1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 1 of 8
Biochem 121.1 Biochemistry of the Gene Laboratory Plasmid DNA Extraction and Restriction Enzyme Digestion 2010-00269, 2010-29246, 2010-48759 Group 4, Ms. Joanne Del Rosario Submitted February 17, 2014 Abstract Plasmids are extra-chromosomal, double-stranded, circular DNA molecules that carry genes that code for a wide array of traits that offer organisms genetic advantages, such as antibiotic resistance. Plasmids are most useful in recombinant DNA technology and in analyses in molecular biology and biochemistry, such as restriction enzyme digestion. Restriction enzymes are enzymes that cleave the DNA sequence at specific nucleotide sequences, making it possible to extract only specific parts of the DNA which are of interest. In this experiment, plasmid DNA was extracted from E. coli. in a procedure that involved alkaline lysis, rapid denaturation and renaturation of chromosomal DNA and its subsequent separation from plasmid DNA. The extracted DNA was then subjected to restriction enzyme digestion by EcoR1. Four samples of digested DNA incubated at 15, 30, 45 and 60 minutes respectively, were made to undergo agarose gel electrophoresis together with the undigested extracted DNA sample. AGE results show that all four digests showed no difference in size and molecular weight, as all of them showed a distinct band of size 2 kbp and molecular weight of 40 ng. The undigested plasmid DNA, however, had a molecular weight of 120 ng. This suggests that the reaction time allotted in the procedure may not have been enough for complete digestion to occur. Keywords: plasmid DNA extraction, restriction enzyme digestion, alkaline lysis, restriction site, agarose gel electrophoresis I. Introduction Virtually all bacterial species contain plasmidsdouble-stranded, typically circular DNA molecules distinct from the main chromosome in a cell. Plasmids account for only a small fraction of the bacterial genome corresponding roughly to a range between 1 and 200 kb. A plasmid of more than 50 kb may be characterized as large, and one of less than 10 kb may be called small. Plasmids are capable of being stably inherited without being linked to the chromosome and can be transferred horizontally between cells between same species or even between different species. (Rohde & Henze, 2011, Rhodes, et al., 2004, Plasmid Isolation, 2014) One of the most important aspects of bacterial plasmids is their carriage and spread of antibiotic resistance genes that ultimately have an impact on the treatment of diseases of animals and humans. They can also carry genes that code for a wide range of metabolic activities, enabling their host bacteria to degrade pollutant compounds, and produce antibacterial proteins. They can also harbor genes for virulence that help to increase pathogenicity of bacteria causing diseases such as plague, dysentery, anthrax and tetanus. Because of their ability to carry genes that provide the cell with genetic advantages, plasmids are used in recombinant DNA experiments to clone, transfer and manipulate genes from other organisms and make large quantities of their DNA. (Rhodes, et al., 2004, Plasmids, 2013) Plasmid DNA extraction and purification is a cornerstone of many molecular biology and biochemistry labs due to its extensive use prior to a variety of applications such as transfection, bacterial transformation, polymerase chain reaction, sequencing, in vitro transcription and restriction endonuclease digestion. Over the years, many methods for plasmid DNA extraction have been made; however, most of these methods have compromisessome can give a Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 2 of 8 low yield, may be time-consuming and produce impure plasmid extracts. In 1979, scientists Birnboim and Doly proposed a method of extracting plasmid DNA involving selective alkaline denaturation of chromosomal DNA while circular DNA remains double-stranded. To this day, alkaline lysis is the preferred method for plasmid DNA extraction from bacteria. (Plasmid DNA Purification, n.d., Birnboim & Doly, 1979) Plasmid DNA extracted using Birnboim and Doly is pure enough to be subjected to restriction enzyme digestion. Restriction enzymes, also called restriction endonucleases, are enzymes that cut the sugar-phosphate backbone of DNA molecules. In order to be able to sequence DNA, it is first necessary to cut it into small fragments. Many DNA-digesting enzymes can accomplish this; however, what is needed is a way to cleave the DNA at specific sites to produce a small set of homogenous fragments. This is why restriction enzymes are of particular importance; they recognize and cut DNA