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 PCR is an technique used to amplify a specific DNA
(target) sequence lying between known positions
(flanks) on a double-stranded DNA molecule.
 PCR was first developed by Karl Mullis in 1983.
 The polymerase chain reaction can be used to amplify
both double and single stranded DNA.
 In order to perform PCR, one must know at least a portion
of the sequence of the target DNA molecule that has to be
copied.
 Generally, PCR amplifies small DNA targets 100-1000 base
pairs long.
 A pair of single stranded oligonucleotide primers, which
have DNA sequences complementary to the flanking
regions of the target sequence, must be synthesized.
 The primers are complementary to either end of the target
sequence but lie on opposite strands. The primers are
usually 20-30 nucleotides long and bind to complementary
flanking region at 3' end and starts polymerase activity.
 Thermal cycler (thermo cycler) ƒ
 PCR amplification mix typically containing: ƒ
1) Sample ds DNA with a target sequence ƒ
2) Thermo stable DNA polymerase ƒ(taq polymerase).
3) Two oligonucleotide primers ƒ
4) Deoxynucleotide triphosphates (dNTPs) ƒ
5) Reaction buffer containing magnesium ions and other
components
1) Initial stage
2) Denaturation of ds DNA
3) Primer annealing
4) Polymerase activity
 This four steps constitutes the single
cycle.
 This stage is only required for DNA polymerases that
require heat activation by hot-start PCR.
 This step consists of heating the reaction to a
temperature of 94–96 °C (or 98 °C if extremely thermo
stable polymerases are used), which is held for 1–9
minutes.
 This step is the first regular cycling event and consists
of heating the reaction to 94–98 °C for 20–30 seconds.
 It causes DNA melting of the DNA template by
disrupting the hydrogen bonds between
complementary bases, yielding single-stranded DNA
molecules.
 The reaction temperature is lowered to 50–65 °C for 20–40
seconds allowing annealing of the primers to the single-stranded
DNA template.
 This temperature must be low enough to allow for hybridization
of the primer to the strand.
 If the temperature is too low, the primer could bind
imperfectly. If it is too high, the primer might not bind.
 Stable DNA–DNA hydrogen bonds are only formed when the
primer sequence very closely matches the template sequence.
 An incorrect annealing temperature will cause an error in the test.
 Taq polymerase has its optimum activity temperature at 75–
80 °C and commonly a temperature of 72 °C is used with
this enzyme.
 At this step the DNA polymerase synthesizes a new DNA
strand complementary to the DNA template strand by
adding dNTPs that are complementary to the template in 5'
to 3' direction.
 Under optimum conditions, i.e., if there are no limitations
due to limiting substrates or reagents, at each extension
step, the amount of DNA target is doubled, leading to
exponential amplification of the specific DNA fragment.
 At the end of cycle one single double stranded DNA
is polymerized into two double stranded DNA.
 This cycle continues to produce billions of ds DNA
molecules.
Polymerase chain reaction(pcr)
Polymerase chain reaction(pcr)

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Polymerase chain reaction(pcr)

  • 1.  PCR is an technique used to amplify a specific DNA (target) sequence lying between known positions (flanks) on a double-stranded DNA molecule.  PCR was first developed by Karl Mullis in 1983.  The polymerase chain reaction can be used to amplify both double and single stranded DNA.
  • 2.  In order to perform PCR, one must know at least a portion of the sequence of the target DNA molecule that has to be copied.  Generally, PCR amplifies small DNA targets 100-1000 base pairs long.  A pair of single stranded oligonucleotide primers, which have DNA sequences complementary to the flanking regions of the target sequence, must be synthesized.  The primers are complementary to either end of the target sequence but lie on opposite strands. The primers are usually 20-30 nucleotides long and bind to complementary flanking region at 3' end and starts polymerase activity.
  • 3.  Thermal cycler (thermo cycler) ƒ  PCR amplification mix typically containing: ƒ 1) Sample ds DNA with a target sequence ƒ 2) Thermo stable DNA polymerase ƒ(taq polymerase). 3) Two oligonucleotide primers ƒ 4) Deoxynucleotide triphosphates (dNTPs) ƒ 5) Reaction buffer containing magnesium ions and other components
  • 4. 1) Initial stage 2) Denaturation of ds DNA 3) Primer annealing 4) Polymerase activity  This four steps constitutes the single cycle.
  • 5.  This stage is only required for DNA polymerases that require heat activation by hot-start PCR.  This step consists of heating the reaction to a temperature of 94–96 °C (or 98 °C if extremely thermo stable polymerases are used), which is held for 1–9 minutes.
  • 6.  This step is the first regular cycling event and consists of heating the reaction to 94–98 °C for 20–30 seconds.  It causes DNA melting of the DNA template by disrupting the hydrogen bonds between complementary bases, yielding single-stranded DNA molecules.
  • 7.  The reaction temperature is lowered to 50–65 °C for 20–40 seconds allowing annealing of the primers to the single-stranded DNA template.  This temperature must be low enough to allow for hybridization of the primer to the strand.  If the temperature is too low, the primer could bind imperfectly. If it is too high, the primer might not bind.  Stable DNA–DNA hydrogen bonds are only formed when the primer sequence very closely matches the template sequence.  An incorrect annealing temperature will cause an error in the test.
  • 8.  Taq polymerase has its optimum activity temperature at 75– 80 °C and commonly a temperature of 72 °C is used with this enzyme.  At this step the DNA polymerase synthesizes a new DNA strand complementary to the DNA template strand by adding dNTPs that are complementary to the template in 5' to 3' direction.  Under optimum conditions, i.e., if there are no limitations due to limiting substrates or reagents, at each extension step, the amount of DNA target is doubled, leading to exponential amplification of the specific DNA fragment.
  • 9.  At the end of cycle one single double stranded DNA is polymerized into two double stranded DNA.  This cycle continues to produce billions of ds DNA molecules.