RNA and DNA primers are short sequences of nucleotides. They serve as starting points for DNA synthesis during replication.
Key Areas Covered
1. What is an RNA Primer
– Definition, Composition, Function
2. What is a DNA Primer
– Definition, Composition, Function
3. Similarities Between RNA Primer and DNA Primer
– Outline of Common Features
4. Difference Between RNA Primer and DNA Primer
– Comparison of Key Differences
RNA Primer, DNA Primer
What is an RNA Primer
RNA primer is an RNA that initiates DNA synthesis. It acts as a binding site for DNA polymerase to initiate DNA replication. RNA primers are typically 10-12 nucleotides long. The enzyme primase synthesizes these RNA primers.
The unwinding of DNA also happens during DNA replication. Each strand of the DNA serves as a template for the synthesis of a new complementary strand; however, DNA polymerase cannot initiate the synthesis of a new DNA strand. It only extends an existing strand. Hence, RNA primers are necessary to start DNA synthesis.
After the synthesis of the RNA primer, DNA polymerase adds nucleotides to the 3’-OH group of the RNA primer, which extends the DNA strand. Then RNase H removes the RNA primer, and the gap left behind by the RNA primer is filled with the nucleotides by the DNA polymerase. We call this process primer removal and DNA repair synthesis.
Moreover, RNA primer is complementary to the template DNA strand. It is synthesized in the 5’ to 3’ direction, just like that of DNA. In addition, defects in the RNA primer synthesis lead to errors in DNA replication. It may also contribute to genetic diseases like cancer. In fact, in various cancers, mutations are identified in the gene encoding the enzyme RNA primase. A few examples of such are ovarian, pancreatic, and lung cancer.
What is a DNA Primer
DNA primer is a short single-stranded DNA fragment. It is useful in certain laboratory techniques, such as polymerase chain reactions (PCR). PCR method involves the hybridization of a pair of primers with a sample DNA. This defines the region that will be amplified; it gives millions of copies in a very short period. There are other uses of primers, such as in DNA sequencing and other experimental processes. They are usually 18 to 25 nucleotides long. Primers can be synthesized in laboratories.
The 3’ end of the primer serves as the starting point for DNA synthesis. The 5’ typically has a fluorescent or radioactive tag to facilitate the detection and analysis of the PCR product. The specificity of the primer is determined by the nucleotide sequence that should be unique to the target DNA region being amplified.
Moreover, the GC content of the primer sequence can affect the efficiency of the PCR amplification. In fact, primers with a high GC content are more likely to form stable duplexes with the template DNA. But primers with high GC content can also form secondary structures such as hairpins, which can interfere with the amplification.
Furthermore, various modifications to these DNA primers can enhance their performance or facilitate downstream analysis of the PCR product. Primers can also be labelled with a fluorescent tag to facilitate the detection and purification of the PCR product.
Similarities Between RNA Primer and DNA Primer
- RNA primers and DNA primers are short strands of nucleotides.
- Moreover, they serve as a starting point for DNA synthesis.
Difference Between RNA Primer and DNA Primer
RNA primers are short strands of RNA, whereas DNA primers are short strands of DNA.
RNA primers consist of ribonucleotides, whereas DNA primers consist of deoxyribonucleotides.
While RNA primers are typically 8-12 nucleotides in length, DNA primers can be longer, often around 18-24 nucleotides.
RNA primers are useful in initiating DNA replication by providing a free 3’-OH group for DNA polymerase to extend form, whereas DNA primers are useful in PCR to target and amplify specific DNA sequences.
Moreover, RNA primers are more prone to degradation than DNA primers due to the presence of hydroxyl groups on the ribose sugar.
Typically, the synthesis of RNA primers is by primase, a specialized RNA polymerase, while there are a variety of methods to synthesize the DNA primers, such as chemical synthesis or enzyme amplification.
In brief, RNA and DNA primers are short strands of nucleotides that serve as a starting point for DNA synthesis. The main difference between RNA primer and DNA primer is that RNA primers consist of ribonucleotides, whereas DNA primers consist of deoxyribonucleotides.