5 Double Helix of DNA

Prof. Sunil Kumar Khare

  1. Objectives
  • Discovery of DNA
  • Structure of DNA
  • Salient Features of DNA Double Helix
  • Helix Geometries
  • From structure to function
  1. Concept Map
  1. Deoxyribonucleic Acid (DNA)

The discovery of the deoxyribonucleic acid (DNA) structure remains one of the most famous scientific discoveries and hall mark of modern molecular biology. In living organisms, DNA molecule is the blueprint for life. It is the repository and carrier of genetic information and plays integral role in its development, functioning and reproduction.

During her research at the King’s college, London, Rosalind Franklin used X-Rays to be beamed through crystals of DNA. She simultaneously used a photographic film to record where the scattered X -Rays would fall. The shadows on the film would show where the dense molecules lie. Cross shaped shadows were found on the X-Ray film, thereby confirming that the DNA molecule was helical in shape (Fig. 3). The X-Ray that resulted from this experiment was named Photograph 51. Maurice shared the image with Watson and Crick.

In 1953, James Watson and Francis Crick proposed a model for the structure of DNA. This proposal was based on the previous assumptions of Chargaff’s experimental finding (that there are equal numbers of A and T bases and of G and C bases in DNA), and the observations made in Photograph 51 (X-Ray data obtained from crystals of DNA by Rosalind Franklin and Maurice Wilkins ). Watson and Crick outlined the theory that DNA molecule comprised of two complementary polynucleotide strands, which wound around each other to form a double helical structure. Their results were published in 1953 in a paper entitled “A Structure for Deoxyribose Nucleic Acid” in Nature. Watson and Crick were awarded the Nobel Prize in Physiology or Medicine along with Maurice Wilkins, for this work in 1962.

3.2 DNA structure

 

As outlined above, the structure of DNA is represented in the form of polynucleotide strands of DNA coiled around each other to form a double helix. The backbone of this helix is formed by sugar-phosphate and the bases lie towards the interior of the helix, extended at right angles (at 90°) to the helix axis. Bases remain stacked over each other in the double helix. Hydrophobic interactions between stacked bases lead to stabilization of the DNA molecule. Overall the sugar phosphate backbone of each strand is negatively charged due to phosphate group (pKa being near to zero). These charges are stabilized by counter ion Mg2+ .

 

The helical structure of DNA and arrangement of bases within the DNA structure is shown in Figure 5.

Both two-dimensional and three-dimensional images are shown.

Complementary bases from opposite helix pair with each other. Purines form base pairs with pyrimidines, that is base A pairs with base T, and base C with base G (Fig.6) This pairing is known as the Watson-Crick base-pairing.

The hydrogen bonding in the base pairs imparts stability to the helical structure of DNA. The base-pairs G and C are bonded to each other by three H-bonds, while A and C are bonded to each other by two H-bonds. Owing to larger number of H-bonds between the two, the G-C base-pairs are therefore stronger than A-T base-pairs. Greater the number of GC base pairs in a DNA molecule, greater will be the stability than a DNA molecule having more AT base pairs.

 

3.3 Features of double helical structure of DNA

 

The key features of the DNA double helix are given below. Please refer to Fig. 5 as the features are studied.

  • The overall structure of DNA is a double helical structure composed of two polynucleotide strands. One polynucleotide chain coils around the second polynucleotide strand in a double helix.
  • Helix is right handed along the axis.
  • The backbone of each polynucleotide is formed by alternate sugar and phosphate, and the bases lie within the helix, arranged at right angles to the helix axis.
  • The phosphate group remains bonded to the 5′ C of one sugar, and to the 3′ C of the next sugar. A common representation of polynucleotide is 5’pApTpGpC OH3′
  • Two strands run antiparallel to each other: one in 5′ —> 3′ direction and the other in the 3′ —> 5′ direction
  • Each base in the DNA double helix forms hydrogen bonds with complementary bases directly opposite it, forming base pairs. A pairs with T and G with C
  • The planes in which the adjacent base pairs are located are separated by 3.6 Å.
  • There are 10 base pairs found per turn of the helix with a rise of 3.6 Å. One turn of the helix measures 36 Å.
  • Each turn of the double helix contains an average of 25 hydrogen bonds to provides a strong stability.
  • The diameter of DNA helix measures 20 Å.
  • Two deep grooves are found on the surface of double helix which are the major and minor grooves.
    • Minor groove exposes edge from which C1’ atoms where Major groove extend exposes opposite edge of base pair
    •  Major group is wider than the minor group
    •  Protein binding to DNA molecule takes place through the major groove.

3.4 Helix Geometries

 

The DNA molecule exhibits conformational flexibility, and could therefore exist in alternative structural forms. There are three conformations of DNA named as A-DNA, B-DNA and Z-DNA (Fig.7)

Under physiological conditions, the B-DNA forms the most stable structure and is therefore considered as a standard reference in any study. It mostly predominates in the cell. The Watson-Crick structure is also the B-form DNA or B-DNA.

 

Apart from the B-DNA, A-DNA and Z-DNA are two other structural variants of DNA. These have been well characterized in crystal structures. They also form helical structures like the B-DNA, but differ in their geometry and dimensions from B-DNA. A comparative understanding of the various properties and parameters of the three different DNA variants is provided in Table 1.

Both A –DNA and B-DNA helix are right handed helix, but the A-DNA is wider and flatter than B-DNA. Earlier it was thought that A-DNA could be observed under dehydrating conditions, but with further studies, later it was proved that DNA dehydration occurs in vivo also. Z-DNA, on the other hand, is a left-handed helix and seen in conditions of high salt concentrations.

 

The other possible DNA conformations which have been described in recent studies are C-DNA, E-DNA, L-DNA, P-DNA, S-DNA forms. However, most of these forms have been created synthetically and have not yet been found to occur naturally in biological systems so far. Triple-stranded and quadruplex forms of DNA are also known.

 

3.5 From structure to function

  • DNA is the storehouse of biological information. The two strands of DNA provide a simple mechanism for copying the molecule. Upon separation, DNA replication occurs and each strand acts a template for creating the other strand. Thus two identical ‘daughter’ molecules are created. Some portions of DNA are non-coding, implying that these sections are not engaged in coding for protein sequences.
  • Within nucleus of cells, DNA is organized into chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each daughter cell its own complete set of chromosomes. While eukaryotes store most of their DNA inside the nucleus and some of their DNA in organelles like mitochondria or chloroplasts, prokaryotes store their DNA only in the cytoplasm. Chromatin proteins (histones) play key role in compacting and organizing the DNA within the chromosomes.
  1. Summary
  • DNA molecule serves as the molecular repository of genetic information in living organisms.
  • The background for the discovery of DNA was formed by several scientific breakthroughs made by four scientists, namely Maurice Wilkins, Rosalind Franklin, Francis Crick and James Watson.
  • Watson and Crick proposed the three-dimensional structure of DNA for the first time in 1953. They outlined the theory that DNA has a double helical structure comprising of two complementary anti-parallel polynucleotide strands, wound around each other in a rightward direction.
  • The helix is right handed and runs antiparallel. The backbone of the helix is sugar-phosphate and the bases in the interior extend perpendicular to the axis of the helix.
  • Complementary bases from opposite helix pair with each other.
  • The planes in which the adjacent base pairs are located are separated by 3.6 Å. 10 base pairs are found per turn with rise of 3.6 Å and one turn of the helix is 36 Å. The diameter of DNA helix is 20 Å.
  • DNA exists in alternative structural forms, namely as A-DNA, B-DNA and Z-DNA. B from is the most stable structure for a random sequence DNA molecule.