Professional Documents
Culture Documents
Submitted by
Arti Vijay
Roll No-1903610540017
In
Department of Biotechnology
(2020-21)
Of
Submitted To
Dheerendra Kumar
(HOD, OF BIOTECHNOLOGY)
1
ACKNOWLEDGEMENT
It was a great pleasure for me to get an opportunity to work for my training at the MRD LIFE
SCIENCESS. It has given me the research experience that will be definitely helpful in my
gratitude to those without whom this training would not have been materialized.
With an overwhelming sense pride and genuine and personal regards to Mr. Manoj Kumar
Verma for his valuable advice and encouragement. With an overwhelming sense pride and
personal regards to my supervisor Mr. Manoj Kumar Verma, Director of MRD LIFE
SCIENCES, Lucknow for her constructive criticism, valuable advice, close supervision,
healthy encouragement, utmost patience and generosity throughout the course of this study.
Additionally, I would like to thank, Mr. RJ Shekhar Mishra, Ms. Pallavi Sharma , MRD
Life Sciences Lucknow. I would like to thank my parents who have supported me
throughout entire process, all by Keeping me harmonious and helping me putting pieces
2
CONTENTS
S.No. Title
1. Introduction
2. Objectives
3. Methodology
4. Result
5. Discussion
6. Conclusion
7. References
ABSTRACT
Name : Arti Vijay
Branch : Biotechnology (2nd year)
College Date : : R.R I M T Sitapur Road Lucknow up. India Date :
Date:
3
First of all, I would like to express my gratitude to almighty GOD to enableing me to
complete this report on “Extraction, purification and quantification of the plasmid
DNA from E.Coli.”
The use of plasmid DNA is the keystone of DNA analysis because it allows easy
manipulation and maintenance of defined heterologous DNA fragments. The E.coli
bacteria system is very versatile, allowing rapid DNA replication and informed gene
manipulation.
The training opportunity I had with MRD Life Sciences was a great chance for
learning and professional development. Therefore, I consider my self very lucky
individual as I was provided with an opportunity to be a part of it. I am also grateful
for having a chance to meet so many wonderful people and professionals in this
epidemic year on this online training platform who led me though this training
period.
Bearing in mind previous I am using this opportunity to express my deepest gratitude
and special thanks to the MD of MRD Life Sciences Lucknow, who in spite of being
extraordinarily busy with her/his duties, took time out to here, guide and keep me to
carry out my project at their esteemed organization and extending during the
training.
I perceive as this opportunity as a big milestone in my career development. I will
strive to use gained skill and knowledge in the best possible way, and I will continue
to work on their improvement, in order to obtain desired career objectives. Hope to
continue cooperation with all of you in the future.
INTRODUCTION
In biochemical aspects, to purify plasmid DNA from bacteria is to isolate only
plasmid DNA from the mixture of Biopolymers such as Protein, ribonucleic acid
(RNA), chromosomal DNA and plasmid DNA, by which bacteria call is composed.
4
To purify plasmid DNA of High Quantity culture condition, or media for E.coli
growth is important.
5
• solution which is separated by centrifugation in the presence of the INSTA-PREP
ge.
• barrier material. This method has been successfully tested on various
environmental.
• Salmonella strains, although it was not suitable for Pseudomonas aeruginosa.
• enterococci strains. The INSTA-MINI-PREPTM method is a new alternative
procedure Summary The INSTAMINI-PREPTM method, a rapid protocol for plasmid
DNA.
• extraction, was originally developed to prepare plasmid DNA from 1 to 3 ml
minaret.
• Escherichia coli cultures, Direct extraction of plasmid DNA is achieved by a two-
phase .
• solution which is separated by centrifugation in the presence of the INSTA-PREP
gel.
• barrier material. This method has been successfully tested on various
environmental.
• Salmonella strains, although it was not suitable for Pseudomonas aeruginosa and
enterococci strains.
• The INSTA-MINI-PREPTM method is a new alternative procedure
• to screen plasmid contents of Salmonella and E. coli strains rapidly and easily.
• Key words Pseudomonas aeruginosa · Escherichia coli · Salmonella · Plasmid
screening procedure ·
• Plasmid extraction to screen plasmid contents of Salmonella and E. coli strains
rapidly and easily Key words Pseudomonas aeruginosa ·
• Escherichia coli ·
• Salmonella ·
• Plasmid screening procedure ·
• Plasmid extraction.
