Optimization Of DNA Isolation Biology Essay

Conservation of sandalwood familial resources is chiefly concerned with keeping all the familial fluctuations contained within and among carefully selected mark species. Hence DNA based markers RAPD which are first-class tools for analyzing diverseness at the DNA degree and aid in riddance of extras in germplasm and discriminating cultivars are widely used. Where we present the optimisation of DNA isolation and PCR status for RAPD analysis of selected Santalum album genotypes collected from Tamil Nadu, Karnataka and Andhra Pradesh.

It is of great economic importance because of its fragrant duramen and oil. ( Rogers, 1996 ) India histories for about 99 per centum of sandal oil manufacturer in the universe. Sandalwood occupies an of import topographic point in the ecological, cultural and religious heritage of India. Extraction of high quality Deoxyribonucleic acid from sandalwood foliages is a hard undertaking due to their stiff cell wall which is composed of complex saccharides.

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Sandalwood foliages are besides rich in secondary metabolites, such as polyphenols, tannic acids and polyoses, which pose major job in DNA purification, as they are hard to divide from DNA. Many of the initial jobs encountered in the extraction of high quality DNA have been attributed to these contaminations ( Murray and Thompson,1980 ) . A modified CTAB method DNA extraction ( Probeski et al.,1997 ) was followed which is comparatively speedy, cheap and consistent for extraction of DNA.Keywords: Deoxyribonucleic acid Isolation, Sandalwood, PCR Amplification, RAPD Analysis, DNA markersIntroductionSantalum album is of great economic importance because of its aroma duramen and oil. Which have high value in the decorative, perfumery and handcraft industries. Santalum album leaves contain high sum of polyphenols, tannic acids and polyoses.

Problems encounter in the isolation and purification of DNA because of debasement of DNA due to endonucleases, extremely syrupy polyoses, inhibitor compounds like polyphenols and other secondary metabolites which straight or indirectly intervention with enzymatic reaction. These contaminant causes many jobs in PCR elaboration, interfere with DNA elaboration affecting random primers and consequence in improper priming of DNA templet during thermic rhythm sequencing Pikkart et al10Assorted protocols for DNA extraction have been successfully applied for this we used four methods 1 and 2 method utilizing CTAB 3 and 4 methods utilizing SDS methods. These are compared for isolation of Deoxyribonucleic acid from sandalwood foliages.

The protocol affecting SDS was uniformly unsuccessful in efforts to pull out high quality DNA. The chief obstruction was trouble in rhenium fade outing Iso propyl alcohol precipitated DNA in TE buffer.Optimization of PCR enzymatic method of doing multiple transcripts of predicted section of DNA. It commence with denaturation measure of the Deoxyribonucleic acid followed by primer tempering temperature, concluding extension and constituents in PCR mixture influence the concluding merchandise. Hence these conditions have to be optimized in order to bring forth enlightening and consistent finger prints.


Plant stuff

Material from different ringers of Santalum album was obtained from germplasm block maintained by Institute of Wood Science and Technology ( IWST ) , Bangalore, were sandalwood genotypes procured from different geographical parts of India are conserved.

The present survey was carried out on a set of 30 indiscriminately selected ringers, collected from different provinces viz. , Karnataka ( 12 ) , Tamil Nadu ( 14 ) , Kerala ( 3 ) and Andhra Pradesh ( 1 ) . Approximately 8-10g of dried foliages were powdered by utilizing “ Mixer ” for 45-60 seconds and sieved through a 60 mm-mesh screen to obtain a all right pulverization. The needed measure of powdery leaf sample was weighed and used for DNA extraction.SolutionThe extraction buffer dwelling of 6 % ( w/v ) CTAB, 5M NaCl, 1M Tris base ( pH 8 ) 0.5 M EDTA ( pH 8 ) ; trichloromethane: Isoamyl alcohol 24:1 v/v solution, 1 % I?-Mercaptoethanol, 3M Sodium ethanoate are prepared.

