What is the Difference Between Oligonucleotide and Polynucleotide

The main difference between oligonucleotide and polynucleotide is that the oligonucleotide is a short sequence of nucleotides typically containing 20 bases whereas polynucleotide is a polymeric macromolecule with many nucleotides. Furthermore, oligonucleotides are important as primers which facilitate the DNA synthesis by DNA polymerases while polynucleotides can be either DNA or RNA, mainly storing genetic information of all living organisms. 

In brief, the oligonucleotide and polynucleotide are two types of polymers of nucleotides. Where, either RNA nucleotides or DNA nucleotides take part in the formation of these polymers. Thus, based on the type of nucleotide in the structure, these polymers are known as RNA and DNA respectively. 

Key Areas Covered 

1. What is an Oligonucleotide
     – Definition, Structure, Role
2. What is a Polynucleotide
     – Definition, Structure, Role
3. What are the Similarities Between Oligonucleotide and Polynucleotide
     – Outline of Common Features
4. What is the Difference Between Oligonucleotide and Polynucleotide
     – Comparison of Key Differences

Key Terms 

DNA, Nucleotide, Oligonucleotide, Polynucleotide, RNA

Difference Between Oligonucleotide and Polynucleotide - Comparison Summary

What is an Oligonucleotide 

Oligonucleotide or oligomer is a short, single-stranded DNA or RNA fragment. In principle, oligonucleotides contain a few repeating units, which can be 10 to 100. Therefore, they undergo an infinite degree of polymerization. Furthermore, oligonucleotides are a type of polynucleotides. Solid-phase chemical synthesis is the method of synthesizing oligonucleotides.

Main Difference - Oligonucleotide vs Polynucleotide

Figure 1: RNA probes in FISH

Furthermore, oligonucleotides are important in genetic testing, research, and forensics. Importantly, they play a key role in artificial gene synthesis by solid-phase chemical synthesis, as primers in DNA replication, PCR, and DNA sequencing, and as molecular probes in in-situ hybridization and gene knockdown assays. Here, oligonucleotides are an indispensable element in antisense therapy, which uses gene knockdown assays. 

What is a Polynucleotide 

A polynucleotide is a polymeric molecule of either DNA or RNA nucleotides. It may compose of 13 or more nucleotides. Polynucleotides, typically, contain an infinite number of nucleotides. DNA and RNA are examples of polynucleotides. In this, the DNA is a double-stranded macromolecule.

Furthermore, there are three main types of RNA molecules; they are the mRNA, tRNA, and rRNA. These are single-stranded molecules, which can often form secondary structures through complementary base pairing.

Difference Between Oligonucleotide and Polynucleotide

Figure 2: DNA and RNA

Moreover, DNA is the universal macromolecule which stores genetic information in all living organisms, in both eukaryotes and prokaryotes. Meanwhile, all three types of RNAs take part in protein synthesis. Basically, the mRNA is the resultant of transcription of protein-coding genes, transporting information for the synthesis of a particular protein from the nucleus to the cytoplasm. In here, both tRNA and rRNA are important in facilitating translation. Typically, tRNA carries corresponding nucleotides to ribosomes where translation occurs. And, the rRNA and its associated proteins make up ribosomes, decoding codons on mRNA. Furthermore, the RNA serves as genetic material in RNA viruses. 

Similarities Between Oligonucleotide and Polynucleotide 

  • Oligonucleotide and polynucleotide are two types of polymers of nucleotides. 
  • However, these nucleotides can be either DNA nucleotides or RNA nucleotides. 
  • In the case of DNA nucleotides, they are DNA molecules and in the case of RNA nucleotides, they are RNA molecules. 
  • Further, both their nitrogenous bases include adenine, guanine, cytosine, and thymine in DNA molecules and adenine, guanine, cytosine, and uracil in DNA molecules. 
  • In the case of RNA polymers, both oligonucleotides and polynucleotides are single-stranded molecules.  
  • Also, both contain a sugar-phosphate backbone, which occurs by the formation of phosphodiester bonds between the 3′ OH on the pentose sugar of the existing nucleotide and 5′ phosphate group on the phosphate sugar of the incoming nucleotide.  
  • Besides, both have different applications in the field of biotechnology. 

Difference Between Oligonucleotide and Polynucleotide 


Oligonucleotide refers to short DNA or RNA molecules with a small number of nucleotides while polynucleotide refers to a biopolymer, containing 13 or more nucleotides. 

Number of Nucleotides 

In general, an oligonucleotide composes of 10 to 100 nucleotides while a polynucleotide composes of 13 or more nucleotides, in principle, infinite. 


While oligonucleotides are short fragments of DNA or RNA, polynucleotides are comparatively large in size. 

Degree of Polymerization 

Moreover, oligonucleotides show a finite degree of polymerization while polynucleotides show an infinite degree of polymerization. 

Molecular Duplex Formation 

Oligonucleotides are generally single-stranded molecules while polynucleotides such as DNA are double-stranded macromolecules. 


Furthermore, oligonucleotides are important as primers for DNA polymerization and probes for in situ hybridization and gene knockdown assays while polynucleotides play a role as molecules, which store genetic information in all living organisms as well as, viruses. 


An oligonucleotide is a type of polynucleotide composed of around 10 to 100 nucleotides, which can be either DNA or RNA nucleotides. Thus, they are short nucleotide fragments with a finite degree of polymerization. Generally, oligonucleotides are single-stranded molecules important as primers in DNA polymerization and probes as hybridization and knockdown assays. In contrast, a polynucleotide is a type of macromolecule, typically composing of 13 or more nucleotides. However, the number of nucleotides in a polynucleotide can be infinite. Furthermore, polynucleotides such as DNA is the universal macromolecule responsible for storing genetic information. Meanwhile, RNA stores genetic information of RNA viruses. Therefore, the main difference between oligonucleotide and polynucleotide is the number of nucleotides and their importance.   


1. “Oligomer.” Wikipedia, Wikimedia Foundation, 27 Apr. 2019, Available Here.
2. “Nucleic Acid.” Wikipedia, Wikimedia Foundation, 29 Oct. 2019, Available Here.

Image Courtesy:

1. “Q-FISH workflow” By Jclam at English Wikipedia (CC BY 3.0) via Commons Wikimedia   
2. “Difference DNA RNA-EN” By File:Difference DNA RNA-DE.svg (CC BY-SA 3.0) via Commons Wikimedia   

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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