scholarly journals Uji Efektivitas Metode Isolasi DNA Genom Kopi Arabika (Coffea arabica L.) Asal Kabupaten Jayawijaya

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Arsyam Mawardi ◽  
Maria L. Simonapendi
Keyword(s):  
Genomic Dna ◽  
Dna Isolation ◽  
Dna Amplification ◽  
Initial Information ◽  
Arabica Coffee ◽  
Modified Method ◽  
Ctab Method ◽  
Young Leaves ◽  
Amplification Technique ◽  
The Difference

Genetic substance of DNA has many functions as a basic component of the organism. DNA can be obtained directly through the isolation of DNA. Isolation of genomic DNA Wamena arabica coffee is done by treating the young leaves to get DNA extract. This reasearch is intended to provide scientific contributions in an effort to screen the best methods of DNA isolation, including a modified extraction of Zheng et al method (2005), a modified method of Doyle and Doyle (1990), and method of George and Khan modificaation (2008) or CTAB method. All of methods were tested on Arabica coffee Jayawijaya Wamena. Testing was done by looking at the difference in quality and quantity of products in the form of genomic DNA concentration and DNA thickness, comparing with the marker DNA then electrophoresis on agarose gel. From the results of testing the effectiveness of three types of isolation methods, it was found that the method of George and Khan (2008) or CTAB genomic DNA  produce the best quality than other methods. In terms of quantity, the criteria in the form of DNA concentrations ranging from 100 ng λ-DNA/ml, λ-DNA 50 ng/ml, λ-DNA 10 ng/ml. Concentration of genomic DNA bands visible when the profile is visualized in gel electrophoresis with UV luminescence. This study will be a step and initial information about the genetic composition of a population of arabica coffee which still exists, and will be developed through DNA amplification technique. Key words: coffee, isolation of genomic DNA, CTAB method, profile band pattern

scholarly journals Optimizing the pure genomic DNA isolation procedure for Plectranthus amboinicus DNA – A prerequisite for further genomic Studies

2017 ◽  
Vol 2 (4) ◽  
Author(s):  
S. Manikandan ◽  
S. Ansarali ◽  
G.M. Alagu Lakshmanan
Keyword(s):  
Dna Barcoding ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Pcr Amplification ◽  
Leaf Tissue ◽  
Isolation Procedure ◽  
Modified Method ◽  
Genomic Dna Isolation ◽  
Young Leaves ◽  
Plectranthus Amboinicus

The DNA isolation procedure for different plant groups have been studied and standardized.  The isolation of pure genomic DNA is the most essential component for any type of molecular studies.  The present work is aimed to identify suitable DNA markers for the amplification of P.amboinicus  DNA  becomes a great hurdle  for DNA barcoding studies carried out by rbcL and matK primers Used in the members of Lamiaceae. To solve this problem, The DNA was extracted by three methods from fresh young leaf tissue of P.amboinicus. After the evaluationthe outcome of these methods, one most suitable modified method was selected for isolating DNA from young leaves of P.amboinicus and selected for suitable DNA barcoding markers for PCR amplification. The quality and quantity of DNAs are a prerequisite for genetic studies for a variety of plants including P.amboinicus. The quantity and quality of the DNA extracted by this method wasused for suitable DNA barcoding markers selection.

scholarly journals An improved method for genomic DNA extraction from strawberry leaves

2011 ◽  
Vol 41 (8) ◽  
pp. 1383-1389 ◽  
Author(s):  
Claudinéia Ferreira Nunes ◽  
Juliano Lino Ferreira ◽  
Mônique Carolina Nunes Fernandes ◽  
Sâmera de Souza Breves ◽  
Andressa Leal Generoso ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Extraction Methods ◽  
Isolation And Purification ◽  
Modified Method ◽  
Freeze Dried ◽  
Ctab Method ◽  
Young Leaves ◽  
Tissue Maceration

Several extraction methods of genomic DNA for identification and characterization of genetic diversity in different plant species are routinely applied during molecular analysis. However, the presence of undesirable compounds such as polyphenols and polysaccharides is one of the biggest problems faced during the isolation and purification of high quality DNA in plants. Therefore, achievement of fast and accurate methods for DNA extraction is crucial in order to produce pure samples. Leaves of strawberry genotypes (Fragaria ananassa) have high contents of polysaccharides and polyphenols which increase the sample viscosity and decrease the DNA quality, interfering with the PCR performance. Thereby, in this study we evaluated the quality and amount of genomic DNA extracted from young leaves of strawberry after tissue lyophilization and maceration in presence of polivinilpirrolidone (PVP). The CTAB method was used as reference procedure and it was modified to improve the DNA extraction. The modifications consisted of tissue lyophilization overnight until it was completely freeze-dried and addition of PVP during the tissue maceration in liquid nitrogen. The results showed the efficiency and reliability of the modified method compared to the unmodified method, indicating that combination of lyophilization and PVP improve the quality and amount of the DNA extracted from strawberry leaves.

scholarly journals Genomic DNA Isolation and Purification of Two Endemic Medicinal Plants (Pterocarpus Santalinus Linn.F & Pimpinella Tirupatiensis Bal&Subr) of Seshachalam Hills, Tirumala.

