Estriction Enzyme Digestion Of Bacteriophage Essay

The molecular biological science industry is immensely increasing due to the increasing usage of limitation enzymes in the coevals of fragments which can farther be used in cistron analysis such as RFLP and cistron cloning techniques. In this practical, limitation enzymes EcoRI, BamHI, and HindIII were used to cut up ? DNA as both individual enzymes and besides a combination of the different enzymes, the mixture of the Deoxyribonucleic acid and the enzymes were so loaded unto 0.8 % agarose gel in order to divide the fragments whose sizes could be measured in order to pull a limitation map. This practical nevertheless was non successful and hence appropriate fragment sizes could non be worked out.

Since its first isolation ( Smith et al 1970 ) limitation enzymes ( RE ) has become a major tool utilised by research worker to cut genomic DNA into smaller fragment utile for look intoing cistron alliance, activity and look through limitation fragment lenght polymorphism [ RFLP ) ( Hartwell et al 2003 ) . RE originates from bacteriums and serves as a signifier of immune defense mechanism against viral infection by digesting the viral DNA. These enzymes recognizes a specific sequence of bases anyplace within the genome and so serves two covalent bond in the sugar-phospahte anchor at a peculiar place within or near that sequence. Over 3000 limitation enzymes have been identified and classified, runing from type I-III based on fractional monetary unit fundamental law, cleavage place, sequence specificity and cofactor demands. Type I RE are rather complex as they cuts Deoxyribonucleic acid at random locations every bit far as 1000bp from the acknowledgment site. They composed three different fractional monetary units M ( alteration ) , R ( limitation ) and S ( specificity ) that form multifunctional enzymes with limitation, methylase and ATPase activities. Type III RE are hetero-oligomeric that composed of two fractional monetary units ( RESs and Mod ) , With similarity to type I enzyme they are besides ATP dependant ( encoded by Res ) , the Mod possess sequence specific methylation limitation and DNA dependent nucleoside triphosphatase activities. These sequence recognises the short 5-6 bp long asymmetric DNA and later split Deoxyribonucleic acid at non-specific loci adjacent to the site 25-28 bp bases 3? ( ) . Type II RE are preponderantly used in biotechnology for DNA analysis and cistron cloning, since 1997 over 1000 new RE has been identified. They recognise short sequence 4-8bp and split within or shut to propinquity of the acknowledgment sequence in the presence of Mg. In this probe Three type II RE ( HIND III, BAMH I, and ECORI ) are used in a series of individual, multiple and ternary enzymatic digest utilizing lambda ( ? ) DNA as a substrate. Bacteriophage ? DNA is a additive molecule incorporating 4800kb that originates from phage Lambda virus. It ‘s a good known substrate for RE digestion. All three enzymes were isolated from bacteriums. EcoRI from Escherichia.coli is specific for cutting GAATTC and produces gluey terminals with the 5 ‘ terminal of DNA ( ) , while HindIII isolated from Haemophillus influenza cleaves between the Adenine- Adenine ( AA ) which causes 5 ‘ terminals to overhang ( ) BamHI isolated from Bacillus.Amiloliquefaciens is an enzyme that ‘s extremely utile ; because of its ability to go forth the GATC hanging after enzymic cleavage therefore able to attach to other enzymes ( Becker et al 1990 ) . These enzymes are used to digest ? DNA and evaluated gel cataphoresis

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Method

SOLUTIONS AND REAGENT

Fast digest enzymes EcoRI® , BamHI® and HindIII® , 10x TE buffer obtained from fermentas. Deoxyribonucleic acid methylated, bacteriophage ( Lambda Phage ) from E. coli host strain W3110 ( 10mM Tris-Hcl at a pH of 8.0 and 1mM EDTA ) and HindIII DNA ladder obtained from SIGMA-ALDRICH. Distilled H20 ( dH2O ) ,0.8 % agrose gel supplied by Kingston university. 7 epoendorf tubings were labelled harmonizing to the limitation enzyme digest reaction. First three ( individual digest check ) tube 1-3 contained 11µl of dH2O, 2µl of ? DNA, 2µl of 10x TE buffer and cleavage were initiated by add-on of 5µl of fast digest EcoRI, BamHI and HindIII severally to a concluding volume of 20µl in each tubing. Tube 4-6 ( dual digest check ) contained 6µl of dH2O, 2µl of ?DNA, 2µl of 10x TE buffer and dual digestion was initiated by add-on of 5µl of EcoRI/BAMHI each, EcoRI/HindIII, and BamHI/HindIII severally to a concluding volume of 20µl in each tubing. The concluding tubing 7 ( ternary digest check ) contained 1µl of dH2O, 2µl of 10X TE buffer, 2µl of ? DNA and ternary digestion was initiated by add-on of 5µl of EcoRI, BamHI and HINDIII each. The tubings were centrifuged and placed in a 650C H2O bath for 5 proceedingss ( mistake as opposed to the 37 0C ) . 2µl of lading dye was added to the tubings and incubated once more at 650C for 10minutes. The tubings were recentrifuged aboard a tubing of ? DNA HindIII digest as a control to extinguish the bubbles. The 22µl of tubing content were loaded into the Wellss of the pre-prepared 0.8 % agarose gel and run at 90volts for 40 proceedingss. gels were viewed under ultraviolet transilluminator and image obtaineWere possible the DNAfragment set were evaluated by scintillation numeration.