Deoxyribonucleic acid ExtractionRecently matured leaves from 3rd to 5th node were collected before blossoming. Processing of excessively immature foliages resulted in charring of tissue while drying14. Leafs are dried in hot air oven at 40°C for 24 hour. Dried foliages were powdered and sieved through 60mm mesh to obtain all right pulverization. Hence, four different genomic DNA purification protocols outlined by different workers with minor alteration were evaluated to insulate high molecular weight Deoxyribonucleic acid from sandalwood foliages.The foliage sample for DNA extraction was prepared by following Tai and Tanksley method15 with minor alterations. They were wiped and dried at 40Es C for 24 hours. The dried foliages were so sealed in plastic bags and used subsequently.

Approximately 8-10g of dried foliages were powdered by utilizing “ Kanchan Mixer ” for 45-60 seconds and sieved through a 60 mm-mesh screen to obtain a all right pulverization. The needed measure of powdery leaf sample was weighed and used for DNA extraction.The protocol outlined by Porebski et al11 was followed with minor changes. 500 milligram of the foliage pulverization with 20 milliliters extraction buffer ( 20 millimeter Ethylene Diamine Tetra Acetic acid pH 8.0, 100 mM Tris-Base pH 8.

0, 1.4 M NaCl, 3 % CTAB and 2 % Poly Vinyl Pyrolidone with 1 % I?-mercaptoethanol ) was incubated on a H2O bath at 65A° C for one hr with intermittent shaking. The mixture was so cooled on ice bath and 10 milliliter of cold trichloromethane: isoamylalcohol ( 24:1 v/v ) was added and the contents were assorted good by inverting the tubing and spun at 9000 revolutions per minute for 20 proceedingss. The supernatant was transferred to a fresh tubing and this measure was repeated four times till clear supernatant was obtained. To the aqueous stage, half the volume of 5 M NaCl was added and gently assorted followed by add-on of one volume of cold propyl alcohol to precipitate the Deoxyribonucleic acid. The solution was kept at 4A° C over dark to speed up the precipitation of DNA. The mixture was spun at 10,000 revolutions per minute for 25 proceedingss to pellet the Deoxyribonucleic acid. The pellet was washed with 70 per cent ethyl alcohol and dried in a vacuity drier for one hr.

The pellet was resuspended in 300 I?l of TE buffer ( 10 millimeter Tris HCI and 1 millimeter EDTA pH 8.0 ) and the samples were stored in eppendorf tubing at -40A° C until farther analysis.


Collection of late matured foliages of Sanatalum album and drying them at 40A° C for 24 hours was found optimum for pulverizing and further processing for DNA extraction ( Fig 4a ) .

Prolonged drying beyond 24 hours was found detrimental for the quality of DNA. Use of high salt concentrations ( 3 % CTAB, 1.4M NaCl ) , 2 per cent PVP, 1 per cent b-mercaptoethanol in 20 ml extraction buffer for 400 milligram of dried foliage pulverization and an drawn-out RNAse intervention followed by phenol-chloroform ( 1:1 ) extraction resulted in high sums of good quality DNA suitable for RAPD analysis. The quality of DNA isolated by method 2 was found good and complete cleavage of Deoxyribonucleic acid by HindIII was observed, where as digestion of DNA was uncomplete, partial for other methods ( Fig. 4b ) .

The OD 260/280 ratios ranged from 1.40 to 1.85 ( Table 3 ) . The success of different protocols was evaluated based on the utility of DNA isolated for PCR elaboration.

Deoxyribonucleic acid purification and appraisal

Since the DNA isolated by the above methods may incorporate considerable sum of RNA, polyoses, phenoplasts and other drosss, the infusion was subjected to farther purification as follows To take RNA, each sample was incubated with 3 g/ml RNAse on a H2O bath at 37A° C for over dark. The proteins were removed by blending the solution with equal volume of phenol, so with phenol: trichloromethane ( 1:1 v/v ) and eventually with trichloromethane ( spun at 10,000 revolutions per minute for 10-15 proceedingss ) . Two volume of cold ethyl alcohol was added to precipitate DNA.

