Difference Between dNTP and DdNTP

The key difference between dNTP and ddNTP is that dNTP or deoxyribonucleotides are the building blocks of DNA and have a 3ʹ-OH group on the pentose sugar structure while ddNTP or dideoxynucleoside triphosphates are nucleotides that lack 3ʹ-OH group and they are used in Sanger dideoxy DNA sequencing technique to produce different length DNA sequences.

dNTP and ddNTP are nucleotides. dNTP refers to deoxyribose nucleotides. They are the building blocks of DNA. dNTPs are used to synthesize DNA. dNTP, on the other hand, refers to dideoxynucleoside triphosphates. They are used in Sanger sequencing to terminate DNA synthesis at different lengths. They lack OH group at 3ʹ position. A hydrogen is present at the position 3ʹ instead of OH group. Therefore, ddNTPs are unable to form a phosphodiester bond with the next nucleotide. dNTP is capable of carrying out the synthesis of DNA, while ddNTP is capable of terminating the polymerization of DNA.

CONTENTS

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

What is dNTP?

dNTP stands for deoxyribose nucleotide or deoxyribonucleotide. It is the building block of DNA. There are four types of dNTPs. They are dATP, dTTP, dCTP and dGTP. They are named according to the purine or pyrimidine nitrogenous bases: Adenine (A), Guanine (G), Thymine (T) and Cytosine (C).

Adenine and guanine are purine bases while thymine and cytosine are pyrimidine bases. The pentose sugar of dNTP is deoxyribose. There is also a phosphate group. Therefore, dNTP is composed of three components: a nitrogenous base, deoxyribose sugar and a phosphate group. These dNTPs combine with each other via phosphodiester bonds. In dNTPs, there is an OH group attached to position 3ʹ of pentose sugar which is required to form a link with the phosphate group attached to the 5ʹ carbon of the sugar of next nucleotide. Since all dNTPs have this 3ʹ -OH group, they are capable of synthesizing and extending DNA strands. Hence, dNTP acts as the basic repeating unit of DNA and chemical matter of genes. The synthesis of DNA always proceeds from 5ʹ to 3ʹ.

What is DdNTP?

Sanger sequencing is a first-generation DNA sequencing method developed by Frederick Sanger and his colleges in 1977. It is also known as Chain Termination Sequencing or Dideoxy sequencing since the basic principle of this method is the chain termination using dideoxynucleoside triphosphates (ddNTPs). ddNTPs are nucleotides used in Sanger sequencing. Sanger sequencing is based on the selective incorporation of ddNTPs and termination of DNA synthesis during the in vitro DNA replication. The speciality of the ddNTPs is that they lack 3ʹ-OH group on the pentose sugar to continue phosphodiester bond formation between the phosphate group of 5ʹ in adjacent nucleotide. Hence, once a ddNTP is attached to the extending strand, chain elongation ceases and terminates from that point. ddNTPs act as chain-elongating inhibitors of DNA polymerase during the Sanger sequencing method.

There are four ddNTPs: ddATP, ddCTP, ddGTP and ddTTP used in Sanger sequencing. These nucleotides stop the DNA replication process when they are incorporated into the growing strand of DNA. As a result, Sanger sequencing produces varying lengths of short DNA. Capillary gel electrophoresis is used to organize these short DNA strands by their sizes on a gel. ddNTPs are radioactively or fluorescently labelled with different colours for the ease of analyzing the DNA sequence. By analyzing the gel, the nucleotide sequence of the unknown DNA strand can be determined.

What are the Similarities Between dNTP and DdNTP?

• Both dNTP and ddNTP are used in Sanger sequencing.
• There are four types of dNTPs and ddNTPs.
• They are composed of three components: a nitrogenous base, deoxyribose sugar and phosphate groups.

What is the Difference Between dNTP and DdNTP?

dNTP is one of the four types of deoxyribonucleotides which are building blocks of DNA. ddNTP is one of the four types of dideoxyribonucleoside triphosphates used in Sanger sequencing technique. dNTP has a 3ʹ-OH group on the pentose sugar while ddNTP lacks 3ʹ-OH group on the pentose sugar. Thus, this is the key difference between dNTP and ddNTP. Moreover, dNTPs carry out DNA polymerization while ddNTPs terminate DNA polymerization. Hence, this is another major difference between dNTP and ddNTP.

The below infographic lists the differences between dNTP and ddNTP in tabular form.

Summary – dNTP vs DdNTP

Normal dNTPs are building blocks of DNA while ddNTPs are nucleotides used in Sanger sequencing technique. dNTP has 3ʹ-OH while ddNTP lacks 3ʹ-OH. Thus, this is the key difference between dNTP and ddNTP. Moreover, dNTP can synthesize a DNA strand while ddNTP can terminate the DNA polymerization. Therefore, ddNTPs are used in Sanger sequencing in order to produce different DNA strands with varying lengths. During the Sanger sequencing, both dNTP and ddNTP are included.

Reference:

1. “Dideoxynucleotide.” Wikipedia, Wikimedia Foundation, 12 July 2020, Available here.
2. “Structure and Function of DNA.” Lumen, Available here.

Image Courtesy:

1. “Desoxyribonucleotides” Par Bionet — Travail personnel (CC0) via Commons Wikimedia

2. “Dideoxy termination of DNA elongation EN” By Michał Sobkowski – Own work (CC BY 3.0) via Commons Wikimedia