DNA Purification
6
• Basic Isolation Procedure
• There are five basic steps of DNA extraction that are consistent across all the
possible DNA purification chemistries:
• 1) disruption of the cellular structure to create a lysate,
• 2) separation of the soluble DNA from cell debris and other insoluble material,
• 3) binding the DNA of interest to a purification matrix,
4) washing proteins and other contaminants away from the matrix and
• 5) elution of the DNaterial,
1. Creation of Lysate
The first step in any nucleic acid purification reaction is releasing the DNA/RNA
into solution. The goal of lysis is to rapidly and completely disrupt cells in a
sample to release nucleic acid into the lysate. There are four general techniques for
lysing materials: physical methods, enzymatic methods, chemical methods and
combinations of the three.
Physical Methods
Physical methods typically involve some type of sample grinding or crushing to
disrupt the cell walls or tough tissue. A common method of physical disruption is
freezing and grinding samples with a mortar and pestle under liquid nitrogen to
provide a powdered material that is then exposed to chemical or enzymatic lysis
conditions. Grinders can be simple manual devices or automated, capable of
disruption of multiple 96-well plates. Physical methods are often used with more
structured input materials, such as tissues or plants. Other devices use bead beating
or shaking in the presence of metallic or ceramic beads to disrupt cells or tissues,
or sonication to disrupt tissues and lyse cells.
Chemical Methods
Chemical methods can be used alone with easy-to-lyse materials, such as tissue
culture cells or in combination with other methods. Cellular disruption is
7
accomplished with a variety of agents that disrupt cell membranes and denatures
proteins. Chemicals commonly used include detergents (e.g., SDS) and chaotropes
(e.g., guanidine salts and alkaline solutions).
Enzymatic Methods
Enzymatic methods are often used with more structured starting materials in
combination with other methods with tissues, plant materials, bacteria and yeast. The
enzymes utilized help to disrupt tissues and tough cell walls. Depending on the
starting material, typical enzymatic treatments can include: lysozyme, zymolase and
liticase, proteinase K, collagenase and lipase, among others. Enzymatic treatments can
be amenable to high throughput processing, but may have a higher per sample cost
compared to other disruption methods .
In many protocols, a combination of chemical disruption and another is often used since chemical
disruption of cells rapidly inactivates proteins, including nucleases.
2. Clearing of Lysate
Depending on the starting material, cellular lysates may need to have cellular
debris removed prior to nucleic acid purification to reduce the carryover of
unwanted materials (proteins, lipids and saccharides from cellular structures) into
the purification reaction, which can clog membranes or interfere with downstream
applications. Usually clearing is accomplished by centrifugation, filtration or
bead-based methods. Centrifugation can require more hands-on time, but it is able
to address large amounts of debris. Filtering can be a rapid method, but samples
with a large amount of debris can clog the filter. Bead-based clearing, like the
method used with Promega particle-based plasmid prep kits, can be used in
automated protocols, but can be overwhelmed with biomass. Once a cleared lysate
is generated, the DNA can then be purified by many different chemistries, such as
silica, ion exchange, cellulose or precipitation-based methods.
8
Regardless of the method used to create a cleared lysate, the DNA of interest can
be isolated using a variety of different methods. Promega offers genomic DNA
isolation systems based on sample lysis by detergents, and purification by binding
to matrices (silica, cellulose and ion exchange), which is where interest has
primarily been focused in recent years .
Each of these chemistries can influence the efficiency and purity of the isolation,
and each have a characteristic binding capacity. Bind capacity is an indication of
how much nucleic acid an isolation chemistry can bind before it reaches the
capacity of the system and no longer isolates more of that nucleic acid. We can
build design features into these chemistries by manipulating the binding
conditions to enrich for different categories of nucleic acid (e.g., chemistries that
selectively bind RNA versus DNA or large versus small fragments).
Solution-Based Chemistry
This type of chemistry does not rely on a binding matrix, but rather on alcohol
precipitation. Following the creation of lysate, the cell debris and proteins are
precipitated using a high-concentration salt solution. The high concentration of
salt causes the proteins to fall out of solution, and then centrifugation separates the
soluble nucleic acid from the cell debris and precipitated protein (1). The DNA is
then precipitated by adding isopropanol to the high-concentration salt solution.
This forces the large genomic DNA molecules out of solution, while the smaller
RNA fragments remain soluble. The insoluble DNA is then pelleted and separated
from salt, isopropanol and RNA fragments via centrifugation. Additional washing
of the pellet with ethanol removes the remaining salt and enhances evaporation.
