Would exonic primers affect gDNA amplification?

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A primer designed for an exonic sequence may not successfully amplify genomic DNA (gDNA) due to potential issues with non-specific annealing sites within the gDNA. While the primer works effectively with complementary DNA (cDNA), the complexity of gDNA can lead to amplification challenges. One suggested solution is to consider using nested PCR, especially if upstream or downstream genetic information is available, as this can enhance specificity and improve amplification results.
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Will a primer designed for an exonic sequence anneal and sucessfully amplify a gDNA strand? I'm having trouble amplifying gDNA using that primer. cDNA with that primer amplifies perfectly. I have no problem amplifying gDNA using another primer that anneals to intronic sequences.
 
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I can't think of a reason why any given primer should work only for cDNA. Maybe the reason why you're having trouble with the genomic DNA amplification has to do with other possible annealing sites on the genomic DNA? I had this problem before. If you have upstream/downstream genetic information, maybe you should try a nested PCR?
 

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