DNA: An Explicit Version

Introduction, History, and Timeline of DNA

DNA is the abbreviation for deoxyribonucleic acid. This name is gotten from the chemical nature of DNA. To break it down;

• De-oxy Ribo = ribose sugar with one less oxygen atom

• Nucleic = related to the nucleus

• Acid = has acidic properties (due to the phosphate group).

In more definitive words, DNA is a biomolecule largely found in the nucleus of prokaryotes, eukaryotes and many viruses [1]. A small quantity of DNA can be found in the mitochondria. DNA found in the nucleus is Nuclear DNA while DNA found in the mitochondria is called Mitochondrial DNA (mtDNA).

There are two types of nucleic acids found in living cells; DNA and RNA.

DNA (deoxyribonucleic acid) has a removed oxygen atom at the C'2 (second carbon atom) of the ribose sugar component (hence the term “de-oxy”) while RNA (ribonucleic acid) has all the oxygen atoms in the ribose hydroxyl group intact. (See article on structure of DNA).

Deoxyribose and Ribose structure. Image source: BYJU'S

DNA is the unique hereditary material of an organism containing information responsible for development, function, and reproduction. In essence, DNA carries the biological instructions for an organism’s function and can be transmitted to offsprings.

---

STUDY QUESTIONS

1. What is the full meaning of DNA?

2. Where is DNA found?

3. How many nucleic acids are there? Name them.

4. What is the difference between ribose and deoxyribose?

5. What’s the essential function of DNA?

---

The Watson and Crick three-dimensional model for the representation of the structure of DNA in space, which was discovered in 1953, has aided the understanding and advancement of DNA studies. However, research around the function, structure, and importance of DNA began decades earlier.

James Watson and Francis Crick were able to come up with the popular double helix model following previous works of scientists like Oswald Avery, Rosalind Franklin, and Maurice Wilkins on DNA. Major breakthroughs were based on the research and publication of various biochemists, and scientists which would be explored in the History of DNA described below.

The Story of DNA

Nuclein to Nucleic Acid: Discovery, Investigation, and Composition

In the 1860s, a serendipitous discovery revolutionized genetic research. Before this time, there had been breakthroughs in cytology as works of scientists like Louis Pasteur [2] and Rudolph Virchow [3] showed that new cells arise from existing cells, however heredity and evolution were still being figured out. This discovery would go on to be to be foundation of so many profound works in genetics studies.

In 1869, a young Swiss physician, Johann Friedrich Miescher moved to Tübingen, Germany, to work in the laboratory of Felix Hoppe-Seyler ( a pioneer of Biochemistry and Molecular Biology). He was researching on leucocytes (white blood cells), determined to find the chemical composition of cells. His source material was pus-coated bandages gotten from a local surgical clinic. He intended to wash the material, filter out the leucocytes (white blood cells), extract, and identify the key components of the cell. He had assumed that the component of interest would be a protein as proteins were the closely associated cell components to cell function at the time.[4]

However, Miescher discovered an unusual substance from the cell nuclei which was unlike any protein. He described this substance in the letter he (Miescher) sent to Wilhelm His in 1869.[5] The chemical properties he discovered about this unusual substance included an unsually high phophorus content, solubility in alkali and reprecipitation on addition of excess acid, and resistance to proteolysis (protein digestion) by protease (pepsin), which ruled out the possibility of this substance being a protein. Dahm (2005) quotes Miescher as stating “We are dealing with an entity sui generis not comparable to any hitherto known group”. [4]Miescher termed this novel substance, nuclein.

Later in 1871, Miescher worked with a considerable amount of the purest nuclein he ever isolated using an abundance of sperm cells gotten from salmon fish in his hometown, Basel. He improved on the protocol he had developed while at Tübingen for further qualitative and quantitative analyses and identified that nuclein contained carbon, nitrogen, hydrogen, was lacking sulfur, and was indeed rich in phosphorus. He also determined correctly that all phosphorus contained in nuclein existed in the form of phosphoric acid. Miescher speculated that nuclein may be responsible for fertilization and that the differences in chemical structure of nuclein which would happen in a limited diversity could account for slight differences in individuals of the same species.