Lastly, the DNA pellet is resuspended in an aqueous buffer like Tris-EDTA or
nuclease-free water and, once dissolved, is ready for use in downstream
applications.
Cellulose-Binding Chemistry
More recently, Promega has commercialized DNA isolation methods that use a cellulose-based
matrix. Nucleic acid binds to cellulose in the presence of high salt and alcohols. Generally
speaking, the bind capacity of cellulosebased methods is very high. Conditions can be adjusted to
preferentially bind different species and sizes of nucleic acid. As a result of the combination of
9
binding capacity and relatively small elution volume, we can get high concentration eluates for
nucleic acids.
4. Washing
Wash buffers generally contain alcohols and can be used to remove proteins, salts
and other contaminants from the sample or the upstream binding buffers. Alcohols
additionally help associate nucleic acid with the matrix.
5. Elution
DNA is soluble in low-ionic-strength solution such as TE buffer or nuclease-free
water. When such an aqueous buffer is applied to a silica membrane, the DNA is
released from the silica, and the eluate is collected. The purified, high-quality
DNA is then ready to use in a wide variety of demanding downstream
applications, such as multiplex PCR, coupled in vitro transcription/translation
systems, transfection and sequencing reactions.
When selecting your elution buffer, it is important to consider the requirements of
your desired downstream processes. Eluting and storing the DNA in TE buffer, for
example, is helpful as long as the EDTA does not impact your chosen downstream
applications. EDTA chelates, or binds, magnesium present in the purified DNA
and can help inhibit possible contaminating nuclease activity. If EDTA is a
concern, we recommend storing DNA in a buffered solution, as the acidic nature
of DNA can lead to autohydrolysis. Alternatively, you can use TE-4 buffer, which
is 10mm TrisHCl, 0.1mm EDTA (pH 8.0)
10
Minute method
Based on the alkaline lysis method, we developed a new plasmid purification
method, which ends within 1 hour and does not need RNase (Figure 5) [22]. The
principle of this method is a combination of the alkaline lysis method, CaCl2
precipitation, and PEG precipitation. Although a sequential combination of these
11
precipitations was already reported [23], our new invention is that we developed a
new composition of solution III. This “super solution III” contains CaCl2 to the
standard solution III (Solution III: 5 M CaCl2: H2O = 2:2:1), which makes not
only protein and genomic DNA debris but also a pellet of RNA in the debris. After
centrifuging and recovering a supernatant, a standard PEG precipitation makes a
plasmid DNA pellet and removes small RNA, which was not precipitated at the
super solution III step. After all, only plasmid DNA remains in the final solution.
Actually, this method needs totally 55 minutes from collecting E. coli pellet to
recovering the final purified plasmid DNA. The great advantage of this method is
that we are able to eliminate the use of RNase. Therefore, even RNase removal
step is also eliminated. A quality and quantity are adequate for doing another
experiment such as transfection into cultured cells.
Samples:-
The broiler cecal samples were collected from a commercial poultry production
unit in the United Kingdom. Samples were lyophilized and stored at −80°C. Each
of the plasmid extraction methods were carried out with the same cecal sample
(Sample A). All methods were also carried out with Escherichia coli NCTC 13400
containing plasmid pEK499 as a control.
12
13
Material and Reagents –
1. Tris base
2. Protinase K
3. Phenol\Chloroform (1:1)
4. Ethanol
5. SdS
6. EDTA
7. Tryptone
8. Yeast extract
9. NaCl
10. LB medium
11. TE buffer
12. Lysis buffer
Equipment
1. Tabletop centrifuge
2. 1.5 ml Eppendrof tube
3. Incubator
4. Gloves
Procedure:-
1) Transfer 1.5 ml of the overnight E.coli culture (grown in LB medium) to a 1.5 ml
Eppendrof tube and centrifuge at max speed for 1 mint to pellet the cell.
2) Discard the supernatent. NOTE: Remove as much of the supernatent as you can
without disturbing the cell pellet.
3) Resuspend the cell pellet in 600 micro litter lysis buffer and vortex to completely
resuspended cell pellet.
4) Incubate 1 hr at 37degree centigrate.
5) Add an equal volume of phenol/chloroform and mix well by inverting the tube until
the phases are completely mixed.
NOTE: do not vertex the tube- it can shear the DNA.
14
6) CAUTION: phenol is a very strong acid that causes severe burn. Chloroforn is a
carcinogenic. So wear gloves, goggles and labe cote and keep tubes capped tightly.
7) Spin at max speed for 5 mint at RT. There is a white layer (protien layer) in the
aqueous:phenol/chloroform interface. 8) Carefully transfer the upper aqueous phase to
a new tube by 1ml of pipetman.
