Difference Between Primer and Promoter

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.

CONTENTS

1. Overview and Key Difference
2. What is a Primer 
3. What is a Promoter
4. Similarities Between Primer and Promoter
5. Side by Side Comparison – Primer vs Promoter in Tabular Form
6. Summary

What is a Primer?

Primers are short DNA sequences designed for the amplification of target DNA sequences. Structurally, they possess short nucleotide sequences complementary to the flanking ends of the DNA double strands. They are usually around 20 nucleotides long. During the PCR, Taq polymerase catalyzes the addition of nucleotides into the preexisting nucleotide sequence. Hence, primers serve as starting points for the synthesis of new strands. Taq polymerase works only in 5’ to 3’ direction. Hence, DNA synthesis also takes place in the same 5’ to 3’ direction. Since DNA is double-stranded, two types of primers are needed in PCR. They are known as the forward primer and reverse primer, based on the direction of the elongation of the primer during the DNA synthesis.

Forward primer anneals with antisense DNA strand and initiates the synthesis of + strand of the gene into 5’ to 3’ direction. It has a short nucleotide sequence which is complementary to the 3’ flanking end of the antisense strand. Reverse primer anneals with the sense strand and initiates the synthesis of a complementary strand of the coding strand, which is – a strand of the gene into 5’to 3’ direction. Thus, reverse primer is designed complementary to the 3’ end of the coding strand. Both reverse and forward primers are important for the production of millions to billions of copies of particular regions of DNA which is targeted or interested.

What is a Promoter?

The promoter is a DNA sequence located upstream or at the 5′ end of the transcription initiation site of a gene. It provides a binding site for RNA polymerase and certain regulatory elements in order to initiate the transcription of the gene. It is a regulatory sequence needed for turning on or off a gene. There is a specific nucleotide sequence in the promoter. It can have 100–1000 base pairs. Promoter shows the direction of transcription. Moreover, it indicates the sense strand which should be transcribed.

There are three types of promoter elements as core promoter, proximal promoter and distal promoter. The core promoter is the minimal portion of the promoter required to initiate transcription. It is located most proximal to the start codon. TATA box is a conserved region found in many eukaryotic core promoters. It is found 25 to 35 base pairs upstream of the transcription start site. The proximal promoter is found more upstream to the core promoter. Generally, it is located 250 base pairs upstream to the start codon and contains primary regulatory elements. The distal promoter is found upstream to the proximal promoter, and it contains additional regulatory elements. Bacterial promoters have two short sequence elements in their promoters. TATAAT is the consensus sequence located at -10 of bacterial promoter while TTGACA is the consensus sequence at -35. They are known as -10 element and -35 element.

What are the Similarities Between Primer and Promoter?

• Primer and promoter are two types of DNA sequences.
• They consist of nucleotide sequences.
• Both primer and promoter are important for gene expression.

What is the Difference Between Primer and Promoter?

Primer is a short nucleotide sequence designed for the amplification of target DNA. In contrast, the promoter is a specific regulatory DNA sequence found upstream to the transcription initiation site of a gene. So, this is the key difference between primer and promoter. Primers are about 20 base pairs long while promoter can have 100 -1000 base pairs. Functionally, primers are served as starting sequences for the new strand synthesis while promoters control gene transcription by providing binding sites for RNA polymerase and other transcription factors.

Moreover, a promoter is defined as the direction of the transcription and indicates the sense strand of a gene. Structurally, primer is a short, single-stranded DNA sequence while promoter is a long double-stranded DNA sequence.

The below info-graphic tabulates more comparisons related to the difference between primer and promoter.

Summary – Primer vs Promoter

Primers are short nucleotide sequences complementary to the flanking ends of the target DNA double-strand. Two types of primers are used in PCR. They serve as the starting sequences for the synthesis of new strands. Primers are commercially designed, and they are temperature stable sequences. On the other hand, the promoter is a regulatory sequence of a gene located upstream to the transcription initiation site. Promoters control the transcription of genes. They provide binding sites for RNA polymerase and transcription factors to initiate transcription. Thus, this is the summary of the difference between primer and promoter.

Reference:

1. “Addgene: Promoters”. Addgene.Org, 2020, Available here.
2. “Primer (Molecular Biology)”. En.Wikipedia.Org, 2020, Available here.

Image Courtesy:

1. “Primers RevComp” By Zephyris – Own work (CC BY-SA 3.0) via Commons Wikimedia
2. “Gene structure eukaryote 2 annotated” By Thomas Shafee – Shafee T, Lowe R (2017). “Eukaryotic and prokaryotic gene structure”. WikiJournal of Medicine 4 (1). DOI:10.15347/wjm/2017.002. ISSN 20024436 (CC BY 4.0) via Commons Wikimedia