only at a particular sequence of nucleotides. Most recognition sequences are palindromesthey read the same forward (5 to 3) and backward (3 to 5). Also, the cuts made by restriction enzymes can generate either sticky ends (with 5 and 3 overhangs) which were cut asymmetrically, or blunt ends which were cut at precisely opposite sites. (Bowen, 1999, Restriction Enzymes, 2013) In this experiment, plasmid DNA was extracted from bacteria in a procedure that used alkaline lysis, and the extracted plasmid DNA underwent restriction enzyme digestion before being subjected to agarose gel electrophoresis. II. Experimental A. Plasmid DNA Extraction Three solutions were made with their respective contents; Solution 1: 50 mM glucose, 25 mM Tris-Cl at pH 7.4 and 10 mM EDTA at pH 8.0; Solution 2: 1 M NaOH and 10% SDS; Solution 3: 6 mL of 5 M potassium acetate, 1.5 mL glacial acetic acid and 2.5 mL sterile distilled water. A single bacterial colony was transferred into 2 mL of LB-ampicillin medium and incubated overnight at 37 o C with vigorous shaking. From the overnight culture, 1.5 mL was pipetted into a microcentrifuge tube. The tube was then centrifuged at 12000xg for 1 minute at 4C. The medium was completely removed by aspiration. The bacterial pellet was resuspended in 400 L of ice-cold Solution 1. The solution was pipetted up and down with a pipette tip to completely resuspend cells. Next, 400 L of freshly prepared Solution II was added. The tube was closed tightly, and the contents were mized by inverting the tube rapidly but gently five times. The tube was stored on ice for 3 minutes. Three hundred microliters of ice-cold Solution III was then added. The tube was closed and vortexed gently in an inverted position for 10 seconds to disperse the solution through the viscous bacterial lysate. The tube was stored on ice for 5 minute without shaking. The tube was then centrifuged at 12000xg for 5 minutes at room temperature. The supernatant was recovered and the pellet discarded. The supernatant was divided into 500 L aliquots in 1.5 mL microcentrifuge tubes. Two volumes of absolute ethanol were added to it at room temperature. The solution was mixed by vortexing and let stand for 5 minutes at room temperature. The tube was centrifuged at 12000xg for 5 minutes at 4C. The supernatant was removed by gentle aspiration and discarded. To the precipitate, 600 L of 70% ethanol was added. The tube was again centrifuged at 12000xg for 5 minutes at 4C and the supernatant was removed by gentle aspiration and discarded. Another round of 600 L of 70% ethanol was added to the precipitate. The pellet was air-dried and was resuspended in 100 L TE buffer, ready for storage. B. Restriction Enzyme Digestion A master mix for 10 reactions was prepared so that each 0.2mL PCR tube contained 2.5 L 10X RE buffer, 18.75 L sddH 2 O, 2.5 L of the extracted plasmid from the previous experiment, and 1.25 L restriction enzyme, EcoR1 (10 U/L). Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 3 of 8 The tubes were incubated at 37C for 1 hour. For every 15 minutes, an aliquot (5 L of the RE reaction) was obtained and loaded to 1% agarose gel together with 1 L of 6X gel loading buffer. AGE was run at 100 volts for 40 minutes. Undigested sample was also included to compare uncut, partially digested, and completely digested plasmid DNAs. III. Results and Discussion Plasmid DNA Extraction Plasmids are small, extra- chromosomal genetic elements that are found in almost all bacterial cells and also in some eukaryotic organisms (Sambrook and Russell, 2001). These are double stranded and circular DNA molecules that range from 1 kb to greater than 200 kb in size (Lipps, 2008). Plasmids are considered to be among the most important contributors in the evolution of prokaryotes as they can serve as vehicles that carry artificially inserted DNA and they provide an essential role in gene manipulation. Plasmids are also considered to be originators of several drug resistance mechanisms. Some strains of bacteria can be resistant to antibiotics either by acquiring several independent plasmids or through acquisition of a single plasmid with many sources of resistance on it. In this experiment, E. coli was used to assimilate the pGEM-1 plasmid which carries the ampicillin resistance gene (pGEM-1, 2011). To better analyze and observe plasmid DNA, a molecular biology technique known as plasmid DNA isolation is employed. In general, this procedure involves four steps: (1) immediate lysis of the bacterial cells, (2) separation of the plasmid from the chromosomal DNA, (3) removal of the cellular components that may alter subsequent test results and lastly, (4) removal of the detergents and