2012 ◽  
Vol 4 (1) ◽  
Author(s):  
S. Vipranarayana ◽  
T.N.V.K. V.Prasad ◽  
A. Rajinikanth ◽  
T. Damodharam
Keyword(s):  
Gel Electrophoresis ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Low Cost ◽  
Isolation And Purification ◽  
Genomic Dna Isolation ◽  
Pterocarpus Santalinus ◽  
Ctab Method ◽  
Endemic Medicinal Plant ◽  
High Level

Ptercarpus santalinus is an important endemic medicinal plant with high medicinal values that interfere with DNA extraction procedures and qualitative, quantitative agaros gel electrophoresis. An effective and low-cost protocol for isolating genomic DNA from the roots of Pterocarpus santilinus and Pimpinella tirupatiensis was described in this paper. It involved a modified CTAB method with distilled water pretreating samples.  The A260/A280 absorbance ratio of extracted DNA was found to be free from polysaccharide, poly-phenols and tannins contaminants ranged from 2.2 to 2.8 within the high level of purity.

scholarly journals OPTIMASI SUHU ANNEALING UNTUK PRIMER g-SSR DAN EST-SSR PADA KACANG HIJAU (Vigna radiata L.)

2019 ◽  
Vol 33 (1) ◽  
pp. 95-102
Author(s):  
Herman Herman ◽  
Lambok Nia Natalya ◽  
Suha Maudina Berampu ◽  
Dewi Indriyani Roslim
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Vigna Radiata ◽  
Genetic Information ◽  
Dna Isolation ◽  
Dna Amplification ◽  
Accurate Data ◽  
Young Leaves ◽  
Total Dna ◽  
Diversity Research

Mungbean (Vigna radiata L.) is one of important legume in Indonesia. G-SSR and EST-SSR markers had been widely used in mungbean genetic diversity research. DNA isolation and DNA amplification are required to obtain genetic information about mungbean to obtain accurate data on the genetic diversity of mungbean. This study aims to determine the Temperature of annealing (Ta) of the g-SSR and EST-SSR primer pairs. The total DNA was isolated from young leaves mungbean origin Pelalawan and the eight primer pairs of the g-SSR and EST-SSR were optimized. The optimal Ta for G2436, G3598, G2516, G7472, G0483. G1671, G3302, and G3427 were 50,55ºC, 51,15ºC,51,25ºC, 51,2ºC, 51,6ºC, 49,0ºC, 49,8ºC, and 52,8ºC respectively. Meanwhile, the optimal Ta for E51985, E19823, E24080, E22860, E26637, E16266, E11659, and E10675 were 52,2ºC, 54,4ºC, 52,5ºC,51,25ºC, 53,25ºC, 54ºC, 54,35ºC, and 53,6ºC respectively.

scholarly journals Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice

2019 ◽  
Vol 39 (03) ◽  
Author(s):  
B Priyadharshini ◽  
M Vignesh ◽  
M Prakash ◽  
R Anandan
Keyword(s):  
Genomic Dna ◽  
Large Scale ◽  
Dna Isolation ◽  
High Throughput Analysis ◽  
Ctab Method ◽  
Maximum Quantity ◽  
Rice Genotypes ◽  
Step Over ◽  
Generation Sequencing

The utilization and conservation traditional rice genotypes have attracted global attention. Optimization of DNA isolation protocol for genetic characterization of plants is a necessary and primary step. Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research, with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated DNA is prerequisite for successful and reliable large-scale genotyping analysis. Therefore, standardization of DNA isolation is a basic requirement. Here we employed three methods of DNA isolation namely, Dellaporta, Hi-purA and modified CTAB techniques for isolation of genomic DNA from 25 indigenous rice genotypes. From the results, it was found that genomic DNA isolated by modified CTAB method to be the most appropriate for extracting high quality and maximum quantity DNA suitable for genotyping. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements and gel electrophoresis.

scholarly journals Comparison of ORAGENE® and Mouthwashed-Based Saliva Collection Methods for Genomic DNA Isolation