As groundbreaking as Miescher’s work was, its relevance not widely known until about half a century after his passing in 1895. However, his research on nuclein provided a foundation for investigation by other scientists into nuclein, which we now know as nucleic acid.

Being more of a meticulous researcher and less of a publisher, much of Miescher’s work is gleaned from letters written to family members and work colleagues which were gathered and published by his uncle, Wilheim His, with the help of Miescher’s colleagues after Miescher’s passing.

In 1881, a German biochemist Albretch Kossel—another scientist from Hoppes-Seylar’s laboratory— extended research on Nuclein. He identified and isolated the five nucleotide bases using cells from thymus gland and yeast; adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) thereby correctly determing the building blocks of Nucleic acids. Kossel is one of the prominent names associated with the study of the composition of nucleic acids as he was one of the first scientists to distinguish between true nucleic acids and para (pseudo) nucleic acids.[6] Kossel went on to recieve a Nobel Prize in Physiology or Medicine in 1910 for this discovery.

In the early 1909, a Russian-born biochemist Phoebus Levene developed an improved method of preparing nucleic acids [6], and found out that the carbohydrate present in yeast nucleic acid is the five-carbon sugar, ribose. Although it was in 1929 that he successfully identified the carbohydrate in thymus nucleic acid as ribose as well, a variant which was lacking an oxygen atom called desoxyribose [7].

In 1909, Levene proposed a tetranucleotide structure for nucleic acids where each of the bases occurred once in each molecule of nucleic acid and was joined by the sugar and phosphate groups, depicting nucleic acid as a structure of repeating tetranucleotides units. This tetranucleotide hypothesis stemmed from his study of yeast nucleic acid where he proposed the empirical formula C38H50O29N15P4 and found the four bases— Adenine, Guanine, Cytosine, and Uracil (from yeast RNA) to be in equimolecular proportions [9], however he could not correctly determine the mode of linkage of individual nucleotides. In 1921, he correctly established the four nucleotide bases in thymus— Adenine, Guanine, Cytosine, and Thymine, with their empirical and structural formulas but was at loss for their mode of linkage. [10]

Although Levene’s tetranucleotide hypothesis seemed to draw focus away from nucleic acid as being the substance of heredity due to its perceived rigidity— and was later established as erronous— the significance of his work was not lost on subsequent scientists in the field like Oswald Avery and Erwin Chargaff. In fact, his results were accurate for the composition of each nucleotide; a phosphate group, a ribose or deoxyribose sugar, and a sigle nitrogen-containing base [11]. Hargittai (2009) quotes the science historian, Robert Olby, as saying about Levene, ‘‘this great chemist lifted the subject out of its confusion and extricated the nucleic acids from their conceptual entanglement with the proteins’’ [7].

In 1944, Oswald Avery together with Colin McLeod, and Maclyn McCarty published the first report to prove that DNA was indeed genetic material following their work on pneumococcus bacteria and identification of a transformation principle (first observed by Frederick Griffith) through which the organism transformed from one type to another. This transformation principle was linked to a white precipitate identifed as the transformation material which was determined analytically to be composed largely of desoxyribonucleic acid and capable of stimulating unencapsulated R variant of Pneumococcus Type II to produce capsulated S variant of Pneumococcus Type III.[12]

The report highlighted the ability of the transforming material to produce biological response identical to type specificity with that of the cells from which the transforming substance was isolated. More striking was that the responses produced were chemically distint with each belonging to a whole different class of chemical compounds. Also, failed attempts to induce transformation in resting cells held under growth and multiplication-inhibiting condition suggested that transformation occured only during active cell reproduction. The changes occurred in predictable patterns that were type-specific and heritable [12].

The publication from the Avery group received immediate, although not as much as expected positive responses. A few scientists in the field like Immunologist Macfarlane Burnet, and Biochemist Howard Mueller, were excited for the implication of this breakthrough, however a good number of scientists were hesitant on acceptance [13]. This transformation principle discovery was corroborated by André Boivin, deputy director of the Institut Pasteur in Paris, who worked with Escherichia coli later in 1945 [14], further presenting nucleic acids as a core component of genes.