salts added in the process (Kieleczawa, 2006). An ampicillin resistant E. coli was used as the specific host of interest and such phenotype was made by adding the antibiotic during the overnight culture preparation. This is to carefully select against the cells that do not produce the - lactamase protein and thus, the ones which are not resistant to the effects of Ampicillin. The gene for antibiotic resistance produces the -lactamase that breaks down any chemical with a beta-lactam ring. Through this, the antibiotic around the E. coli will become degraded and the bacteria will be able to survive. The extraction procedure utilized in this experiment is called the alkaline lysis method. The alkaline lysis preparation is considered to be the most commonly used method for isolating small amounts of plasmid DNA. Procedures such as this are generally based on the fact that plasmids usually occur in the covalently closed circular configuration within the host cells. Figure 1. A schematic representation showing the mechanism of resistance of bacteria to penicillin, an ampicillin- like antibiotic. Retrieved from: http://www.wiley.com/college/ pratt/0471393878/instructor/activities/bacterial_drug_resistanc e/index.htmlssss Three solutions having their own specific modes of action were prepared and used to facilitate the complete lysis of the bacterial cells. Solution 1, comprising of glucose, Tris-Cl and Ethylenediaminetetraacetic acid (EDTA), is considered to be the resuspension buffer and has a mechanism that is mainly directed towards the cell wall. Glucose functions to maintain the necessary osmotic pressure for the rest of the reactions to proceed. It usually makes the solution isotonic. However, for most bacteria including E. coli DH5a, isotonicity is not required since they contain cell wall that can withstand a wide range of solution concentration (Boffey, 1983). With the use of Tris-Cl and EDTA, cell lysis is further enhanced as they disrupt the outer envelope and expose the peptidoglycan. Tris is known as an ideal buffering agent as it buffer the cell at pH 8 while EDTA chelates with divalent cations (Ca 2+ , Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 4 of 8 Mg 2+ , Mn 2+ ) which are released upon bacterial lysis. The action of EDTA results in inactivation of many enzymes which may possibly harm the plasmid DNA if not removed (Birnboim and Doly, 1979). The Alkaline lysis solution 2 was a freshly-prepared combination of SDS and NaOH. Sodium dodecyl sulfate is a weak, anionic detergent that dissolves the lipid components of the cell membrane and cellular proteins. Denaturing action of SDS also releases proteins from DNA, leaving the DNA free from contaminating proteins. Conversely, sodium hydroxide denatures both the chromosomal and plasmid DNA into single strand by weakening the hydrogen bonds that hold the two strands together (Birnboim and Doly, 1979). It is of great importance that this solution is freshly prepared to take into account the presence of NaOH and the tendency of water to react with carbon dioxide. If not freshly prepared, it is of great possibility that NaOH can also react with carbon dioxide. Carbon dioxides reaction with alkalis can lead to the production bicarbonates whereas its response to water is to produce carbonic acid (Pauling, 1988). These two reactions are illustrated below: CO 2 + H 2 O H 2 CO 3
CO 2 + NaOH NaHCO 3
The last solution, solution 3, contains potassium acetate and acetic acid. The addition of acetic acid neutralizes the high pH due to NaOH so that DNA strands can rapidly renature. Potassium ions interact with the SDS to make this detergent insoluble from the solution. The SDS then easily precipitates and is separated through centrifugation. Furthermore, the insoluble SDS traps the larger genomic DNA to remove it from the supernatant. This enables the plasmid DNA to remain in solution (Birnboim and Doly, 1979). Aside from the fact that biological activity is maintained at approximately 4 o C, it is essential for solutions 1 and 3 to be stored in an ice-cold environment so that each of them can serve its purpose well. Note that storing solution 2 in such environment is not that compulsory since it is expected that it is freshly prepared. Maintaining this temperature for Solution 1 inhibits the nucleases that may cleave the plasmid DNA of interest. Conversely, for Solution 3, the precipitation of the chromosomal DNA and the SDS-protein complexes is facilitated at this temperature. Also, since DNA is very sensitive to mechanical stress, shearing forces caused by techniques such as vortexing and fast pipetting are avoided as soon as cell lysis occurs. All mixing steps during and