9) Steps 4.6 can be repeated until the white protein layer disappears.
10) To remove phenol an add equal volume of chloroform to the aqueous layer. Agai
mix well by inverting the tube.
11) Spin at max speed at 5 min .
12) Remove aqueous layer to new tube.
13) To precipitate the DNA add 2.5 or 3 volume of cold 200 proof ethanol (store
ethanol at 20 degree C freezer) and mix gently (DNA precipitation can be visible).
14) Icubate the tube at 20 degree C for 30 min. or more.
15) Spin at max speed for 15 min. at 4 degree C.
16) Discard the supernatent and rinse the DNA pellet with 1 ml 70% ethanol.
17) Spin at the max speed for 2 min. Carefully discard the supernatent and dry the
DNA pellet. To be faster, dry the tube at 37 degree C incubator.
18) Resuspend the DNA in TE buffer.
19) Check isolated Genomic DNA on agrose gel.
15
Result
16
17
Discussion
Purification of plasmid DNA from Escherichia coli using alkaline lysis is based on the
two. Bacteria are lysed with a solution containing sodium dodycyl sulfate (SDS) and
sodium hydroxide. During this step, chromosomal as well as plasmid DNA are
covalently closed plasmid DNA to reanneal and to stay solubilized. Most of the
chromosomal DNA and proteins precipitated in a complex formed with potassium and
SDS, which is removed by centrifugation. The plasmid DNA is concentrated from the
supernatant by ethanol precipitation. Using this procedure, 2-3 micro gram of DNA
can be obtained from a 1.5 mili litre culture of E.coli containing a pBR322-derrived
plasmid, and 3-5 fold higher yields can be expected from pUC-derrived plasmids.
Conclusion
18
In a course of doing plasmid purification for every day, I noticed several tips for the
definitive method for plasmid purification. None of another methode will take over
the alkaline lysis method. However, RNA is not removed in alkaline lysis method, so
RNA removal step should be applied in a course of plasmid isolation by alkaline lysis
method. Rnase completely digests unwanted RNA from the plasmid sample. But this
enzyme is very stable and very hard to inactivate, even disturbing RNA experiment in
the laboratory . Moreover, Rnase is usually isolated from animals such as bovine,
which may induce allergy to the human in gene therapy. Based on these tips, we
to purify plasmid DNA without adding of Rnase. This method does not need any
special columns or resins, but plasmid DNA purified by this method has enough
quality for applying transfection to the cultured cell, injection into the nematode, and
so on. Our result indicates that plasmid DNA purification without phenol/chloroform
References
19
Plasmid DNA Extraction
Plasmid have been found to be wide distribution in bacteria. They are
autonomously replicating extrachromosomal elements which are not essential for the
their host cells. However, they may encode a wide range of genetic products which
may permit their host to adopt conditions, for example, in the presence of antibiotics.
In cloning work, very often the recombinant plasmids have to isolated from their
transformed host in order to characterize by restriction analysis and sequencing, The
information from these analyses provides a basis for the mode of their presentation to
the transformants and the planning of future experiment for the recombinant
molecules.
Among the various methods are available for the presentation oh plasmid DNA
for rapid screening, a protocol involving the use of an alkaline solution to lyses the
cells, salt precipitation to remove cell debris and chromosomal DNA and application
to hibind DNA column to eliminate protein and others contaminants has been widely
employed.
Instrumentation
• ANALYTICAL CENTRIFUGE INVENTED BY :.A centrifuge is a device that
uses centrifugal force to separate various components of a fluid. This is achieved by
spinning the fluid at high speed within a container, thereby separating fluids of
different densities (e.g. cream from milk) or liquids from solids.
20
Fluorescence Microscope: A fluorescence microscope is an optical microscope that
uses fluorescence and phosphorescence instead of, or in addition to, reflection and
absorption to study properties of organic or inorganic substances.
21
22
Autoclave- (Labtech):- An autoclave is a device used to sterilize equipment and
supplies by subjecting them to high pressure saturated steam at 121 °C for around 15–
20 minutes depending on the size of the load and the contents.
