The key difference between primer and promoter is that primer is a commercially synthesized short DNA sequence which is used in PCR for amplification of a target DNA sequence while promoter is a specific DNA sequence which provides a secure initial binding site for RNA polymerase and transcription factors in order to initiate transcription.
Primer and promoter are two types of DNA sequences. Primer is a small fragment of DNA needed for polymerase chain reaction (PCR). It has short nucleotide sequences complementary to the flanking end of the DNA strand. There are two types of primers, and they work as starting points for the synthesis of new DNA strands. In contrast, a promoter is a specific DNA sequence located upstream to the transcription initiation site of a gene. It directly interacts with the transcription mechanism components such as RNA polymerase and transcription factors in order to control DNA transcription. Therefore, RNA polymerase and other transcription factors bind to the promoter sequence and initiate transcription.
