Dna Extraction And Purification Of Plant Samples Biology Essay
Holy and sweet basil workss were grown at the National Plant Protection Experimental Station Reduit ( Ministry of Agro-Industry & A ; Food Security ) . All the necessary conditions such as foods and pesticides were given to the workss for good growing and development of healthy workss.
Young, stamp, unbruised and healthy foliages were picked in the forenoon from the Experimental Station, kept between damp tissue paper in a plastic bag kept off from sunshine and the fresh samples were brought to the research lab placed on an ice box for DNA extraction and farther analysis.
Genomic DNA was isolated from O.tenuiflorum, o. sanctum and O.basilicum specimems utilizing three protocols: the modified hexadecyltrimethylammonium bromide ( CTAB ) mini readying described by Doyle and Doyle 1990, with 1 % 2-mercapthoethanol as a reducing agent, the modified Na dodecyl ( SDS ) mini readying method of Edwards et Al. ( 1991 ) with 1 % 2-mercapthoetnahol as reducing agent and utilizing the modified Dellaporta and Doyle & A ; Doyle protocol method which are described below.
The samples isolated utilizing the above methods were purified as elaborate. To each tubing, 500 milliliter trichloromethane: iso-amylalcohol ( CIA 24:1 ) was added and the contents mixed by agitating for 15 min, followed by centrifugation at 12000 revolutions per minute for 15 min. The aqueous stage was transferred to a new tubing and so 200 milliliters 1M NaCl-TE added to the old tubing and shaken for 15 min. The old tubing was centrifuged for 15 min at 12000 revolutions per minute. The aqueous stage was transferred to the new tubing and assorted, followed by centrifugation at 12000 revolutions per minute for 15 min in order to settle any staying dust. The supernatant was so transferred to a new tubing. Ice cold isopropyl alcohol ( 700 milliliter ) was added to the sample and assorted gently, and centrifuged at 10,000 revolutions per minute for 5 min and the supernatant discarded. Cold 75 % ethyl alcohol ( 1000 milliliter ) was added to the pellet to rinse it thrice, and contents centrifuged at 5000 revolutions per minute for 5 min. The ethyl alcohol was discarded and the pellet air dried. The pellet was re-suspended in 200 milliliter sterile distilled H2O ( SDW ) and incubated overnight at 55A°C.
Note: Alterations were brought to process for the extraction of Deoxyribonucleic acid with the mini CTAB and SDS protocol every bit good for its purifications ; the nightlong incubation was non done alternatively after adding the sterile distilled H2O the pellet was kept frozen at -20A°c overnight and was so subjected for farther analysis.
126.96.36.199 RNase intervention for the mini CTAB and SDS readying
The Deoxyribonucleic acid was treated with DNase free Ribonuclease A ( 10 mg/ml ) . Large sums of RNA in the sample can chelate Mg2+ and cut down the output of the PCR ( Padmalatha and Prasad, 2006 ) . This measure removes RNA from the stray genomic DNA. RNase ( 10 I?l of 10 mg/ml ; Sambrook et al. , 1989 ) was added to 100 I?l of re-suspended DNA pellet and so incubated at 37°C over dark. Equal volume of ice-cold absolute ethyl alcohol was added to each sample and so centrifuged at 10,000 revolutions per minute for 10 min to re-precipitate the Deoxyribonucleic acid. This was done twice. The supernatant was poured away and the DNA pellets air-dried and re-suspended in 100 I?l dual unfertile distilled H2O ( dSDW ) .
2.3 RNASE TREATMENT OF GENOMIC DNA
100 I?l ( 0.1 milliliter ) of Deoxyribonucleic acid was put in an eppendorf tubing ( 6 eppendorf tubings in entire each incorporating DNA sample of several basil assortment ) .
1 I?l RNAse was added in the eppendorf incorporating the Deoxyribonucleic acid and the mixture was incubated at 37 A°C for 1 hr.
10 I?l of 3M Na ethanoate was so added.
100 I?l of phenol: trichloromethane: isoamyl ( 25:24:1 ) was added and assorted good by inverting the eppendorf tubing.
The eppendorfs were spinned at 10,000 revolutions per minute for 5 proceedingss.
The supernatant was collected and 100 I?l of trichloromethane: isoamyl ( 24:1 ) was added.
The eppendorfs were spinned once more at 10,000 revolutions per minute for 5 proceedingss.