Between 1945 and 1948, and impelled by the Avery group’s work, focus returned to nucleic acids. Over 260 papers were published on Nucleic acids and four major international scientific conventions were held on the subject and at prestigious locations; at Cambridge in 1946, at Cold Spring Harbor in 1947 and 1948, and in Paris in 1948 [13].

The work of the Avery group did not receive as much accolades as it deserved in the scientific community until the 1970s, and after Avery’s passing. The major arguments against their discovery (raised by Alfred Mirsky) were based on the stubborn presence of protein components in their nucleic acid isolates (although Avery’s collaborator, Rollin Hotchkiss had succeeded in reducing the protein content of their DNA extract to about 0.2% which was published much later [15]). With the traditional focus on proteins, it seemed logical to assume that the protein content of the DNA extract was an active component of the transformation material.

Arguments for the Avery group’s painstaking research from André Boivin [16], brilliant chemist Masson Gulland [17] (whose tragic death in 1947 was a huge loss to the scientific community), and subsequents works from Erwin Chagaff and the work of Hershey-Chase (Al Hershey and Martha Chase) lent eventual credibility to the group’s incredible work. It was later agreed that the Avery group had made a very significant discovery which had been way ahead of their time [13].

In 1944, Erwin Chargaff, a professor of Biochemistry at Columbia University, read the Avery group’s report stating that hereditary units were made up of DNA and this sparked his interest into the investigation of the chemical composition of nucleic acids [18]. Chargaff was convinced that if DNA from different species exhibited different biological type-specific responses, there should also be chemically distinguishable differences between the DNA from different species.

In 1948, Chargaff and Vischer published their report on the study of pentose nucleic acids (RNA) of yeast and pancreas [19]. They found that under the common method employed in the release of pyrimidines ie. prolonged autoclaving with mineral acid at high temperature, cytosine in the nucleic acid was being converted to uracil. Therefore, an alternative procedure for hydrolysis was developed using concentrated formic acid. Chromatographic seperation as well as spectroscopic controls were applied in this study of the composition of RNA.[19]

The results showed that the sugar composition of RNA was identical to the one reported by Levene and Jacobs (D-ribose) [20], however the purines and pyrimidines composition disproved Levene’s tetranucleotide hypothesis. From 10gm of ribonucleic acid, the percentage distribution of the nitrogenous bases per mole of P were as follows: adenine 7.1% (0.19 mole) ; guanine, 10% (0.24 mole); cytosine 9.8% (0.32 mole); and no value could be assigned to uracil. The results of the experiment pointed to the possibility of uracil being a constituent of pentose nucleic acids, although in minute amounts.

In a later publication on the composition of desoxypentose nucleic acids (DNA) of calf thymus and spleen [21], Chargaff et. al showed that the assumption of previous workers that DNA behaved as a single chemical entity regardless of the source from which it was isolated, was incorrect. The qualitative analysis of their work showed that the desoxypentose nucleic acid of spleen contained carbohydrate similiarly isolated from thymus DNA andthe sugar component was identified as 2-desoxyribose. The purines and pyrimidines found in the hydrosylates were adenine and guanine, and cytosine and thymine respectively, with no demonstration of uracil in the chromatograms.

Regarding the composition of the desoxypentose nucleic acid, the report stated, “The composition of both the thymus and spleen desoxypentose nucleic acids was found closely similar, but it was not in accord with the expectations derived from the tetranucleotide hypothesis. For 10 molecules of cytosine, 16 molecules of adenine, 13 of guanine, and 15 (or 13) of thymine were found.” [21]

In 1950, Chargaff published a paper reviewing his findings on the study of the chemical composition of the nucleic acids [22] which is now known as Chargaff’s Rules: 1) that in any double-stranded DNA the number of adenine units equals the number of thymine units and the number of guanine units equals the number of cytosine units and (2) that the composition of DNA differs from one species to another, hence effectively disproving the tetranucleotide hypothesis.

With a seeming saturation of investigation into the composition of nucleic acids, investigations into the structure and mode of linkage of DNA components were taken up by William Astbury, Rosalind Franklin, and Maurice Walkins, before the advent of the famous Watson and Crick DNA model proposed by James Watson and Francis Crick in 1953.

