fidelity thermophilic DNA polymerases.
Materials and Methods
Thermocycler
DNA amplification was performed on MJ Research PTC-200 thermocyclers that had recently been calibrated by the
manufacturer. Reactions
to
prevent evaporation if not using a thermocycler with
a heated lid.
4. The amplification parameters will vary depending
on the primers and the thermocycler used. It may
be necessary to optimize
reagents in a PCR-designated hood in a template-free PCR room (recommended).
2. Program thermocycler with conditions described in Table 7. Start the program and pause the
thermocycler at 96°C to preheat
will vary depending on the primers and the thermocycler used. It may be
necessary to optimize the system for individual primers, template, and thermocycler.
Common cycling parameters are:
a. Denature
will vary depending on the primers and the thermocycler used. It
may be necessary to optimize the system for individual primers, template, and thermocycler.
Common cycling parameters are:
a. Denature
10X PCR
buffers for evaluation.
2. Layer 25 µl of mineral oil over the reaction mix in
every tube if using a thermocycler without a heated
lid.
3. Place the tubes in the thermocycler
will vary depending on
the primers and the thermocycler used. It may be
necessary to optimize the system for individual
primers, template, and thermocycler.
Common cycling parameters are:
a. Denature
reagents in a PCR-designated hood in a template-free PCR room (recommended).
2. Program thermocycler with conditions described in Table 7. Start the program and pause the
thermocycler at 96°C to preheat
reagents in a PCR-designated hood in a template-free PCR room (recommended).
2. Program thermocycler with conditions described in Table 7. Start the program and pause the
thermocycler at 96°C to preheat
will vary depending
on the primers and the thermocycler used. It may
be necessary to optimize the system for individual
primers, template, and thermocycler.
Common cycling parameters are:
a. Denature
Mineral Oil, Product Code M 8662 (optional)
• 0.5 ml or 0.2 ml thin-walled PCR tubes, Product
Codes P 3114 and P 3364
• Thermocycler
• Primers
• DNA to be amplified
• Chloroform, Product Code C 7559 (
, pH 7.0 (e. g., PCR Nucleotide Mix*)
• Water, PCR Grade*.
Depending on the type of thermocycler, the usage of mineral is
optional. Mineral oil must be used in case a thermocycler without
heating lid
polymerase for reliable PCR
amplification, DNA contaminants can be introduced into
PCR through a number of other reagents.2 To further
minimize the risk of contaminant DNA during PCR, we
include 10× MTP
be omitted if you are using a PCR cycler that does not require an oil overlay, according to the
recommendations of the manufacturer.
Place the sample in a thermocycler and start an appropriate cycling
Vortex thoroughly, centrifuge briefly, and begin
thermocycling. The following profile has been
optimized for a PE 9700 or equivalent
thermocycler:
Initial Denaturation 95 C for 3 minutes
time.
Recommendations for hold times are based on the ramp
rate of the thermocycler, as well as the yield required.
Thermocyclers with ramp speeds higher than 3°C/sec are
considered fast, while slow cyclers
Little or no PCR
product is
detected.
Extract was not
neutralized
Make sure SRE0087, Neutralization Solution for Blood was added
to the extract before PCR was performed.
PCR reaction is
Little or no PCR
product is
detected.
Extract was not
neutralized
Make sure SRE0087, Neutralization Solution for Blood was added
to the extract before PCR was performed.
PCR reaction is
performed in a standard thermocycler,
heating block, or waterbath, after which the sample
is centrifuged and the DNA-containing supernatant
recovered. Extracts may be used directly in PCR, without
quantification
performed in a standard thermocycler,
heating block, or waterbath, after which the sample
is centrifuged and the DNA-containing supernatant
recovered. Extracts may be used directly in PCR, without
quantification
centrifuging.
3. Transfer the tubes to a PCR machine and
begin thermocycling using the following
conditions as defined in Table 2.
Table 2.
Thermocycle Program for PCR Reactions
Cycle Step Temp Time
Little or no PCR
product is detected.
Extract was not neutralized
Make sure Cat. No. SRE0087, Neutralization
Solution for Blood was added to the extract before
PCR was performed.
PCR reaction
Little or no PCR
product is detected.
Extract was not neutralized
Make sure Cat. No. SRE0087, Neutralization
Solution for Blood was added to the extract before
PCR was performed.
PCR reaction
time. Recommendations for hold times are based on the
ramp rate of the thermocycler, as well as the yield required.
Thermocyclers with ramp speeds higher than 3°C/sec are
considered fast, while slow cyclers
time. Recommendations for hold times are based on the
ramp rate of the thermocycler, as well as the yield required.
Thermocyclers with ramp speeds higher than 3°C/sec are
considered fast, while slow cyclers
suming steps such as washing (Figure 1). In addition, all
incubation steps can be performed in a thermocycler.
In the work presented here, the effect of gibberellic acid
(GA3) treatment or pollination
or
unmodified Normal control DNA) to each control tube.
e. Place tubes in the thermocycler block, and perform PCR under the following
conditions:
Denature:
for Taq Polymerase 95°C / 5 minutes
the tubes in the thermocycler block.
2. Set-up the real-time experiment to include the following PCR parameters.
30°C 30 min 1 cycle
95°C 2.0 min 1 cycle
45 cycles
94°C
(modified U and M, unmodified W) to
each control tube.
e. Place tubes in the thermocycler block, and perform PCR under the following
conditions:
Denature:
for Taq Polymerase 95°C / 5 minutes