The supernatant was collected into another clean eppendorf and 100 I?l of cold isopropyl alcohol was added ( left overnight at -20 A°C for DNA precipitation )
The eppendorfs were centrifuged at maximal R autopsy for 30 proceedingss after which the isopropyl alcohol supernatant was discarded.
The DNA pellet was washed with 70 % intoxicant and the pellet was dried in the centrifugal evaporator.
The DNA pellet was dissolved in 100 I?l sterile distilled H2O.
Samples were stored in -20A°c.
2.4 Evaluation of quality and measure of Deoxyribonucleic acid
Quality Assessment of DNA
In the experiment carried out, 10 I?l Deoxyribonucleic acid was assorted with 990 I?l unfertile distilled H2O in a vitreous silica cuvette for each assortment and the optical density of DNA was read at wavelengths 230, 260 & A ; 280 nanometer severally in the spectrophotometer. The optical density reading of all the 3 species were taken and the pureness and measure of stray DNA were determined spectrophotometrically.
Wavelength ratios demoing quality of Deoxyribonucleic acid
OD260/OD280 =1.8 or 1.9 Pure Deoxyribonucleic acid
OD260/OD280 & gt ; 1.8 Deoxyribonucleic acid contaminated with RNA
OD260/OD280 & lt ; 1.8 Phenol or protein taint
OD260/OD230 & lt ; 1.8 Polysaccharides or amylum taint
Quantity finding of Deoxyribonucleic acid
The expression used to cipher the Deoxyribonucleic acid concentration:
Deoxyribonucleic acid concentration ( I?g/I?l ) = Optical denseness value at 260 nm x 0.05 ten dilution factor.
The dilution factor is 1000 divided by 10, since 10 I?l DNA was diluted with 990 I?l Sterile distilled H2O doing a entire volume of 1000 I?l.
2.5 Electrophoresis Analysiss
The Deoxyribonucleic acid samples were assorted with the gel lading buffer and loaded onto a 1.5 % agarose gel and left to migrate for about one hr at 90 Vs. The volumes used were 7I?L of Deoxyribonucleic acid and 3I?L of Dye. The Deoxyribonucleic acid was so stained with Ethidium Bromide and viewed under UV visible radiation.
2.6 Preparation of an Agarose gel medium of 1.5 % concentration ( See Appendix ) .
2.7 RAPD Marker Analysis
A set of 12 primers ( OPK-05 ; OPL-05 ; OPO-03 ; OPC-08 ; OPW-04 ; OPC-03 ; OPC-16 ; OPP-20 ; OPA-18 ; OPA-10 ; OPB-11 and OPD-13 ) were used.
The DNA sample was diluted from the stock with nanopure H2O doing up 50 I?l and placed on ice.
Dilution of DNA sample = 20 ng/ I?l x 50 I?L + dilution with nanopure H2O
[ DNA ] 260 nanometer
Table 5. Optimization Protocol for RAPD Reaction mixture
Volume per reaction tubing ( I?l )
Volume for 3 tubings ( I?l )
Chemical reaction buffer
Deoxyribonucleic acid Taq
Template Deoxyribonucleic acid
The maestro mix was prepared on ice for a sum of 3 PCR tubings as follows:
Two PCR tubings were used for each primer:
1st PCR tubing: Positive control which contained 2 I?l of the diluted DNA.
2nd PCR tubing: Negative control which contained no Deoxyribonucleic acid.
2.8 Detailed Stairss of PCR ( See Annex )
Deoxyribonucleic acid elaboration was carried programmed with 3 min at 94A°C for initial denaturation, followed by 35 rhythms of 54sec at 94A°C, 45 sec at 43A°C, 2 min at 72A°C, and a concluding 5 min extension at 72A°C. After elaboration, the Deoxyribonucleic acid fragments were separated by cataphoresis for about 3hours under changeless electromotive force ( 90 V ) in 1.5 % agarose gel submersed in 1X TBE buffer. The gels were stained with ethidium bromide solution and observed under ultraviolet visible radiation. A 1 kilobit fragment size marker was used as a mention to let comparing among the different gels ( 1kb ladder ) .
2.9 Different molar concentrations of Template DNA were used for showing of primers
[ ng/I?l ]
Final molar concentration
[ nanogram ]
Volume of diluted DNA per
reaction tubing [ I?l ]