Below is a comprehensive timeline of advances in heredity and nucleic acid investigation from Darwin to present times.

DNA through Time

1859: Charles Darwin proposes the theory of evolution through Natural Selection in his paper, The Origin of Species.

1865: Gregor Mendel discovers how traits are inherited by studying pea plant, Pisum sativum.

1866: Ernst Haeckel proposes the recapitulation theory, “Ontogeny recapitulates phylogeny”.

1869: Friedrich Miescher identifies and extracts DNA.

1882: Walther Flemming describes chromosomes’ behaviour during cell division and called the process mitosis.

1884–1885: Oscar Hertwig, Albrecht von Kölliker, Eduard Strasburger, and August Weismann’s independent works show that the basis of heredity is in the cell nucleus.

1885-1901: Albrecht Kossel discovers the chemical composition of DNA; the five nitrogenous bases (Adenine, Guanine, Cytosine, Thymine, and Uracil).

1889: Richard Altmann changed the name “nuclein” to “nucleic acid” based on the acidic properties of the substance.

1900: Carl Correns, Erich von Tschermak, and Hugo de Vries independently rediscover Mendel’s Laws while working on different plant hybrids.

1902 & 1903: Theodor Boveri and Walter Sutton independently propose that genes are found in the chromosomes, ie., the chromosome theory of inheritance.

1902–1909: Archibald Garrod proposes that genetic defects result in hereditary metabolic diseases and the loss of enzymes which he described as the Inborn errors of Metabolism.

1909: Wilhelm Johannsen distinguishes between genotype and phenotype, coining the term “gene” to describe units of heredity.

1909: Phoebus Levene discovers ribose sugar in nucleic composition, and proposes tetranucleotide hypothesis.

1910: William Bateson co-discovers genetic linkage between Mendelian Laws and Darwin’s theory of evolution with Reginald Punnett and Edith Sauders. The term “genetics” is coined.

1910: Thomas Hunt Morgan discovers sex-linked trait for eye colour while studying fruit fly, Drosophila.

1913: Alfred Sturtevant produces the first genetic linkage map from studying patterns of Thomas Hunt Morgan’s Drosophila melanogaster.

1921: Theophilus Painter first counts the number of human chromosomes (48 but incorrect number). Joe Hin Tjio publishes correct number (46) in 1956.

1921: Frederick Banting and Charles Best succesfully isolate hormone, insulin.

1928: Frederick Griffith discovers “transforming principle” in bacteria which allows properties from one bacteria type (heat-inactivated virulent Streptococcus pneumoniae) to be transferred to another (live nonvirulent Streptococcus pneumoniae) to change their characteristics.

1929: Phoebus Levene discovers deoxyribose sugar in DNA composition.

1937: Florence Bell obtains first DNA X-ray diffraction images.

1941: George Beadle and Edward Tatum propose the one gene, one enzyme hypothesis (each gene encodes for a single enzyme).

1944: Oswald T. Avery, Colin MacLeod, and Maclyn McCarty establish that Griffith’s “transforming principle” is not caused by a protein, but rather DNA, suggesting that DNA maybe the genetic material.

1949: André Boivin, Colette, and Roger Vendrely discover that the nuclei of germ cells contain only half the amount of DNA in somatic cells.

1949–1950: Erwin Chargaff demonstrates that the DNA nitrogenous base composition varies between species but that within a species the bases in DNA are always present in fixed ratios, proposes Chargaff’s Rules; the number of A= the number of T, and number of C= the number of G.

1952: Alfred Hershey and Martha Chase confirm DNA as the genetic material using bacteriophage T2. Viral protein does not enter bacteria during infection but viral DNA does.

1953: Rosalind Franklin and Maurice Wilkins demonstrate regular repeating helical structure of DNA using X-ray crystallography.

1953: James Watson and Francis Crick discover the tertiary structure of DNA: a double helix in which Adenine (A) always pairs with Thymine (T), and Cytosine (C) always pairs with Guanine (G).

1955: Severo Ochoa and Marianne Grunberg-Manago discover RNA polymerase.

1956: Arthur Kornberg discovers DNA polymerase I, an enzyme responsible for DNA replication.

