Understanding PCR A Practical Bench Top Guide 1st Edition Maddocks instant download
Understanding PCR A Practical Bench Top Guide 1st Edition Maddocks instant download
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Sarah Maddocks
Cardiff Metropolitan University, United Kingdom
Rowena Jenkins
Cardiff Metropolitan University, United Kingdom
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ISBN: 978-0-12-802683-0
ix
Chapter 1
1.1 INTRODUCTION
So, you have decided to tackle the polymerase chain reaction (PCR); this is an
extremely powerful technique that will enable you to amplify fragments of
DNA. PCR is also incredibly versatile, and once you have mastered the basics,
you will be able to apply the techniques you have learned to a host of mo-
lecular techniques including genetic profiling, detection, gene expression, and
genetic modification. The world of PCR can be overwhelming, from deciding
on your primer design, to where to buy your polymerase. It is therefore
important that you understand the fundamental requirements necessary to
prepare and carry out PCR, to avoid months of frustration or results you can
not even begin to comprehend.
There are a number of factors to consider when planning to undertake PCR
for the first time, and if these are addressed prior to putting on your lab coat
and picking up your pipette, then the whole process will run much more
smoothly, meaning you are more likely to be successful. Such considerations
include aspects of safety, preparation of reagents, and consideration of reaction
parameters and organization of your work area. This chapter will describe
some of the considerations you need to address before heading into the lab; it
is a good idea to equip yourself with a pen whilst reading through this chapter
so that you can begin to plan your first PCR.
PCR tubes that you have. This avoids inaccuracies during pipetting, or
problems if reagents have not properly mixed.
When using the PCR recipe list, you will most likely still be planning your
PCR “on paper,” designing primers and reaction parametersdif you are using
a predesigned set of primers with known reaction parameters you can move
onto the wet work and skip to Chapter 3 which describes how to analyze the
results of the PCR reaction.
you can always prepare your own by autoclaving nanopure water. Again, it is
advisable to prepare small aliquots of between 10 mL and 20 mL for this
purpose. It is always the best to purchase things like reaction buffers for en-
zymes and magnesium solutions, and most of these will come with the enzyme
when you buy it (see Section 1.6 for where to buy reagents and supplies).
As mentioned previously, if possible, it is a good idea to use filter tips when
setting up PCR reactions to help you to maintain a nuclease-free environment;
these prevent aerosols associated with your pipettes from getting into your
PCR reaction and therefore contaminating it. These can be purchased from a
wide range of suppliers. DNase-free and RNAse-free PCR tubes can also be
purchased from numerous suppliers (see Section 1.6), these usually arrive in
large bags so it is a good idea to portion them out into smaller, sterile con-
tainers (if you prefer, you can autoclave them as you would any other
microcentrifuge tube). Because you can introduce nucleases to your working
environment, it is important that you always wear a lab coat and gloves when
handling any PCR reagents, more specifically ensure you wear a “fresh” pair
of gloves when beginning PCR work and that your lab coat is not filthy!
Unless you have a dedicated bench space that is only used for molecular
work, it is wise to clean your bench space before setting up your reaction;
you can use disinfectant or 70% ethanol to do this, but there are some
commercially available sprays that are specifically designed to remove nu-
cleases and can be used to surface treat benches and equipment such as pi-
pettes or PCR tube racks. Below is a recipe to prepare a solution that will do
this job; if you choose to make this solution ensure that it is prepared using
nanopure water and in a glass container, then sterilized by autoclave for
15 min at 121 C prior to use. Treat it as you would any other nuclease-free
reagent and prepare only small “working” volumes. If at any point you think
you might have contaminated your work space or equipment, it is advisable
to clean everything again as there is nothing more frustrating than running a
PCR to find later that there are problems associated with the presence of
nucleases or other contaminants.
rushing and making mistakes. If you are using predesigned primers and pre-
optimized reaction parameters you can head straight into the lab and get started.
However, if this is not the case then there are a few more things to consider.
Depending on the gene you are investigating, you may need to find and
identify the gene sequence and design primer pairs (Chapter 2). If you are
using novel or newly designed primers, they may not work first timedthe
concentration, thermal cycling conditions, or other parameters might need
optimizing (see Chapter 2 for common problems and troubleshooting). You
might find cross-priming if you are looking for more than one gene at a time or
the primers you have designed may dimerize (Chapter 2).
You will need to prepare template DNA; this can be done using a com-
mercial kit or you can use your own “in-house” methods (Section 1.4). Either
way, this will take time, 30 min to a couple of hours with a commercial kit
(depending on the kit you use), or half to a full day, if using your own method.
After extracting the DNA, you will have to check its concentration and purity
(Chapter 3), and if there are problems at this stage, you might need to repeat
the extraction. Each of these adjustments could take a day or more of your
time so it is easy to see how, if everything does not run perfectly first time,
things might take longer than expected.
