Structure and Components of DNA

DNA (deoxyribonucleic acid) is a hereditary material commonly found in the nucleus of a cell. It is also present in mitochondria, which is called mitochondrial DNA (mtDNA). DNA is a polymer of the many mono-deoxy ribonucleotides, covalently linked by 3′-5′ phosphodiester bonds. It is a double-stranded molecule in which two strands wind around each other and form a double helix. Whereas some viruses like Parvovirus have a single-stranded DNA molecule.

DNA consists of deoxyribose sugar, nitrogenous bases (purine and pyrimidine), and phosphoric acid. Information is encoded in the DNA as the sequences of ATGC. Adenine (A) pairs with thymine (T) with the double hydrogen bonds, whereas guanine (G) pairs with cytosine (C) with the triple hydrogen bonds. The arrangement of the nucleotides (ATGC) in two strands gives rise to the spiral structure of DNA, commonly known as the double helix.

Structure of DNA
Structure of DNA,
Courtesy: National Human Genome Research Institute

Components of DNA

The essential components of DNA are acid (phosphoric acid), pentose sugar (deoxyribose sugar), and nitrogen bases; purine (adenine and guanine) and pyrimidine (cytosine and thymine).

phosphoric acid , deoxyribose sugar, and nitrogenous bases
Phosphoric acid, deoxyribose sugar, and nitrogenous bases

Phosphoric acid

It contains the three monovalent hydroxyl groups and one divalent oxygen atom linked to the pentavalent phosphorus atom. The molecular formula of phosphoric acid is H3PO4.

Pentose sugar

Deoxyribose sugar is the pentose sugar present in the DNA. Since it lacks one oxygen atom in carbon-2, it is known as deoxyribose. Pentose sugar forms the ester with phosphoric acid and forms the 3’-5′ phosphodiester bond. 

3′-5′ phosphodiester bonds

Phoshpodiester bond is present between the 5’-hydroxyl group and the 3’-hydroxyl group of the deoxypentose of the nucleotides. The phosphate group joins these hydroxyl groups in the adjacent nucleotides. In the DNA, the sequences are encoded in the 5′ end to the 3′ end of the chain. E.g., 5’-ATGC-3′

Nitrogenous bases 

There are two types of nitrogenous bases: purine and pyrimidines. The purine derivatives present in the DNA are adenine (A) and guanine (G). The pyrimidine derivatives present in the DNA are thymine (T) and cytosine ( C). In the case of the RNA, thymine (T) is absent, which is replaced by the uracil (U).

Base-compositions of DNA (Chargaff rule)

The Chargaff rule was given by Erwin Chargaff and his colleagues in the 1940s and has given the following conclusions:

  • The base composition of DNA generally varies from one species to another.
  • DNA specimens isolated from the different tissues of the same species have the same base composition.
  • The base composition of DNA in a given species does not change with the organism’s age, nutritional state, or changing environment.
  • The number of adenine is equal to thymine (A=T), and guanine is equal to cytosine (G=C), i.e., A+G=T+C.

Proportion of the nitrogenous bases in human and E.coli are:

  • Human: A-30.9 T-29.4 G-19.9 C-19.8
  • E.coli: A-24.7 T-23.6 G-26.0 C-25.7

Primary structure of DNA

The primary structure of DNA consists of the linear sequence of nucleotides linked together by phosphodiester bonds. Nucleotides is composed of three components; nitrogenous bases, 5-carbon (pentose) sugar, and phosphate groups.

primary structure of DNA
Primary structure of DNA

Secondary structure of DNA

The secondary structure of DNA is a set of interactions between the bases, i.e., two linear strands bound to each other by phosphodiester bonds forming the double helical structure of the DNA. The secondary structure is responsible for maintaining the shape of the nucleic acid.

Tertiary structure of DNA

The tertiary structure of DNA is the most common double helix structure which includes the 3-forms of the DNA; A, B, and Z form. The handedness (left or right) of the DNA, length of helix turn, and the number of bases per turn are the basis for the different forms. It is the location of the atom in the 3-dimensional space.

Double helix: Watson and Crick’s model

Watson and Crick’s model of double helical DNA was postulated by James D. Watson and Francis H.C. Crick in 1953. According to this model, the two helical DNA chains are wound around each other in the same axis of symmetry.

Watson and crick's model of DNA
Watson and Crick’s model of double-helical DNA, source: Nature

The purine and the pyrimidine bases in both the strands are hydrophobic and stacked inside the double helix. Deoxyribose and phosphate groups are the backbone of the DNA outside the double helix, which are hydrophilic.

When these two helices are wound around each other, two types of grooves are formed: major groove and the minor groove.

  • Major groove: width-12 nm, depth-8.5 nm
  • Minor groove: width-6 nm, depth-7.5 nm

The diameter of the helix is 20 Å (Angstrom). The bases are 3.4 Å apart on the helix axis. The length of each helical turn is 34 Å. In each of the complete turns of the double helix, 10 base pairs are present in it.

The hydrogen bond present in the double helix confers stability in the DNA. There is a double hydrogen bond between adenine and guanine, whereas triple hydrogen bonds are present between cytosine and thymine. The B-form of DNA (Watson-Crick structure of DNA) is the most stable form of DNA.

A-DNA

  • The size of the A-DNA is about 26 Å.
  • It is a right-handed double helix. 
  • It contains 11 base pairs per helical turn.

B-DNA

  • The size of the B-DNA is about 20 Å.
  • It is a right-handed double helix.
  • It contains 10 base pairs per helical turn.

Z-DNA

  • The size of the Z-DNA is about 18 Å.
  • It is a left-handed double helix.
  • It contains 12 base pairs per helical turn.
different forms of DNA
Different forms of DNA

Some viruses like Parvoviruses contain single-stranded DNA.

The difference between double-stranded DNA and single-stranded DNA

Although double stranded and single stranded DNA has same composition, these have different strand (single stranded has one and double stranded has two) aligned in different shapes. Likewise, the A/T and G/C ratio also differs. A detailed difference is given below:

ds DNA (double stranded DNA)ss DNA (single stranded DNA)
Double-stranded DNA is a linear or filamentous type.It is stellate-shaped (star-like)
DNA double helix behaves as a rigid rod.It behaves as a randomly coiled polymer.
A/T ratio approaches unity.A/T ratio is 0.77
G/C ratio also approaches unity.G/C ratio is 1.3
It is resistant to the action of formaldehyde.It reacts readily with formaldehyde.
Ultraviolet absorption increases from 0℃ to 80 ℃.Ultraviolet absorption increases from 20℃ to 90℃.

Functions of DNA

The DNA carries and transfers the genetic material from the parent cell to its offspring during replication. DNA also carries all the genetic codes for synthesizing RNA. The RNA then codes proteins essential for the growth, development, and proper functioning of any cell. So, DNA can be termed an instruction manual for cells.

References

  • Watson, J., Baker, T., Bell, S., Gann, A., Levine, M., & Losick, R. (2004). Molecular biology of the gene (5th ed.). Pearson Education.
  • Deoxyribonucleic Acid (DNA). Genome.gov. (2022). Retrieved 4 August 2022, from https://www.genome.gov/genetics-glossary/Deoxyribonucleic-Acid.
  • Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Structure and Function of DNA. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26821/
  • Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100

Sushmita Baniya

Hello, I am Sushmita Baniya from Nepal. I am a postgraduate student of M.Sc Medical Microbiology. I am interested in Genetics and Molecular Biology.

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