2015 ◽  
Vol 8 (2) ◽  
Author(s):  
Ayesha A. Hassan
Keyword(s):  
Genomic Dna ◽  
Dna Isolation ◽  
Cost Effective ◽  
Non Invasive ◽  
Genomic Dna Isolation ◽  
Invasive Method ◽  
Saliva Collection ◽  
The Difference ◽  
Collection Methods

In recent years, saliva has been used as a non-invasive method of obtaining genomic DNA. Two common collection methods include mouthwash and commercially produced saliva kits. Here, a novel comparison between these two collection methods, using Scope® mouthwash and the Oragene®-Discover kit (OGR-250) from DNA Genotek Inc., was conducted to analyze differences in the quantity and quality of the DNA isolated, and cost effectiveness. The Oragene® kit yielded greater quantity of DNA, while Scope® mouthwash was more cost effective. The difference in yield was attributed to the larger volume of saliva obtained from the Oragene® kit. Isolation from both collection methods resulted in similar DNA quality.    Depuis quelques années, la salive est utilisée comme une méthode non-invasive pour obtenir de l’ADN génomique. Deux méthodes de collection communes sont par rince-bouche et par des trousses commerciales de collection de salive. Ici, une comparaison entre ces deux méthodes, utilisant la rince-bouche Scope et la trousse Oragene-Discover (OGR-250) de DNA Genotek Ink, a été conduite afin d’analyser les différences dans la quantité et la qualité d’ADN isolée ainsi que dans l’efficacité du coût.  La trousse Oragene a recueilli plus d’ADN, alors que Scope était moins cher. La différence en quantité est attribuée au plus grand volume de salive qui est obtenu grâce à l’Oragene. L’isolation par les deux méthodes résultait en une qualité similaire d’ADN.

scholarly journals DNA Isolation And Amplification of the rbcL (ribulose-1,5- bisphosphate carboxylase/oxygenase large subunit) gene of Caulerpa sp., Gracilaria sp., And Sargassum sp.

2020 ◽  
Vol 8 (2) ◽  
pp. 214
Author(s):  
Biondi Tampanguma ◽  
Grevo S. Gerung ◽  
Veibe Warouw ◽  
Billy Th Wagey ◽  
Stenly Wulllur ◽  
...  
Keyword(s):  
Target Gene ◽  
Dna Isolation ◽  
Large Subunit ◽  
Dna Amplification ◽  
Ammonium Bromide ◽  
Rbcl Gene ◽  
Bisphosphate Carboxylase ◽  
Plant Dna ◽  
Ctab Method ◽  
Amplification Process

DNA isolation and gene amplification of algae are significantly influenced by various factors such as characteristics and components of the algae cell wall. Therefore techniques and methods of DNA isolation in certain algae, sometimes only succeed in one particular species and can not be applied to another algae species. Based on that issue, this study was conducted with the aims to determine the succeed of DNA isolation and amplify the rbcL gene as a target gene for identification. Algae DNA was isolated by using innuPrep Plant DNA commercial kit, and the second one with a modified conventional Cetyl Trimetyl Ammonium Bromide (CTAB) method,  for the amplification process was using rbcL gene (ribulose-1,5-bisphosphate carboxylase / oxygenase large subunit) with two pairs of primers : rbcL 7F-753R and rbcL 577F-rbcSR. The results showed that the DNA of Gracilaria sp was succeed isolated by using CTAB method and it was denoted by the presence of DNA bands in agarose gel. Meanwhile DNA amplification for Gracilaria sp., and Sargassum sp., were succeed amplified with the appearance of DNA bands. But in algae Caulerpa sp., was only succeed on 1 pair of primary rbcL 7F and 7.Keywords : DNA, gene rbcL, algae Caulerpa sp., Sargassum sp., Gracilaria sp;AbstrakIsolasi DNA dan amplifikasi gen pada alga sangat dipengaruhi oleh beberapa faktor seperti karakter dan komponen pada dinding sel alga. Oleh karena itu proses isolasi DNA terkadang bisa berhasil pada satu jenis alga, namun tidak berhasil pada jenis alga lainnya. Oleh karena alasan tersebut, maka penelitian ini dilakukan untuk menentukan keberhasilan Isolasi DNA dan mengamplifikasi gen rbcL sebagai gen target identifikasi. Penelitian ini dilakukan dengan tahapan awal Isolasi DNA yang menggunakan kit komersil innuPrep Plant DNA Kit, dan metode konvensional Cetyl Trimetyl Ammonium Bromide (CTAB) yang telah dimodifikasi. Sedangkan untuk proses amplifikasi, menggunakan gen rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) digunakan dua pasang primer yaitu rbcL 7F-753R dan rbcL 577F-rbcSR. Hasil isolasi DNA dari alga Gracilaria sp berhasil diisolasi menggunakan metode CTAB yang ditandai dengan adanya pita DNA pada gel agarose. Amplifikasi DNA pada alga Gracilaria sp., dan Sargassum sp., berhasil diamplifikasi dengan munculnya pita DNA. Namun pada alga Caulerpa sp. hanya berhasil pada 1 pasang primer rbcL 7F dan753R.Kata kunci : DNA, gen rbcL, alga Caulerpa sp., Sargassum sp., Gracilaria sp.

scholarly journals AMPLIFIKASI DNA ALGA MERAH (RHODOPHYTA) Eucheuma sp.

