Optimization of DNA Extraction Methods from Garcinia species for ISSR-PCR, RAPD-PCR and DNA Barcoding

Anerao, Jayesh; Jha, Vikas; Desai, Nitin

doi:10.3923/ajbkr.2017.35.42

Cited by 13 publications

(9 citation statements)

References 13 publications

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“…The method is developed especially when morphology based taxonomy is insufficient to resolve taxonomic problems. PCR success is one of important level to obtain robust sequence for barcoding research [16]. In this study, PCR amplification for all regions were successful in producing bands for all samples.…”

Section: Discussionmentioning

confidence: 67%

“…Numerous studies have been documented to detect standards of an ideal DNA extraction method. High DNA yield, low price, less laborious are accepted an important part of these standards [16]. Commercial kits tested here have comparable price and GeneAll and Gene Matrix are the minimum prices.…”

Section: Discussionmentioning

confidence: 93%

“…DNA barcoding is a tool for fast and accurate identification of organisms. The main goal of plant DNA barcoding is to use short and standardized DNA fragments promoted by CBOL (Consortium for the Barcode of Life) for identification and particularly, plant DNA barcoding researches depend on high yields of pure genomic DNA [16]. An efficiency of different extraction methods have been also tested several times using leaves for different purposes [e.g., 13,[17][18][19][20][21] and some of them were specifically focused on suitable DNA isolation methods for DNA barcoding research [e.g., 16,22].…”

Section: Introductionmentioning

confidence: 99%

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DNA from Leaf or Stem: A Comparative Work on Dianthus L. for DNA Barcoding Analysis with Four Commercial Extraction Kits

Aydın

Şenova

Koch

et al. 2020

Hacettepe Journal of Biology and Chemistry

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yaprak ve gövde dokusu DNA barkodlama çalışmaları için kaliteli ve yüksek genomik DNA elde etmek amacıyla test edilmiştir. Geleneksel olarak yaprak dokusu genomik DNA kaynağı olarak kullanılmaktadır fakat Dianthus taksonları yaprak sklerankima dokusu nedeniyle bu bakımdan sorunludur. Genomik DNA, üretici firmaların sağladığı protokole göre elde edilmiştir ve yedi barkod bölgesi PCR yöntemiyle çoğaltılmıştır. İzole edilen DNA konsantrasyonu florometrik yöntemle ölçülmüş, PCR ürünleri agaroz jelde görüntülenmiştir. Sonuçlar, DNA barkodlama çalışmalarında kullanılabilecek PCR başarısı bakımından değerlendirilmiştir. Ayrıca, kullanılan ekstraksiyon kitleri iş gücü, fiyat ve zaman bakımından değerlendirilmiştir. Sonuçlarımıza göre, yaprak ve gövde dokusundan genomik DNA ekstraksiyonu başarıyla gerçekleştirilmiştir. Tüm ekstraksiyon kitleri PCR amplifikasyonu bakımından başarılı olmasına rağmen en yüksek verim GeneMATRIX kiti kullanılarak elde edilmiştir.

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Section: Discussionmentioning

confidence: 67%

Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

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DNA from Leaf or Stem: A Comparative Work on Dianthus L. for DNA Barcoding Analysis with Four Commercial Extraction Kits

Aydın

Şenova

Koch

et al. 2020

Hacettepe Journal of Biology and Chemistry

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“…Unlike the completely white precipitates obtained from the double-lysis method (Fig. 1b), conventional Trizol-extraction produced more voluminous, yet dark reddishly colored sediments, indicative of coprecipitated polyphenols [16,17]. The integrity of isolated RNA from strawberry leaves was then visualized by gel electorphoresis on a 1.5% agarose gel (Fig.…”

Section: Discussionmentioning

confidence: 99%

Double lysis: an integrative time-saving method yielding high-quality RNA from strawberry

Hazman

Kabil

Elhamid

et al. 2020

Journal of Genetic Engineering and Biotechnology

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Background: The isolation of high-quality RNA from strawberry leaves and fruits is notoriously cumbersome. Both tissues are extremely rich in active secondary metabolites, as phenolics and pigments that inevitably perturb the isolation of RNA. Many protocols have been developed to address this problem. However, they are either costly, or time-consuming, in particular for high number of many plant samples. We describe here a new method with an easy-to-handle approach to obtain high-quality RNA from strawberry leaves and fruits. The method, referred to as double lysis, uses a novel combination of CTAB and Trizol protocols. Results: Compared to conventional Trizol-dependent protocols, either used individually, or in a commercial spincolumn kit, the new method yields RNA at lower costs, but of significantly improved quality. The RNA obtained by double lysis was very pure as indicated by 260/280 ratios of 2.06 (leaves) and 2.07 (fruits), while 260/230 ratio was 2.07 and 1.75, respectively. Also visually, RNA sediments from double lysis showed a white color, indicative of efficient elimination of polyphenolics and pigments. In contrast, traditional Trizol method produced reddish precipitates. The purity of RNA isolated by double lysis enabled successful removal of genomic DNA and, thus, allowed for more efficient cDNA synthesis and RT-PCR. In addition, the suggested method is able to yield RNA with fully preserved integrity from strawberry leaves, fruits in addition to petals and roots. Conclusion: Double lysis is a new RNA isolation protocol developed through the integrative coupling of CTAB and Trizol reagents. The method is cost-effective, robust, time-saving, and can cope even with recalcitrant plant tissues with high contents of phenolics and pigments, such as strawberry leaves and fruits.

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“…Other study carried out in Litchi chinensis (Arruda et al, 2017;Puchooa, 2004) also reported that increase in the concentration of β-mercaptoethanol helped to extract clear DNA pellet. Polyphenols often damage extracted genomic DNA and make some enzymes inaccessible (Anerao et al, 2016). The use of phenol: choloroform: isoamyl alcohol effectively removed polyphenols and yielded pure genomic DNA.…”

Section: Discussionmentioning

confidence: 99%

DNA isolation and optimization of PCR protocol for ISSR analysis of Girardinia diversifolia: A medicinal and economic plant species from Nepal Himalaya

Subedee¹,

Tripathi²,

Chaudhary³

2020

Afr. J. Biotechnol.

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Optimization of DNA Extraction Methods from Garcinia species for ISSR-PCR, RAPD-PCR and DNA Barcoding

Cited by 13 publications

References 13 publications

DNA from Leaf or Stem: A Comparative Work on Dianthus L. for DNA Barcoding Analysis with Four Commercial Extraction Kits

DNA from Leaf or Stem: A Comparative Work on Dianthus L. for DNA Barcoding Analysis with Four Commercial Extraction Kits

Double lysis: an integrative time-saving method yielding high-quality RNA from strawberry

DNA isolation and optimization of PCR protocol for ISSR analysis of Girardinia diversifolia: A medicinal and economic plant species from Nepal Himalaya

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