23
24
25
26
27
28
29
30
31
PH-METRE:-
32
LAB EQUIPMENT IN BIOTECHNOLOGY:
Safety glasses
33
Erlenmeyer flask
Transfer pipet(te)
Beaker
Graduated cylinder
Volumetric pipet(te)
Wire / inoculating loop
Graduated pipet(te)
Bunsen burner
Volumetric flask(with a calibration mark)
Bench top bin
Safety gloves
Disinfectant spray= incidin® foam
Pipette bulb= pipette filler
Pasteur Pipet(te)
Petri dish
Sterile pipet(te) =serological pipet
Pipettor= automatic pipet
Pipet tip(s)
Test tube rack
Tweezers
Lab slides = microscope slides
Laboratory shaker
Wash bottle
Funnel
Biohazard bag
Precision scale
Microscope
Lab coat
Broth cultures
Staining reagents
Absorbent tissue
34
Agar plate
Fume hood
Incubator
Swab
Stoppers = lab caps
UV TRANSILLUMINATOR
UV-transilluminators are used in molecular biology labs to view DNA (or RNA)
that
has been separated by electrophoresis through an agarose gel.
• PRINCIPLE :
During or immediately after electrophoresis, the agarose gel is stained with a
fluorescent dye
which binds to nucleic acid. Exposing the stained gel to a UVB light source causes
the
DNA/dye to fluoresce and become visible.
35
Air displacement micropipettes are a type of adjustable micropipette that deliver a
1000 µl (1 ml).These pipettes require disposable tips that come in contact with the
airtight sleeve. As the piston moves upward, driven by the depression of the plunger, a
vacuum is created in the space left vacant by the piston. The liquid around the tip
moves into this vacuum (along with the air in the tip) and can then be transported and
released as necessary. These pipettes are capable of being very precise and accurate
Eppendorf, Dr. Heinrich Netheler, inherited the rights and initiated the global and
36
The instrument group ULT freezer is defined as freezers for -80 to -85°C. ULT is the
shortcut for ultra low temperature.There are upright and chest freezers.The inner
volume is in general between 300 and 800 L. • Principle: The refrigeration system of
the ultra freezers basic cascade refrigeration principle, the choice of two hermetic
system is also equipped with gas heat exchanger, allows low- pressure gas from the
evaporator heat exchange with the highpressure gas condensate evaporator, it will not
only reduce the heat load of the condensate evaporator, and the full use of the heat .
• Uses: for long term storage for biological samples like DNA, RNA, proteins, cell
extracts, or reagents.To reduce the risk of sample damage, these types of samples need
INCUBATORS
cultures. The incubator maintains optimal temperature, humidity and other conditions
37
is a simple device used commonly in laboratories to mix small vials of liquid. It
consists of an electric motor with the drive shaft oriented vertically and attached to a
cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece
is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the
liquid inside and a vortex is created. Principle: vortex, In fluid dynamics, a vortex is a
region in a fluid in which the flow rotates around an axis line, which may be straight
or curved.[ The vortex mixer was invented by the Kraft brothers (Jack A. Kraft and
manufacturer).[1] A patent was filed by the Kraft brothers on April 6, 1959 and
granted on October 30, 1962.[2] Scientific Industries still makes a version of this
38
A mortar and pestle is a kitchen device used since ancient times to prepare ingredients
or substances by crushing and grinding them into a fine paste or powder.The mortar is
a bowl, made of hardwood, ceramic or stone.The pestle is a heavy blunt club shaped
• Uses it is used for grinding plant samples which lead to disrupting cellular
membranes and specially cell wall. Or in other words to release biological molecules
• Are small capped plastic tubes used for centrifuge or in pcr apparatus.
• Available in different volumes like 0.5 ml, 1.5 ml, 2 ml but the most comman size is
1.5 ml
EPPENDROFFTUBES
Are small capped plastic tubes used for centrifuge or in pcr apparatus.
• Available in different volumes like 0.5 ml, 1.5 ml, 2 ml but the most comman size is
1.5 ml
39
Laboratory gloves are made of latex and nitrile.They protect the hands of wearer
Do not use vinyl gloves which can transmit significant amount of uv.
• Uv glasses or face shields : use poly carbonate face shields that are rated for uv
protection. It should be marked with Z87 to indicate that the shield meets the standard.
also known as Gel Documentation System, Gel Image System or Gel Imager, is
widely used in molecular biology laboratories for the imaging and documentation of
nucleic acid and protein polyacrylamide or agarose gels typically stained with
ethidium bromide or other fluorophores such as SYBR Green. Generally, a Gel Doc is
ultraviolet-visible spectral region. This means it uses light in the visible and adjacent
(near-UV and near-infrared (NIR)) ranges. The absorption or reflectance in the visible
range directly affects the perceived color of the chemicals involved. In this region of
40
THANKING
YOU..!
41