Consequence

L1 L2 L3 L4 L5 L6 L7 L8

Figure 1: Conventional diagram of agrose gel separation of ? DNA digested by three different limitation enzyme EcoRI, BamHI, and HINDIII. First three lane show individual digest of DNA severally. lane 4-6 contains dual digest reaction EcoRI/BamHI, EcoRI/HindIII and BamhHI/HindIII repectively. Lane 7 contains ternary digest reaction with all three enzymes EcoRI/BamHI/HindIII. Lane 8 contain HindIII DNA marker.The fragments were separated by agarose gel ( 0.8 % ) cataphoresis and the visualised under ultraviolet transilluminator. L- ( LANE ) gel16.jpg From the agrose gel image obtained ( fig 1 ) it can be seen that lane 1 ( EcoRI ) presents really weak 5 sets nevertheless it and it seems like the set has non separated down the good decently in order to separate single set, the same can besides be said for lane 2 ( BamHI ) as merely 3 thick distinguishable set can seen opposed to 5 that was expected. Lane 3 ( HindIII ) present 7 fragment set although besides faint the 6 sets can be seen alternatively of 7 expected. Lane 4 -6 incorporating the dual digests as reference in the methodological analysis, did non demo sets that were typical as some of this sets were suppose to match to two or three more set from the individual digest nevertheless some of the sets in these lanes appears thicker and brighter likely bespeaking dual digest of both enzyme film editing at the same site.. Lane 7 demoing set for the ternary digest were really ill-defined sets were excessively close to each other and unable distinguish they did non separate decently. It dye tallies can be seen on al the first set aside from the 8th lane which was the Ladder and all set in this were separated decently. Figure 2 is demoing a limitation map obtained from a web site which shows all the points all three enzymes were suppose to cut and how many set was suppose to demo on our gel in order to pull a limitation map.

Figure 2: conventional Map of ? DNA digested with three different enzyme BamHI ( GGATCC acknowledgment site found in ? Deoxyribonucleic acid at 5 locations ) , EcoRI ( GAATTC-5 location ) and HindIII ( AAGCTT-7 location ) besides demoing size of each fragment size. Map obtained from hypertext transfer protocol: //ww w.apsnet. org/edcenter/K-12/TeachersGuide /Plan t Biote chnol ogy/Pa ges/Act ivity3.aspx and modified.

DISCUSSSION

This experiment was generated to originate series of individual, dual and ternary limitation enzymatic digest on bacteriophage DNA lambda, in order to find how all three enzymes will split and digest Deoxyribonucleic acid ? . The terminal consequence from this experiment was unsatisfactory ; nevertheless this was partly expected due to the figure of mistakes that occurred during methodological analysis procedure. Ideally if the experiment had run swimmingly and clear sets were obtained the set on each lane of the gel image in Fig 1 would be measured ( distance travelled from good ) and each set ( fragment ) size would hold been extrapolated from a standard curve drawn utilizing the DNA HindIII ladder, and a proper genome map would be constructed. However the consequences obtained were unequal hence could non be done. It is clear from first sets on each lane of the gel image that deficiency of pippetting accomplishment into gel Wellss has notably affected the visual image of the sets. This was likely done by delving pipette tip into the well therefore leting important sum of the sample to run under the gel. Optimality and keeping the right environment for each reaction is important for this process, nevertheless this was breach when the samples were by chance placed at 65oC to originate enzyme digestion. Consequently doing denaturation of enzymes which might be the ground why the fragment were non separated decently. Although fermentas merchandise sheet province enzyme inactivation at 80oC. Another procedure that might hold affected the consequence negatively is delayed incubation clip ( 10min ) before gel cataphoresis, which could hold affected breakage H bond keeping the terminals of the additive DNA together in a circle.