Comparison of Different DNA Extraction Methods from Leaves and Roots of <i>Eurycoma longifolia</i> Plant

Abubakar, Bashir Mohammed; Izham, Nur Hazwani Mohd; Salleh, Faezah Md; Shamsir, Mohd Shahir; Wagiran, Alina

doi:10.1166/asl.2018.11456

Cited by 7 publications

(13 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The concentration of NaCl varied in lysis buffers. Using high concentrations of NaCl in the lysis buffer reduces polysaccharide coprecipitates in the extractant (Syamkumar et al, 2003 ; Abubakar et al, 2018 ), but as with high concentrations of CTAB, care must be taken to thoroughly clean the extraction as carryover can inhibit PCR amplification (Demeke and Jenkins, 2010 ). The Doyle and Doyle ( 1987 ) protocol called for 1.4 M NaCl, which is the most common concentration, but protocols ranged between 0.7–4 M (Saghai‐Maroof et al, 1984 ; Tel‐Zur et al, 1999 ).…”

Section: Discussionmentioning

confidence: 99%

“…Mixing during incubation varied among protocols. Abubakar et al ( 2018 ), for example, shook the tubes every 10 min during incubation, whereas Japelaghi et al ( 2011 ) shook and vortexed every 5 min. Vortexing has been shown to provide some benefits but risks shearing the DNA (Sharma et al, 2000 ).…”

Section: Discussionmentioning

confidence: 99%

“…Lysates become discolored as they oxidize, even turning black in some reactions. During oxidation, phenolic compounds covalently bond with DNA, and these bonds cannot be broken with traditional extraction protocols (Loomis and Battaile, 1966 ; John, 1992 ; Varma et al, 2007 ; Abubakar et al, 2018 ). Consequently, the DNA–phenol complexes formed during oxidation are discarded during the cleaning process due to their high molecular weight (Japelaghi et al, 2011 ), ultimately yielding little to no DNA.…”

mentioning

confidence: 99%

See 2 more Smart Citations

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

et al. 2023

View full text Add to dashboard Cite

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

et al. 2023

View full text Add to dashboard Cite

show abstract

“…In the current study, when the content of C. molybdites DNA added to the reaction system was 100 ng, the LAMP reaction was inhibited, and the color of the final product was an intermediate color of pink and yellow instead of yellow, which was consistent with the findings of Njiru et al (2008) (results were not shown in Figure 4 ). This is presumably due to the complexity of the mushroom matrix, which contains many polysaccharides and polyphenols ( Abubakar et al, 2018 ). Polyphenols can be oxidized after a long time, with irreversibly bound proteins and nucleic acids forming high molecular weight complexes ( Newbury and Possingham, 1977 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid and Visual Identification of Chlorophyllum molybdites With Loop-Mediated Isothermal Amplification Method

et al. 2021

View full text Add to dashboard Cite

Chlorophyllum molybdites is a kind of common poisonous mushroom in China that is widely distributed in different areas. Food poisoning caused by accidentally eating C. molybdites has become more frequent in recent years. In 2019, there were 55 food poisoning incidents caused by eating this mushroom in China. Mushroom poisoning continues to be a common health issue of global concern. When mushroom poisoning occurs, an effective, simple, and rapid detection method is required for accurate clinical treatment or forensic analysis. For the first time, we established a loop-mediated isothermal amplification (LAMP) assay for the visual detection of C. molybdites. A set of specific LAMP primers was designed, and the specificity was confirmed against 43 different mushroom species. The LAMP method could detect as low as 1 pg of genomic DNA. Boiled mushrooms and artificial gastric-digested mushroom samples were prepared to test the applicability of the method, and the results showed that as low as 1% C. molybdites in boiled and digested samples could be successfully detected. The LAMP method can also be completed within 45 min, and the reaction results could be directly observed based on a color change under daylight by the naked eye. Therefore, the LAMP assay established in this study provides an accurate, sensitive, rapid, and low-cost method for the detection of C. molybdites.

show abstract

“…As a medicinal plant, E. longifolia has been used in Malaysia for its anti-malarial property, anti-cancer property, and toxicity effect [1,4]. It is still more widely used due to its aphrodisiac property, mostly contributed by its root part [5]. Presently, over 200 commercialize Herbal Medicinal Products (HMPs) from this plant, especially the roots, are available in the market.…”

Section: Introductionmentioning

confidence: 99%

Comparative Evaluation of Different DNA Extraction Methods from E. Longifolia Herbal Medicinal Product

Abubakar

Salleh

Wagiran

et al. 2021

eFood

Self Cite

View full text Add to dashboard Cite

The aphrodisiac property of Eurycoma longifolia has led to an increase in the demand for its Herbal Medicinal Products (HMPs). However, the efficiency of such HMPs depends on the usage of their genuine raw materials. The conventional methods cannot identify species in processed form. The authentication of HMPs can be achieved effectively using DNA barcoding as the method species-specific. However, the use of this method solely relied on the extraction of high-quality DNA from the HMPs. Therefore, it is necessary to establish a satisfactory method for extracting high-quality DNA from the HMPs. Here, four DNA extraction methods were compared to evaluate the best protocol in yield, purity, polymerase chain reaction (PCR) amplification, sequencing, and species identification. The spectrophotometer analysis showed that the Nucleospin Plant II extraction kit has the best purity as this can be severely affected by the presence of various contaminants in the HMPs. Our findings reveal that DNA purity was more important as a predictor for PCR amplification than yield. Therefore, the present study results demonstrate that the Nucleospin Plant II extraction kit is the best because it produces the purest, amplifiable, and sequenceable DNA for identification and authentication of E. Longifolia HMPs.

show abstract

Comparison of Different DNA Extraction Methods from Leaves and Roots of Eurycoma longifolia Plant

Cited by 7 publications

References 0 publications

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Rapid and Visual Identification of Chlorophyllum molybdites With Loop-Mediated Isothermal Amplification Method

Comparative Evaluation of Different DNA Extraction Methods from E. Longifolia Herbal Medicinal Product

Contact Info

Product

Resources

About