Something that people tend to forget to factor in is the delivery time for the
reagents. Depending on your ordering system and the supplier, sometimes
reagents can take a couple of weeks to arrive; it is always best to ask the
company when ordering to see if they can tell you the expected delivery time.
However, if you have everything in the lab and your template DNA was
successfully extracted, you should be able to perform a standard PCR and gel
analysis within a day.
Reagent Checklist
For PCR:
DNA extraction kit (if using)
Glass beads (if not using a kit)
Lysis buffer (if not using a kit)
RNAse A, proteinase K (if not using a kit)
Phenol:chloroform:isoamyl alcohol (25:24:1; pH, 7.5e8 for DNA)
Ethanol (100% and 70%)
Sodium acetate (3 M; pH, 5.5dcan be purchased or made)
Polymerase enzymes and associated buffers (usually supplied as
enzyme þ tube of concentrated reaction buffer þ Mg2þ solution)
Primers (purchased as lyophilized powder you will need to reconstitute)
dNTPs (mixed or individually)
Nuclease-free water (or use nanopure water)
Reaction tubes (normally nuclease-free PCR tubes)
Filter tips
All of these reagents can be purchased from numerous suppliers; it is
usually the best to see if anyone else has been working with PCR within your
department, as there may be a preferred supplier. It is also always worth
speaking to a few companies, to see which have the best deals on the products
you are interested in. Some (but by no means all) of the companies you are
likely to come across when shopping for these reagents are given below. Each
will have their own regional website depending on the country you are in; you
can link through to these from the webpages in the following list:
Bio-Raddwww.biorad.com
Sigmadwww.sigmaaldritch.com
Qiagendwww.qiagen.com
Thermo Scientificdwww.thermoscientificbio.com
Promegadwww.promega.com
GE Healthcare Lifesciencesdhttp://www.gelifesciences.com
Life Technologiesdhttp://www.lifetechnologies.com
Biolinedwww.bioline.com
Planning for PCR Chapter j 1 9
SUMMARY
With the exception of your primer pairs, you will by now have designed,
prepared, and ordered all of the things you need to undertake your first PCR
and will also have your template DNA ready to usedthis can be stored at
either 4 C (short term) or 20 C (long term). In the next chapter, you will
learn how to design primer pairs and analyze (quantify and assess purity) the
template DNA and PCR product.
Chapter 2
2.1 INTRODUCTION
In order to amplify a gene of interest you need to know the gene sequence so
that you can design primers. Primers are short sequences of DNA that are
designed to be complementary to regions of your gene of interest; the area of
DNA sequence in between the primers is the part that is amplified by poly-
merase chain reaction (PCR) and is referred to as the amplicon or PCR
product. If your primers are not correctly designed, you can run into problems
such as mispriming (where the primer binds to the wrong bit of DNA), mul-
tiple priming (where the primer binds many regions of DNA) or no priming at
all (if the primers, for example, form a secondary structure rather than
annealing to your template DNA).
Once you have designed and ordered your primers you must handle and
store them correctly as they can degrade fairly quickly. Short pieces of DNA
are ideal targets for DNases which can be inadvertently introduced into your
primer stock. So always make sure you handle your primers in a “clean” way
(as described in Chapter 1), wearing gloves, and using filter tips. Prepare a
working stock of the primers (see Section 2.10) and store the master stock,
relatively untouched.
This chapter will guide you through the basic parameters for primer design,
handling, and preparation; by the end of it you should be able to confidently
design PCR primers pairs that work!
FIGURE 2.1 Gene sequence showing primers designed to prime at the beginning and end of the
gene, thus amplifying the entire gene.
Primer Parameters Chapter j 2 13
start. On this figure, the start and stop codon are highlighted in bold, and the
selected primer sequence is highlighted in yellow. If you are not amplifying an
entire gene, decide the length of your required amplicon and pick an area that
you would like to be your forward primer and another that will be your reverse
primerdyou will invariably make adjustment to this initial choice, but again,
this gives you something to start with.
The GþC content of the genome you are working with can cause problems
for primer design. An “ideal” organism will have a typical GþC ratio of about
50%. Organisms with high GþC ratios mean that you can end up with primers
that have very high annealing temperatures. Try to avoid regions of DNA that
are highly repetitive or have runs of any one basedthis can be tricky if you are
attempting to amplify an intergenic region of sequence. If the odds are stacked
against you in terms of the sequence you have to work with, then design the
best primer pair that you can and then adjust your PCR parameters to maxi-
mize your chances of success (see Section 2.12 for common problems and
troubleshooting).
M o tt o:
Die Schriften des Hippokrates gaben
das Muster, wie der Mensch die Welt
anschauen und das Gesehene, ohne
sich selbst hineinzumischen,
überliefern sollte.
————————————
Der Verstand mischte sich indessen
auch in die Sache, alles sollte auf
klare Begriffe gebracht und in
logischer Form dargelegt werden,
damit jedes Vorurteil beseitigt und
aller Aberglaube zerstört werde.
Goethe.
Zur Hygiene.
Pulslehre.