I am facing problem to amplify full length gene (around 1.5 kb) using cDNA with primer length varying from 24-28 decamer( attached with adapter) at tm 62 degree celsius. What PCR profile I should follow please suggest.
When amplifying a full-length gene (around 1.5 kb) from cDNA using primers with varying lengths (24-28 nucleotides) and a melting temperature (Tm) of 62°C, it's important to design a PCR profile that optimizes the amplification process. Here's a suggested PCR profile:
Initial Denaturation:95°C for 3-5 minutes. This step ensures complete denaturation of the template DNA and helps inactivation of any potential carryover contaminants.
Cycling Conditions: Denaturation (Step 1):95°C for 15-30 seconds. Ensure thorough denaturation of the template DNA. Annealing (Step 2):Use the Tm of your primers as a starting point. Since your primers have a Tm of 62°C, set the annealing temperature initially around 3-5°C below the lowest primer Tm (e.g., 58-60°C). Optimize the annealing temperature by running a gradient PCR or a series of reactions with different annealing temperatures to find the most suitable condition for specific primer sets. Extension (Step 3):72°C for 1 minute per kb of your expected product length. Ensure sufficient time for complete extension of the PCR product.
Number of Cycles:Perform 25-35 cycles. The actual optimal cycle number may need to be determined experimentally, and it can vary based on the efficiency of your reaction.
Final Extension:72°C for 5-10 minutes. Allow for complete extension of any remaining incomplete PCR products.
Hold at 4-10°C:Hold the reaction at 4-10°C until you are ready to analyze or store the PCR products.
Additional Considerations:
Primer Design: Ensure that the primers are designed to have similar melting temperatures (Tm). The Tm of the primers can affect the efficiency of PCR.
PCR Optimization: If the initial PCR does not yield the desired product, consider optimizing reaction conditions, such as primer concentration, MgCl2 concentration, and annealing temperature.
PCR Clean-up: After successful amplification, consider using a PCR purification kit to remove any remaining primers or nucleotides before downstream applications.
Remember that the optimal PCR conditions may need to be determined empirically, and some degree of optimization might be necessary based on the specifics of your reaction. Running a gradient PCR can be particularly useful in finding the optimal annealing temperature for your specific primer pairs.
Generally, the normal PCR profile works perfectly for such amplifications. You did not mention the polymerase you used. If any HF polymerase (Q5/Phusion etc) is available in your lab, proceed with it once per the manufacturer's instructions. Otherwise, you need to recheck your primers, say for GC content etc. Generally, 1.5 kb amplicon size is not an issue.