Secondary Structure of DNA

Nucleic acids (both DNA and RNA) have primary, secondary, and tertiary structures. The two strands of DNA in a double helix are bonded together by hydrogen. The nucleotides on one strand pair with those on the opposite strand. This makes the secondary structure which is solely responsible for the nucleic acid’s shape. Here, let’s learn more about the secondary structure of DNA.

Table of Contents

What is the Primary Structure of DNA?

DNA is a living organism’s genetic blueprint in which all hereditary information is stored and passed on. The primary DNA structure mainly refers to the linear nucleotide sequences that are held together by strong phosphodiester bonds. A nucleotide comprises three components – sugar, nucleobase and a phosphate group. The phosphodiester bond is present between the 3′ carbon of one nucleotide and the 5′ carbon of the adjacent nucleotide. The sugar and the phosphate backbone are held together by these strong covalent bonds.

The shape of the nucleotide monomer causes the double-helix shape of DNA. A helix is frequently formed when asymmetrical molecules are placed one on top of the other. Each DNA strand runs antiparallel to the other strand in the opposite directions. Let’s learn more about the double helix structure of DNA.

DNA – Secondary Structure

The set of interactions between nucleobases, phosphate backbone and sugar molecules forms the crux of DNA’s secondary structure. These three units together form nucleotides. DNA is a long chain molecule formed by the end-to-end polymerisation of a large number of repeated nucleotide units. Watson and Crick presented the secondary structure of DNA based on X-ray crystallographic studies.

  • The 2 strands of DNA are twisted in a helical configuration and are held strongly by hydrogen bonds.
  • The nucleotides present on one strand pair with those on the opposite strand. These 2 strands run antiparallel to each other.
  • Purines and pyrimidines are the two types of nucleobases found in DNA. Adenine and guanine are the purines. Purines have a double ring structure with a nitrogen-containing six-membered and five-membered ring. Cytosine and thymine are pyrimidines. Pyrimidines are a single ring structure which is a nitrogen-containing six-membered ring.
  • Guanine (G) always pairs with cytosine (C), and thymine (T) always pairs with adenine (A). Here, the hydrogen bonds are specific to the base. Adenine and thymine pair with two hydrogen bonds, while cytosine and guanine pair with three hydrogen bonds.
  • Apart from hydrogen bonds, the stacking interactions present between the bases that are stabilised by Van der Waals forces also play a vital role in holding the strands. Base-pairing of the 2 polynucleotide strands coiled around each other to form a double helix determines the secondary structure of DNA.
  • The double helix also has two grooves, which are referred to as major and minor grooves based on the relative size of the grooves. The former is approximately 22 â„« wide and the latter is 12 â„« wide.
  • One turn (360°) of the spiral has approximately 10 nucleotides on each DNA strand occupying a distance of approximately 3.4 nm.

What is Tertiary Structure?

The next level above the secondary structure is the tertiary structure. It describes the conformation of the entire nucleic acid. The tertiary structure usually refers to the 3-D shape of a DNA polymer. Secondary structure is largely limited to a small number of conformations but tertiary is virtually unlimited.

Also see: Structure of RNA

DNA structure

DNA Packaging

DNA packaging is a critical process in all living cells. DNA packaging tightly packs a large amount of DNA into the small nucleus of every cell. DNA is wrapped around proteins called histones during DNA packaging.

Each nucleosome is made up of 1.65 loops of DNA wrapped around eight histone proteins (histone octamer). Nucleosomes are then packaged like beads on a string (thread-like structure). This fibre compresses and folds into a chromosome’s chromatid. The process culminates in the formation of chromatin fibre.

This packaging also makes it easier to separate the correct chromosomes during cell division. Because of the highly packed DNA structure, it is simple to turn genes on and off as needed.

Keep exploring BYJU’S Biology to learn more such exciting topics.

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Related Concepts:

Difference between Gene and DNA

Difference between DNA and RNA

Difference between Replication and Transcription

Frequently Asked Questions

Q1

What are the three configurations of DNA?

Z-DNA, A-DNA, and B-DNA are examples of the three configurations of the double helix in space. B-DNA which is a right-handed double helix is the common form of DNA whereas Z-DNA is a left-handed helix. A-DNA is also right-handed like B-DNA but it is a more compact and shorter helical structure.
Q2

What are purines and pyrimidines?

The nitrogenous bases can be pyrimidines or purines. Pyrimidines are thymine and cytosine and the purines are guanine and adenine. According to Chargaff’s rule, the amount of pyrimidines in a DNA is equal to the amount of purines (C+T = A+G). Also, the amount of thymine is equal to adenine and cytosine is equal to guanine. Thus the pyrimidine and purine bases should be present in a 1:1 ratio in the DNA of an organism.
Q3

What is a nucleosome?

In eukaryotes, the DNA is tightly bound to an equal mass of histones which serve to form a repeating array of DNA protein particles called nucleosomes. Thus it is the basic structural unit with regard to DNA packaging. It is also a fundamental subunit that makes the chromatin.
Q4

What is DNA supercoiling?

DNA supercoiling refers to the tertiary interwinding of the double-helical DNA axis. It is the amount of twist in a specific DNA strand that determines the expression of strain on it. A strand can be either negatively supercoiled (less tightly wound) or positively supercoiled (more tightly wound).