2018 ◽  
Vol 6 (2) ◽  
pp. 26
Author(s):  
Paratiti Dewi Djakatara ◽  
Grevo S Gerung ◽  
Elvy L Ginting ◽  
Calvyn F.A. Sondak ◽  
Natalie D.C. Rumampuk ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Vitamin C ◽  
Red Algae ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Water Movement ◽  
Morphological Characteristics ◽  
Dna Amplification ◽  
Production Quality ◽  
Genomic Dna Isolation

Indonesia is a rich source of biodiversity and having a richness species of marine organisms. Indonesia has around 17,000 islands, a suitable place for seaweed growth because of its long coastline. There are around 782 species of seaweed in Indonesia with 196 species of green algae, 134 species of brown algae, and 452 red algae. Any of various seaweeds that potential sources of revenue and mostly can be found around Indonesian waters is Eucheuma sp. including in red algae and can produce carrageenan. Algae Morphological characteristics can be influenced by environmental factors among others: water movement, sunlight, temperature, salinity, and degree of acidity (pH). Beside environmental factors, genetic factors can influence differences in production quality and morphological characteristics of algae. To distinguish morphological characteristics can be analyzed molecularly. In molecular analysis, important steps that must be taken are DNA isolation and genomic DNA amplification. Isolation of red algae DNA in this study using the CTAB method which was modified from Doyle and Doyle (1987), Allen (2006) and Nugroho et al. (2015). Amplification of red algae genomic DNA (Eucheuma sp.) Using COX2 and rbcL genes on PCR. The success of the genomic DNA isolation process and the amplification of COX2 and rbcL genes from Eucheuma sp. detected through UV transilluminator after going through a gel electrophoresis process. Based on this study, several modifications need to be carried out in the DNA isolation stage Eucheuma sp. by using the method of Doyle and Doyle (1987) modifications that need to be carried out include adding vitamin C and liquid nitrogen. Furthermore DNA of Eucheuma sp. successfully amplified by using F-577 and R-753 primers. Indonesia merupakan negara yang kaya akan sumber keanekaragaman hayati dan memiliki kekayaan spesies laut tertinggi. Indonesia memiliki sekitar 17.000 pulau, menjadi tempat yang cocok untuk pertumbuhan rumput laut karena garis pantainya yang panjang. Terdapat sekitar 782 spesies rumput laut di Indonesia dengan 196 spesies alga hijau, 134 spesies alga cokelat, dan 452 alga merah.  Salah satu jenis rumput laut yang potensial dan banyak dijumpai di perairan Indonesia adalah Eucheuma sp. yang termasuk dalam alga merah dan  dapat menghasilkan karaginan. Karakteristik morfologi alga dapat dipengaruhi oleh faktor lingkungan antara lain : gerakan air, cahaya matahari, suhu, salinitas dan derajat keasaman (pH). Selain faktor lingkungan, faktor genetik dapat mempengaruhi perbedaan kualitas produksi dan karakteristik morfologi pada alga. Untuk membedakan karakteristik morfologi dapat dianalisis secara molekuler. Dalam analisis molekuler, langkah penting yang harus dilakukan adalah isolasi DNA dan amplifikasi DNA genomik. Isolasi DNA alga merah dalam penelitian ini menggunakan metode CTAB yang di modifikasi dari Doyle dan Doyle, (1987), Allen, (2006) dan Nugroho dkk, (2015).  Amplifikasi DNA genomik alga merah (Eucheuma sp.) menggunakan gen COX2 dan rbcL pada PCR. Keberhasilan proses isolasi DNA genomik dan amplifikasi gen COX2 dan rbcL dari Eucheuma sp. dideteksi melalui UV transilluminator setelah melalui proses elektroforesis gel. Berdasarkan penelitian ini, beberapa modifikasi perlu dilaksanakan dalam tahap isolasi DNA Eucheuma sp. dengan menggunakan metode Doyle dan Doyle, (1987) modifikasi yang perlu dilaksanakan meliputi penambahan vitamin C dan nitrogen cair. Selanjutnya DNA Eucheuma sp. berhasil diamplifikasi dengan menggunakan primer F-577 dan R-753.

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