates the constraint on the size of the digitized target, which was determined by the dimension of the microwells for its counterparts. Moreover, the capacity for hydrodynamic droplet trapping allows the chip to operate in a one-droplet-to-one-trap manner. This microfluidic chip may therefore become a promising device for digital LAMP-based diagnostics in the near future.
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Affiliation(s)
- Yu-Dong Ma
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
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45
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Lu Y, Yao B, Wang G, Hong N. The detection of ACLSV and ASPV in pear plants by RT-LAMP assays. J Virol Methods 2017; 252:80-85. [PMID: 29180245 DOI: 10.1016/j.jviromet.2017.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV) and Apple stem pitting virus (ASPV), two important viruses frequently occurring in pear trees. A set of four RT-LAMP primers designed based on the highly conserved region of each CP gene of the two viruses showed high specificity and feasibility for ACLSV and ASPV detections. The RT-LAMP assays for ACLSV and ASPV in pear samples were 104 and 103 times more sensitive than that of conventional RT-PCR assays. The RT-LAMP under optimal reaction condition was subsequently utilized in the detection of the two viruses in-vitro cultures of pear and field pear samples. This study provides a rapid and sensitive tool to determine the infection statues of the two viruses in pear certification program.
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Affiliation(s)
- Yongcan Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bingyu Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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46
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Yang S, Kim H, Lee KJ, Hwang SG, Lim EK, Jung J, Lee TJ, Park HS, Kang T, Kim B. Attomolar detection of extracellular microRNAs released from living prostate cancer cells by a plasmonic nanowire interstice sensor. NANOSCALE 2017; 9:17387-17395. [PMID: 29095457 DOI: 10.1039/c7nr04386d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Prostate cancer (PC) is the second leading cause of cancer death for men worldwide. The serum prostate-specific antigen level test has been widely used to screen for PC. This method, however, exhibits a high false-positive rate, leading to over-diagnosis and over-treatment of PC patients. Extracellular microRNAs (miRNAs) recently provided valuable information including the site and the status of the cancers and thus emerged as new biomarkers for several cancers. Among them, miR141 and miR375 are the most pronounced biomarkers for the diagnosis of high-risk PC. Herein, we report an attomolar detection of miR141 and miR375 released from living PC cells by using a plasmonic nanowire interstice (PNI) sensor. This sensor showed a very low detection limit of 100 aM as well as a wide dynamic range from 100 aM to 100 pM for all target miRNAs. In addition, the PNI sensor could discriminate perfectly the diverse single-base mismatches in the miRNAs. More importantly, the PNI sensor successfully detected the extracellular miR141 and miR375 released from living PC cell lines (LNCaP and PC-3), proving the diagnostic ability of the sensor for PC. We anticipate that the present PNI sensor can hold great promise for the precise diagnosis and prognosis of various cancer patients as well as PC patients.
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Affiliation(s)
- Siyeong Yang
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea.
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Hayward BE, Kumari D, Usdin K. Recent advances in assays for the fragile X-related disorders. Hum Genet 2017; 136:1313-1327. [PMID: 28866801 DOI: 10.1007/s00439-017-1840-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 12/17/2022]
Abstract
The fragile X-related disorders are a group of three clinical conditions resulting from the instability of a CGG-repeat tract at the 5' end of the FMR1 transcript. Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are disorders seen in carriers of FMR1 alleles with 55-200 repeats. Female carriers of these premutation (PM) alleles are also at risk of having a child who has an FMR1 allele with >200 repeats. Most of these full mutation (FM) alleles are epigenetically silenced resulting in a deficit of the FMR1 gene product, FMRP. This results in fragile X Syndrome (FXS), the most common heritable cause of intellectual disability and autism. The diagnosis and study of these disorders is challenging, in part because the detection of alleles with large repeat numbers has, until recently, been either time-consuming or unreliable. This problem is compounded by the mosaicism for repeat length and/or DNA methylation that is frequently seen in PM and FM carriers. Furthermore, since AGG interruptions in the repeat tract affect the risk that a FM allele will be maternally transmitted, the ability to accurately detect these interruptions in female PM carriers is an additional challenge that must be met. This review will discuss some of the pros and cons of some recently described assays for these disorders, including those that detect FMRP levels directly, as well as emerging technologies that promise to improve the diagnosis of these conditions and to be useful in both basic and translational research settings.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA.
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Schwinefus JJ, Baka NL, Modi K, Billmeyer KN, Lu S, Haase LR, Menssen RJ. l-Proline and RNA Duplex m-Value Temperature Dependence. J Phys Chem B 2017; 121:7247-7255. [PMID: 28737394 DOI: 10.1021/acs.jpcb.7b03608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temperature dependence of l-proline interactions with the RNA dodecamer duplex surface exposed after unfolding was quantified using thermal and isothermal titration denaturation monitored by uv-absorbance. The m-value quantifying proline interactions with the RNA duplex surface area exposed after unfolding was measured using RNA duplexes with GC content ranging between 17 and 83%. The m-values from thermal denaturation decreased with increasing GC content signifying increasingly favorable proline interactions with the exposed RNA surface area. However, m-values from isothermal titration denaturation at 25.0 °C were independent of GC content and less negative than those from thermal denaturation. The m-value from isothermal titration denaturation for a 50% GC RNA duplex decreased (became more negative) as the temperature increased and was in nearly exact agreement with the m-value from thermal denaturation. Since RNA duplex transition temperatures increased with GC content, the more favorable proline interactions with the high GC content duplex surface area observed from thermal denaturation resulted from the temperature dependence of proline interactions rather than the RNA surface chemical composition. The enthalpy contribution to the m-value was positive and small (indicating a slight increase in duplex unfolding enthalpy with proline) while the entropic contribution to the m-value was positive and increased with temperature. Our results will facilitate proline's use as a probe of solvent accessible surface area changes during biochemical reactions at different reaction temperatures.
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Affiliation(s)
- Jeffrey J Schwinefus
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Nadia L Baka
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Kalpit Modi
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Kaylyn N Billmeyer
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Shutian Lu
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Lucas R Haase
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
| | - Ryan J Menssen
- Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States
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Ishihara S, Kotomura N, Yamamoto N, Ochiai H. Ligation-mediated PCR with a back-to-back adapter reduces amplification bias resulting from variations in GC content. Anal Biochem 2017; 531:37-44. [DOI: 10.1016/j.ab.2017.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022]
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50
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Rani A, Taha M, Venkatesu P, Lee MJ. Coherent Experimental and Simulation Approach To Explore the Underlying Mechanism of Denaturation of Stem Bromelain in Osmolytes. J Phys Chem B 2017; 121:6456-6470. [DOI: 10.1021/acs.jpcb.7b01776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjeeta Rani
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Mohamed Taha
- Department
of Chemistry, College of Science, Sultan Qaboos University, PO Box 36, PC 123 Muscat, Oman
| | | | - Ming- Jer Lee
- Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei 10607, Taiwan
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