DNA Synthesis

What is DNA?

Deoxyribonucleic acid (DNA) is the carrier of genetic information in all living organisms. It holds the necessary instructions for an organism to grow, develop, function, and reproduce. DNA is a polymer consisting of repeating units known as nucleotides. A nucleotide is made of three components: one of four nitrogen-containing bases (adenine, cytosine, guanine, and thymine), a deoxyribose sugar, and a phosphate group. The sugars and phosphates form a backbone to which the bases are connected. The unique order of these bases forms genes which tell cells which proteins to synthesize. Nucleotides are strung together to form two long strands that run in opposite directions which spiral into a double helix (Franklin and Gosling, 1953; Watson and Crick, 1953; Wilkins et al., 1953).

The double-helical shape of DNA can be visualized as a twisted ladder. The sugars and phosphates are the sides and the nitrogenous bases are the rungs. The bases on one strand bond with the bases on the other. In a fundamental rule of biology known as complementary base-pairing, cytosine always pairs with guanine, and adenine always pairs with thymine (Chargaff, 1950). Figure 1 illustrates the structure of a molecule of DNA.

Figure 1. The double-helical structure of DNA. a) A ribbon and ladder representation of a DNA molecule. b) A stick representation of the same DNA molecule (PDB ID: 1zf0, Hays et al., 2005).
Figure 1. The double-helical structure of DNA. a) A ribbon and ladder representation of a DNA molecule. b) A stick representation of the same DNA molecule (PDB ID: 1zf0, Hays et al., 2005).

Discovery of the double-helical structure of DNA in 1953 was significant because it suggested a mechanism to copy the genetic material (Watson & Crick, 1953). During DNA replication, the two strands separate and complementary bases are added to synthesize new strands. The replication process is an accurate and efficient way to replicate an organism’s genome.

Structure of DNA

DNA nucleotides are composed of a five-carbon deoxyribose sugar, a phosphate group, and one of four nitrogenous bases. Each carbon on the sugar is labeled following organic chemistry rules. Multiple nucleotides are covalently linked through their phosphates and sugars, forming a backbone of alternating phosphates and sugars. A special type of covalent bond, known as a phosphodiester bond, is created when the 5’ phosphate of one nucleotide attacks the 3’ hydroxyl of the sugar of another nucleotide. Phosphodiester bonds are created in a 5’-3’ direction, which gives each DNA strand a chemical polarity (Travers et al., 2015). One end of the DNA strand contains a 5’ phosphate while the other contains a 3’ hydroxyl. The two strands in a DNA molecule are antiparallel, meaning that the 5’ end of one strand is adjacent to the 3’ end of the other strand.

The three-dimensional structure of DNA arises from the chemical features of both chains. They are held together by hydrogen bonds between the nitrogenous bases on each strand. The chemical structures and shapes of each base dictate that adenine can only bond with thymine, and cytosine can only bond with guanine. The hydrogen bonding between bases is shown in Figure 2.

Figure 2. Complementary base-pairing. Guanine, cytosine, adenine, and thymine nucleotides are labeled. Hydrogen bonds between the bases are colored pink (PDB ID: 1zf0, Hays et al., 2005).
Figure 2. Complementary base-pairing. Guanine, cytosine, adenine, and thymine nucleotides are labeled. Hydrogen bonds between the bases are colored pink (PDB ID: 1zf0, Hays et al., 2005).

To maximize the efficiency of base pairing, the phosphate-sugar backbones twirl around each other to form a double helix. The double-helical structure provides many advantages for an organism. First, the bases face inward which shields them from solvents and possible chemical damage. Second, the complementarity of the genome provides a simple mechanism for DNA replication, and it allows for mistakes to be recognized and repaired (Schoeffler et al., 2008).

DNA Synthesis

DNA replication is the biological process through which a DNA molecule is created. The double-helical structure provides a simple mechanism for creating identical copies of the genome. Both strands of DNA separate from each other and serve as templates for new complementary strands. As shown in Figure 3, a DNA molecule contains one “parent” strand and one “new” strand. This concept is known as semiconservative replication (Meselson and Stahl, 1958).

Figure 3. A model for semiconservative replication. The parent strand is colored in dark blue and the newly synthesized strands are colored in cyan. The base pairs are shown in the ladder representation (PDB ID: 1zf0, Hays et al., 2005). The 5' and 3' ends are shown.
Figure 3. A model for semiconservative replication. The parent strand is colored in dark blue and the newly synthesized strands are colored in cyan. The base pairs are shown in the ladder representation (PDB ID: 1zf0, Hays et al., 2005). The 5' and 3' ends are shown.

The process of DNA replication is complex and differs between all types of organisms. For example, prokaryotes and eukaryotes have different types of DNA polymerase enzymes and helicases (Leipe et al., 1999). Furthermore, replication occurs in the nucleus in eukaryotes but in the cytoplasm in prokaryotes. As a result, antibiotics exploit the differences in DNA replication machinery between humans and bacteria (Drlica, 1999). Common to all organisms, however, are challenges during replication. The following list details the major difficulties and the mechanisms to resolve them.