after cell lysis was carefully performed by inverting the tubes several times. Vigorous vortexing is avoided as it can damage or shear the extracted DNA (Clewell, 1972). A primary alcohol, such as ethanol is the most commonly used component in the precipitation of DNA. Due to the structural differences between ethanol and water, ethanol has much lower dielectric constant than water does (Maniatas, Fritsch, Sambrook, 1982). Water is considered to have a high dielectric insulator, which means that the electrostatic force existing between two ions of opposite charge is very low in comparison with that in ethanol. Adding ethanol lowers the dielectric constant in the solution so water no longer insulates individual ions. Because of this, the Coulomb force of attraction increases between the cations and the negatively charged nucleic acid backbone. Once their interaction begins, nucleic acids are neutralized such that they no longer dissolve in water and hence are precipitated out of solution (Pikur and Rupprecht 1995). Afterwards, the isolated DNA was suspended in a Tris-EDTA buffer for long-term storage. The EDTA in TE buffer chelates Mg 2+ and other divalent metal ions responsible for DNA and RNA degradation, thus suppressing these processes (Birnboim and Doly, 1979). Restriction Enzyme Digestion Restriction endonucleases or enzymes are naturally occurring enzymes that cut double stranded DNA at specific sites called recognition sequence which are usually 4-8 nucleotides long and are palindromes, meaning that the sequence reads the same when read from 5 to 3' at each strand. Restriction endonucleases cleave DNA by Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 5 of 8 catalyzing the hydrolysis of the sugar-phosphate backbone (Berg, Tymoczko, & Stryer, 2002). Restriction enzymes are isolated from different bacterial species wherein they play a role in the defense mechanism of the bacteria against invading foreign DNA such as viruses. Restriction endonucleases, together with the enzyme methylase, comprise the host-controlled restriction modification systems of certain bacterial species including Escherichia coli. When a bacteriophage inserts its DNA into the host cell, the endonuclease synthesized by that cell would cleave the foreign DNA thereby restricting the infecting virus. The host DNA however contains the same recognition sequence, so the cell produces a corresponding methylase which would add methyl groups to cytosine or adenine bases to protect the host DNA from the action of its own endonuclease (Kumar & Garg, 2005). There are of four types of restriction ennzymes namely, Type I, Type II, Type III and Type IV which differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements. Type I and Type III are large, multi-subunit enzymes that cut DNA at random, far from their recognition sequences; Type I cuts DNA locations as far as 1000 or more base-pairs from the recognition site while Type III cuts at approximately 25 base-pairs from the site. Both types carry restriction and methylase activities and are ATP dependent. Type II restriction enzymes cut DNA within or with a short distance from the recognized sequence and are the predominantly used restriction enzyme in DNA analysis and cloning studies. They are smaller and simpler, with subunits of 200 to 350 amino acids. Type II enzymes do not require ATP. Type IV enzymes recognize modified or methylated DNA. Type I, II, and III all requires a cofactor, usually Mg 2+ . (New England Biolabs, 2014) Upon RE digestion, DNA may generate blunt ends, 5 or 3 sticky ends or overhangs depending on the position of the cutting site within the recognition sequence (Kumar & Garg, 2005). Cleaved DNA sequences with sticky ends will easily anneal through ligation than those with blunt ends. Hence, restriction enzymes which produce sticky ends or overhangs are of great use in the recombinant DNA technology. In this experiment, a plasmid DNA isolated from E. coli was subjected to restriction enzyme digestion. The restriction enzyme used is EcoR1, a Type II enzyme which produces 5 overhangs. EcoR1, isolated from Escherichia coli RY13, has a recognition sequence and restriction site shown below:
If the plasmid has only one GAATTC sequence, EcoRI would cut the plasmid once, converting it to a linear piece of DNA. When visualized using agarose gel electrophoresis, a single band should be observed having a molecular weight same as that of the extracted plasmid DNA. Presented in the results in Figure 1, all four RE digests showed a distinct band with size of 2 kbp and molecular weight of 40 ng. This result however is inconsistent with the molecular weight of the plasmid DNA which is 120 ng.