The precipitation was improved by maintaining at -20A° C for 1 hr. Then spun at 12,000 revolutions per minute for 20 proceedingss to pellet the Deoxyribonucleic acid. The pellet was washed with 70 per cent ethyl alcohol and dried in a vacuity drier for one hr. The pellet was dissolved in 300 I?l of TE buffer and to it l/10th volume of 3 M Na ethanoate was added and left overnight. The supernatant was collected after 24 hours by whirling at 12,000 revolutions per minute for 20 proceedingss. The Deoxyribonucleic acid was quantified by utilizing “ ELICO Double beam Spectrophotometer ” and verified by cataphoresis on 0.8 % agarose gel ( Bangalore Genie ) based on the strengths of set when compared with the lambada DNA marker used to find the concentration. The pureness of sandalwood genomic DNA was evaluated by mensurating optical density ( A260 nm/A280 nm ratio ) with a Double Beam UV spectrophotometer.

Pure DNA readyings show a ratio between 1.8 to 2.0.

Optimization of RAPD reaction

Polymerase concatenation reaction is powerful engineering used in many countries of molecular biological science which allows in vitro elaboration of specific DNA sequence7. Deoxyribonucleic acid extracted from assorted Santalum album species, oligonucliotide primers from a to omega series ( Operon Technologies Inc, USA ) were used for elaboration and to standardise the PCR conditions.

The reactions were carried out in DNA thermo cycler ( MJ Research Inc, USA ) . The PCR reactions were carried out in a concluding volume of 25 Aµl reaction mixture incorporating 25 ng templet DNA 2.5 Aµl 10x buffer, 4.3 Aµl of 1.25mM dNTPs, 1 unit of Taq DNA polymerase, 3mM Mgcl2 and 5 pico moles primer ( Integrated DNA engineerings Inc ) .

The PCR reaction was evaluated for 30, 40 and 45 rhythms. The PCR mixture was overlaid with hot burn cap. Amplification was achieved in a MJ Research Thermalcycler ( PTC-100 ) programmed for initial denaturation at 95A°C for four proceedingss, followed by 45 rhythms ; each rhythm dwelling of denaturation at 94A°C for one minute, primer tempering at 35A°C for 2 proceedingss, primer extension at 72°C for 2 proceedingss, and a concluding extension of 10 proceedingss at 72A°C.

The PCR reactions were repeated three timesAmplification merchandise were resolved by cataphoresis in 1.2 per centum agarose gel containg ethidium bromide ( 0.5Aµg/ml ) utilizing 1x TBE buffer Wellss were loaded with 25 Aµl of reaction mixture assorted with 5 Aµl of lading buffer. Electrophoresis was run at changeless electromotive force of 60 Vs for 5 to 6 hour in 1x TBE buffer after that photographed under UV visible radiation by utilizing Entire Lab Gel certification system.


The pureness of the stray Deoxyribonucleic acid of Santalum album checked utilizing dual beam spectrophotometer to look into the quality as it showed a reading between 1.

8 to 2.0, after ciphering the 260/280nm optical density. The Deoxyribonucleic acid outputs obtained were ranged from the 1 to 2 Aµg/Aµl. The size, pureness and unity of DNA isolated were determined by agarose gel ( 0.

8 % ) cataphoresis utilizing I» phage DNA cleaved with HindIII as a size criterion. The quality of DNA obtained by different methods was compared by curtailing with 2 units of HindIII limitation enzyme per mcg of DNA. Chemical reactions were incubated at 37°C for nightlong and so subjected to agarose gel cataphoresis, which was carried out in a horizontal gel system on 0.8 per cent with 1 Tens TBE buffer at changeless electromotive force of 60v for 4 to 6 hours and staining the gel with ethidium bromide ( 0.5 Aµg/ml ) . The size of the amplified fragment 100bp to 4kbp.


First and foremost my thanks must travel to my supervisor Dr. R.

Nelson M.sc. , Ph.D. for his counsel and great support throughout my surveies. I would besides widen my thanks to the A. Prasad Babu, DRR, Hyderabad for his valuable suggestions.

And thanks to Institute of Wood Science and Technology, Research Divisions, Bangalore-560 003, India. For their sort aid in sample aggregation.

Table 3.