  • Supercoiling: when a DNA molecule is unwound and separated by a helicase, it begins to overwind and tighten ahead of the replication fork (Kim and Wang 1998; Liu and Wang 1987). Bacterial type IIA topoisomerase enzymes remove these supercoils which allows the DNA to be easily accessed by helicase (Schoeffler et al., 2008).
  • RNA primers: DNA polymerase III, the main bacterial enzyme that adds nucleotides, cannot work de novo. It can only add bases to an existing hydroxyl group. Primase synthesizes a short RNA primer, allowing DNA polymerase III to recognize a hydroxyl group and add DNA nucleotides (Kelman et al., 2014).
  • Leading and lagging strands: DNA polymerase III can only work in a 5’ to 3’ direction. On the leading strand, DNA polymerase works towards the replication fork, continuously adding nucleotides until termination. On the lagging strand, however, DNA polymerase works away from the replication fork. To overcome this challenge, it synthesizes short strands of DNA, moves back toward the fork, and then adds bases to a new primer (Kelman et al., 2014).

A schematic summary of prokaryotic replication is provided below in Figure 4.

Figure 4. A model for DNA replication. Key enzymes and directions are labeled. The parent strand is colored in dark blue, the newly synthesized DNA is colored in cyan, and the RNA primer is colored in dark green. Portions of the figure were adapted from Servier Medical Art.
Figure 4. A model for DNA replication. Key enzymes and directions are labeled. The parent strand is colored in dark blue, the newly synthesized DNA is colored in cyan, and the RNA primer is colored in dark green. Portions of the figure were adapted from Servier Medical Art.
  1. Helicase unwinds the DNA and separates the two strands by breaking the hydrogen bonds between the nitrogenous bases.
  2. Gyrase and topoisomerase IV work ahead of the replication fork to relieve strain and overwinding caused by helicase’s enzymatic activities. The double-helical structure leads to supercoiling during DNA replication, and gyrase/topoisomerase IV resolves these topological problems.
  3. Single-stranded binding proteins prevent the degradation of DNA and the reforming of the double-helix.
  4. DNA polymerase III adds nucleotides in a 5’-3’ direction to synthesize a new strand of DNA. It must start at the 3’ end of an RNA primer.
  5. Primase synthesizes RNA primers needed to start elongation so DNA polymerase III can add DNA nucleotides
  6. DNA polymerase I removes the RNA primers and replaces them with DNA.
  7. DNA ligase seals the gaps between Okazaki fragments on the lagging strand to create a continuous strand of DNA.

DNA Synthesis as Targets of Antibiotics

DNA synthesis is fundamental for the replication of all organisms with DNA genomes. Given that the machinery for replication in prokaryotes and eukaryotes are different, bacterial DNA synthesis is an excellent target for antimicrobial action. Several antimicrobials targeting DNA replication proteins have been developed to date, of which the gyrase or type II topoisomerase inhibitors are the only class widely used in the clinic (van Ejik, et al., 2017). Since there are many essential proteins in the bacterial replisome, these may also serve as suitable targets for developing new drugs. However, it can be challenging to identify/design antimicrobials that are specific to pathogenic bacteria and do not develop resistance.

References

Chargaff, E. (1950). Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia, 6(6), pp.201-209. https://doi.org/10.1007/bf02173653

Drlica, K. (1999). Mechanism of fluoroquinolone action. Current Opinion in Microbiology, 2(5), pp.504-508. https://doi.org/10.1016/s1369-5274(99)00008-9

Franklin, R. E., Gosling R. G. (1953) Molecular configuration in sodium thymonucleate. Nature. 171(4356):740-1. https://doi.org/10.1038/171740a0

Hays, F. A., Teegarden, A., Jones, Z. J., Harms, M., Raup, D., Watson, J., Cavaliere, E., Ho, P. S. (2005). How sequence defines structure: A crystallographic map of DNA structure and conformation. Proceedings of the National Academy of Sciences of the United States of America, 102(20), 7157–7162. https://doi.org/10.1073/pnas.0409455102 PDB ID: 1zf0

Kelman, L., Kelman, Z. (2014). Archaeal DNA Replication. Annual Review of Genetics, 48(1), pp.71-97. https://doi.org/10.1146/annurev-genet-120213-092148

Kim, R. A., Wang, J. C. (1989) Function of DNA topoisomerases as replication swivels in Saccharomyces cerevisiae. J Mol Biol. 208(2):257-67. https://doi.org/10.1016/0022-2836(89)90387-2

Leipe, D. D., Aravind, L., Koonin, E. V. (1999) Did DNA replication evolve twice independently? Nucleic Acids Res. 27(17):3389-401. https://doi.org/10.1093/nar/27.17.3389

Liu, L. F., Wang, J. C. (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 84(20):7024-7. https://doi.org/10.1073/pnas.84.20.7024

Meselson, M., Stahl, F. W. (1958) The replication of DNA in Escherechia coli. Proc Natl Acad Sci U S A. 44(7):671-82. https://doi.org/10.1073/pnas.44.7.671

Schoeffler, A., Berger, J. (2008). DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Quarterly Reviews of Biophysics, 41(1), pp.41-101. https://doi.org/10.1017/s003358350800468x

Travers, A., Muskhelishvili, G. (2015). DNA structure and function. FEBS Journal, 282(12), pp.2279-2295. https://doi.org/10.1111/febs.13307

van Eijk, E., Wittekoek, B., Kuijper, E.J., Smits, W.K. (2017) DNA replication proteins as potential targets for antimicrobials in drug-resistant bacterial pathogens. J Antimicrob Chemother. 72, 1275-1284. https://doi.org/10.1093/jac/dkw548

Watson, J., Crick, F. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171(4361), pp.964-967. https://doi.org/10.1038/171964b0

Wilkins, M. H., Stokes, A. R., Wilson, H. R., (1953) Molecular structure of deoxypentose nucleic acids. Nature. 171(4356):738-40. https://doi.org/10.1038/171738a0

March 2025, Steven Arnold; Reviewed by Dr. James Berger
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/dna-synth