Sequencing: Setting Up the PCR Reaction
PCR Component 1: Primer Pair
A PCR primer pair consists of two oligonucleotides, typically 15–30 nucleotides long, which hybridize to complementary strands of the DNA template and flank the region of interest. Recommendations for good PCR primer design include:
Primer Design Software
Primer design software, such as OligoPerfect™ software (available at www.invitrogen.com/oligoperfect), can automatically evaluate a target sequence and design primers for it based on the criteria listed above. To confirm the specificity of your primers, a BLAST® search may be performed against public databases to be sure that your primers only recognize the target of interest.
You can synthesize a PCR primer that has a universal sequencing primer binding site added to the 5´ end. Universal-tailed PCR primers are useful in the following scenarios:
PCR Component 2: DNA Polymerase
PCR performance is often related to the DNA polymerase, so enzyme selection is critical to success. One of the main factors affecting PCR specificity is the fact that Taq DNA polymerase has residual activity at low temperatures. Primers can anneal nonspecifically to DNA, allowing the polymerase to synthesize nonspecific product. This complication can be minimized by the inclusion of a hot-start enzyme. Using a hot-start enzyme helps ensure that no active Taq is present during reaction setup and the initial DNA denaturation step.
PCR Component 3: MgCl2
MgCl2 a co-factor of AmpliTaq® polymerase, is critical for good enzyme activity. MgCl2 is chelated by dNTPs, so an increase in dNTP concentration requires an increase MgCl2 concentration.
PCR Component 4: Buffer
An optimized buffer is provided with the enzyme.
PCR Component 5: Additives
Some other additives may be incorporated to facilitate amplification of difficult templates (i.e., DMSO for GC-rich templates)
Performing the PCR Reaction
There are three major steps that make up a PCR reaction. Reactions are generally run for 30 cycles.
- Denaturation—the temperature should be appropriate to the polymerase chosen (usually 95°C). The denaturation time can be increased if template GC content is high.
- Annealing—use appropriate temperatures based on the calculated melting temperature (Tm) of the primers (5°C below the Tm of the primer).
- Extension—at 70–72°C, the activity of the DNA polymerase is optimal, and primer extension occurs at rates of up to 100 bases per second.
PCR amplicons are typically evaluated using agarose gel electrophoresis. To obtain a good sequencing reaction, the PCR product should appear as a single band on an agarose gel. Multiple bands indicate sequence duplications (Figure 1).
The goal of PCR cleanup is to remove the excess PCR primers (one primer is used in each sequencing reaction) and dNTPs (to preserve the ratio of the dNTP to ddNTP necessary for efficient BigDye® Cycle Sequencing reactions). There are several methods for purifying PCR products. Select a method based on the amounts of components carried over from the PCR reaction and on the sequencing chemistry you plan to use:
- Ethanol precipitation
- Gel purification
- Enzymatic purification: involves shrimp alkaline phosphatase (SAP) and Exonuclease I (Exo I) treatment before sequencing; the SAP/Exo I method degrades nucleotides and single-stranded DNA (primers) remaining after PCR
IMPORTANT! If more than one PCR product is present, column purification, ethanol precipitation, or enzymatic purification will not isolate the desired product. Use gel purification to isolate the desired product or reoptimize the PCR to obtain a single product. Ultrafiltration may work if the contaminating PCR products are much smaller than the desired PCR product.