Comparison of DNA outputs from sandalwood foliage tissue utilizing different methods of DNA isolation.

SI.NOPurification MethodDry weight of leaf tissue( milligram )DNA output ( mg/g dry tissue ) *OD ratio 260/280PCRAmplification1CTAB50045.21.





3South dakota5007.01.


4South dakota50022.51.55


* Average of 7 reproductions,+ Poor elaboration,- No elaboration++ Good elaboration,The pureness of DNA obtained from assorted ringers varied from 1.

70 to 2.01 ( Table 4 ) indicating that the Deoxyribonucleic acid was comparatively of high pureness and was suited for PCR elaboration.

Table 4.Absorbance and yield ratios of Deoxyribonucleic acid from genotypes obtained after purification




Deoxyribonucleic acid output

( I?g/g dry wt. )

OD ratio

( 260:280 )

1T1 Kumbakonam682.002T2 Coimbatore1021.863T3 Hosur961.

914T4 Vellore931.865T7 Vellore681.806T9 Salem851.817T15 Theosophical socity, Madras741.

908T21 Tirunelveli981.809T24 Dharmapuri1101.7010T25 Thombakal RF, shanimadu, Harur, Chitteri, Dharmapuri1202.

011T26 Dharmapuri952.0112K3 Hallihatti, Rani bennur, Gadag799.513K7 Banglore851.9814K9 Banglore1201.

8015K14 Kolar901.9116K25 Kuderekonda ayanur Shimoga1021.8017KL1 Munnar951.8818KL2 Anackelpety maryur Munnar841.8819KL3 Munnar1201.8620AP4 Nehru menagerie Hyderabad961.9621K6 Banglore982.

0122K8 Banglore1141.7223K10 Banglore891.8824K11 Chamarajanagar971.

8925K13 Chamarajanagar1021.9126K16 Chamarajanagar921.8027K27 Sagar861.8028T12 Salem961.8629T13 Salem921.9630T19 Tirunelveli1221.91

Agarose ( 0.

8 % ) gel cataphoresis of sandalwood genomic DNA isolated by different methods

1 2 3 4 5 6 7 8 9 10

Figure- 4a

Lanes 1 & A ; 2: Deoxyribonucleic acid obtained by method 1 ( Doyle and Doyle, 1987 )Lanes 3 & A ; 4: Deoxyribonucleic acid obtained by method 2 ( Porebski et al. , 1997 )Lanes 5 & A ; 6: Deoxyribonucleic acid obtained by method 3 ( Edwards et al. , 1991 )Lanes 7 & A ; 8: Deoxyribonucleic acid obtained by method 4 ( Do and Adams, 1991 )Lanes 9 & A ; 10: Deoxyribonucleic acid obtained by method 2 ( Porebski et al. , 1997 )

Agarose ( 0.8 % ) gel demoing HindIII digestion of sandalwood genomic DNA Isolated by different methods

M 1 2 3 4

Figure- 4b

Lane M: cubic decimeter DNA/HindIII digest markerLanes 1: Deoxyribonucleic acid obtained by method 1 ( Doyle and Doyle, 1987 )Lanes 2: Deoxyribonucleic acid obtained by method 2 ( Porebski et al. , 1997 )Lanes 3: Deoxyribonucleic acid obtained by method 3 ( Edwards et al.

, 1991 )Lanes 4: Deoxyribonucleic acid obtained by method 4 ( Do and Adams, 1991

Table- 5

PCR Optimum concentration and conditions for RAPD analysis


PCR elaboration

Hot start ( 95A°C )Denatruration ( 94A°C )Annealing ( 35A°C )Extension ( 72A°C )Number of rhythms2min, 3min, 4min, 5min30sec, 1min, 1.5min1min,1.5min,2.0min1min,1.5 min,2.0min30,40,45 Cycles4min1min2.0min2.0min45 Cycles

RAPD Protocol

Template Deoxyribonucleic acidMgcl2dNTPsTaq polymerase10-15ng,25-30ng,40-50ng1.0mM,1.5mM,2.0mM,2.5mM150mM,200mm,215mM,225mM5 pico moles25-30ng2.0mM215mM5 pico


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