1957: Francis Crick proposes that genetic information flows in one direction; DNA — RNA — Protein or, RNA — Protein known as the “central dogma” of molecular biology.

1958: Matthew Meselson and Franklin Stahl describe the semiconservative mode of DNA replication.

1961–1966: Marshall W. Nirenberg, Robert W. Holley, Severo Ochoa, Har Gobind Khorana, Heinrich Matthaei, and colleagues crack the genetic code.

1968–1970: Hamilton Smith, and Daniel Nathans Werner Arber, first isolate restriction enzyme from Haemophilus influenzae and use it to cut DNA in specific places.

1972: Paul Berg creates first piece of recombinant DNA.

1973: Robert Boyer and Stanley Cohen carry out the first gene splicing experiment.

1977: Frederick Sanger & Allan Coulson, and Allan Maxam & Walter Gilbert develop DNA sequencing techniques.

1978: Eli Lilly, a medical firm, produces first genetically engineered, synthethic insulin using Escherichia coli.

1982: Insulin drug becomes commercially available.

1983: Huntington disease is genetically mapped using DNA polymorphisms.

1983: Kary Mullis invents PCR technique of DNA amplication over a short period of time.

1990: Sequencing of the human genome, the International Human Genome Project begins.

1994: Biotech firm, Calgene, introduces first genetically engineered food, the Flavr Savr tomato, to the market.

1995: First genome sequence of a free-living organism, Haemophilus influenzae, is completed and published by The Institute for Genomic Research.

1996: First genome sequence of a eukaryotic organism, the yeast S. cerevisiae, is completed and published.

1998: Next-generation sequencing (NGS) technologies are developed.

1998: First genome sequence of multicellular organism,the nematode worm Caenorhabditis elegans, is completed and published.

1999: First whole human chromosome, chromosome 22, is sequenced and published.

2000: The genome sequences of the fruit fly, Drosophila, and the first plant, Arabidopsis, are completed and published.

2001: The first working draft of the complete sequence of the human genome is published.

2002: First genome of a mammalian model organism,the mouse, is completely sequenced and published.

2003: Full sequence of the human genome is completed and published.

2003: Tropical fluorescent fish becomes first commercially available genetically modified pet.

2012: Emmnuelle Charpentier, and Jennifer Doudna develop CRISPR genome editing tool.

2013: Twins are discovered and proved to have differences in their genetic makeup.

2014: First organism with artificially expanded genetic code is created.

2014: Study on genetic basis of mental illness reveal 100 genes linked to schizophrenia.

2014: Study of identical twins on epigenetics reveal mechanisms behind development of type II diabetes.

2019: First organism with fully redesigned DNA, Escherichia coli Syn61, is created.

2021: The African Biogenome Project is started.

2023: The first drug for treatment of Alzheimer’s disease, Leqembi, is approved.

2023: The world’s first CRISPR-based gene therapy, CASGEVY, is approved and becomes commercially available.

2023: Unconventional breeding, two fathers and no female, is used to produce healty mice pups.

2023: First complete brain mapping of an insect, fruit fly, is published.

2023: Bacteria is shown to help aggressive spread of cancer cells.

2023: “Stuck” melanocytes are shown to cause gray hair.

2023: Artificial intelligence (AI) tool is used to predict pancreatic cancer.

References

1. Britannica, T. Editors of Encyclopaedia. DNA. Encyclopedia Britannica. Retrieved 22 Oct. 2023 from https://www.britannica.com/science/DNA

2. Pasteur’s “col de cygnet” (1859). (n.d.). British Society for Immunology. Retrieved 16 Jan. 2024 from https://web.archive.org/web/20190811175656/https://www.immunology.org/pasteurs-col-de-cygnet-1859

3. Schultz M. (2008). Rudolf Virchow. Emerging Infectious Diseases, 14(9), 1480–1481. https://doi.org/10.3201/eid1409.086672

4. Dahm R. (2005). Friedrich Miescher and the discovery of DNA. Developmental biology, 278(2), 274–288. https://doi.org/10.1016/j.ydbio.2004.11.028

5. Miescher, F. (1869). Letter i; to wilhelm his; tübingen, february 26th, 1869. Die histochemischen und physiologischen arbeiten von Friedrich Miescher-aus dem wissenschaftlichen Briefwechsel von F. Miescher, 1, 33-38.