Figure 1.Plasmid DNA extract and RE digest resolved under 1.0 % agarose gel. Lane 1 represents the 2-log DNA ladder, Lanes 2 and 3, extracted plasmid DNA and Lanes 4, 5, 6 and 7 the restriction enzyme digest at 15, 30, 45 and 60 minutes, respectively. Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 6 of 8 Each restriction enzyme has optimal reaction conditions; factors including pH, reaction temperature and time, and enzyme concentration affect the results of DNA digestion. For EcoR1 and most other restriction enzymes, the optimal pH of the RE buffer is 7.5 and incubation temperature is 37 C; these conditions generally reflects the growth requirement of the bacterial strain from which the enzyme is derived. Incubation time was set to one hour, and to monitor the restriction enzyme activity, aliquots of the reaction mixture were obtained every fifteen minutes and then loaded on the agarose gel. The results then suggest that the reaction time might not have been enough for complete digestion. Under optimal conditions the difference there is a high difference between the cleavage rates at the recognition or cognate site and the next best site (with a single base substitution). The rate difference of EcoRI at its cognate site (5-GAATTC-3) and next best site (5-TAATTC- 3) is of the order of 10 5 (Promega, 2014). However, when restriction enzyme digestion is done under non-standard or non-optimal conditions, the specificity of the endonuclease decreases and would cleave the DNA at sites different from the normal recognition sequence. This non-specific cutting is called "star activity", a property which is exhibited by EcoRI. Factors that cause star activity include extremely high concentration of the restriction enzyme, prolonged reaction time, non-optimal pH, and presence of organic solvents (New England Biolabs, 2014). Restriction endonucleases as well as many other enzymes that act on phosphate- containing substrates require Mg2+ or some other similar divalent cation for activity (source: journal). However, use of other divalent cation such as Mn 2+ , Co 2+ , and Fe 2+ may also cause relaxation of specificity, and consequently result to star activity. This is because other divalent cations may not fit correctly into the active site of the restriction enzyme, interfering with proper recognition (New England Biolabs, 2014). Appearance of extra bands on the agarose gel can be attributed to star activity, as well as to partial digestion, wherein longer reaction time is recommended, and also to the binding of enzyme to substrate DNA, which could be resolved by lowering the enzyme concentration or by adding SDS to the loading buffer to separate the enzyme and substrate. Other problems encountered in RE digestion include incomplete restriction enzyme digestion or no digestion at all, which could be due to insufficient enzyme concentration, short reaction time, or may be due to methylation; the plasmid DNA isolated from E. coli may be blocked by Dam and Dcm methylation, hence blocking the cleavage by endonucleases. Another is having diffused DNA bands or smears which could be attributed to contamination or to enzyme- substrate binding as well (Fermentas Life Sciences, 2014). IV. Conclusions and Recommendations The method used for plasmid DNA extraction involved the addition of three solutions with distinct roles: the first solution is a buffer that resuspends the DNA in optimum conditions to prevent degradation; the second solution separates contaminating lipids and proteins from the DNA and denatures the DNA; and the third solution rapidly renatures the DNA and separates the chromosomal DNA from the plasmid DNA. The extracted plasmid DNA was then made to undergo restriction enzyme digestion before being subjected to agarose gel electrophoresis. The results suggest that an hour of reaction time was not able to completely digest plasmid DNA, and that 15-min. incubation intervals would not make a significant difference in the rate of digestion. This also suggests that standard and optimum conditions may not have been achieved during restriction enzyme digestion. V. References Bacterial Drug Resistance. Retrieved February 15, 2014 from http://www.wiley. com/college/pratt/0471393878/instructor/ activities/bacterial_drug_resistance/index. html Birnboim, H.C. and Doly, J. 1979. A rapid alkaline procedure for screening recombinant Biochem 121.1 Plasmid DNA Extraction and Restriction Enzyme Digestion Page 7 of 8 plasmid DNA. Nucleic Acids Res. 7: 15131523. Boffey, S. (1983). Techniques in Molecular Biology. In J. Walker, & W. Gaastra. Bristol: Leaper and Gard Ltd. Bowen, R. (1999). Biology and Activity of Restriction Endonucleases. Retrieved February 16, 2014 from http://www.viv o.colostate.edu/hbooks/genetics/biotech/e nzymes/renzymes.html Clewell. D.B. 1972. Nature of ColE1 plasmid replication in Escherichia coli in the presence of chloramphenicol. J. Bacteriol. 110, 667-676. Ethanol precipitation of DNA with salts - Theory. Retrieved February 16, 2014, from http://www.nhm.ac.uk/resources- rx/files/ethanol-precipitation-of-dna-with- salts---theory_aug12-118483.pdf Kieleczawa, J. (2006). DNA sequencing II: Optimizing Preparation and Cleanup, Volume 2. Jones & Bartlett Learning. Kumar, A., & Garg, N. (2005). Genetic Enginee- ring. Nova Science Publishers, Inc. Lipps, G. (2008). Plasmids: Current Research and Future Trends. Horizon Scientific Press. Maniatis, T, E F Fritsch, and J Sambrook. Molecular Cloning. A Laboratory Manual. New York: Cold Spring Harbor Laboratory, 1982. Pauling, L. (1988). General Chemistry. Courier Dover Publications. pGEM-1. (2011). 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