6. Levene, P. A., & Bass, L. W. (1931). Nucleic Acids (pp. 243-256). American Chemical Society Monograph Series, No. 56.

7. Hargittai, I. (2009). The tetranucleotide hypothesis: A centennial. Structural Chemistry. 20. 753-756. https://doi.org/10.1007/s11224-009-9497-x.

8. Phoebus Aaron Theodor Levene. Oxford Reference. Retrieved 19 Dec. 2023, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803100102247.

9. Levene, P. A., & Jacobs, W. A. (1909). Über die Hefe‐Nucleinsäure. Berichte der deutschen chemischen Gesellschaft, 42(2), 2474-2478.

10. Levene, P. A., J. BioZ. Chem., 48, 177 (1921).

11. Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100

12. Avery, O. T., Macleod, C. M., & McCarty, M. (1944). STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY A DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III. The Journal of experimental medicine, 79(2), 137–158. https://doi.org/10.1084/jem.79.2.137

13. Cobb, M. (2014). Oswald Avery, DNA, and the transformation of biology. Current Biology, 24(2), R55–R60. https://doi.org/10.1016/j.cub.2013.11.060

14. Boivin, A., Vendrely, R., & Lehoult, Y. (1945). L’acide thymonucléique hautement polymerisé, principe capable de conditionner la specificité sérologique et l’équipement enzymatique des Bactéries. Conséquences pour la biochimie de l’hérédité. Comptes Rendus de l'Acad Sci de Paris, 221, 646-648.

15. Hotchkiss, R. D., & Ephrussitaylor, H. (1951, January). Use of serum albumin as source of serum factor in pneumococcal transformation. In Federation Proceedings (Vol. 10, No. 1, pp. 200-200). 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998: FEDERATION AMER SOC EXP BIOL.

16. Boivin, A., Vendrely, R., & Vendrely, C. (1948). L'acide désoxyribonucléique du noyau cellulaire, dépositaire des caractères héréditaires; arguments d'ordre analytique. Comptes rendus hebdomadaires des seances de l'Academie des sciences, 226(13), 1061–1063.

17. Gulland J. M., Jordan D. O., & Threlfall C. J., (1947) Deoxypentose nucleic acids. Part I. Preparation of the tetrasodium salt of the deoxypentose nucleic acid of calf thymus. Journal of Chemical Society 25, 1129–31

18. Kresge, N., Simoni, R., & Hill, R. (2005). Chargaff’s Rules: the Work of Erwin Chargaff. The Journal of Biological Chemistry, 280(24), 172–174. https://doi.org/10.1016/S0021-9258(20)61522-8

19. Vischer, E., & Chargaff, E. (1948). The composition of the pentose nucleic acids of yeast and pancreas. Journal of Biological Chemistry, 176(2), 715-734.

20. Levene, P. A., & Jacobs, W. A. (1909). Über Inosinsäure. Berichte Der Deutschen Chemischen Gesellschaft, 42(1), 1198–1203. doi:10.1002/cber.190904201196 

21. Chargaff, E., Vischer, E., Doniger, R., Green, C., & Misani, F. (1949). The composition of the desoxypentose nucleic acids of thymus and spleen. Journal of Biological Chemistry, 177(1), 405-416.

22. Chargaff, E. (1950) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 6, 201–209

23. Pickrell, J. (2006). Timeline: Genetics. New Scientist. https://www.newscientist.com/article/dn9966-timeline-genetics/

24. Admin. (2015). The history of DNA timeline. DNA Worldwide. https://www.dna-worldwide.com/resource/160/history-dna-timeline

25. Conocimiento, V. A. (2021). Interactive timeline: 150 Years of DNA | OpenMind. OpenMind. https://www.bbvaopenmind.com/en/science/bioscience/history-dna-timeline/

26. Mishra, S. (2023). 7 medical breakthroughs that gave us hope in 2023. Premium. https://www.nationalgeographic.com/premium/article/medical-breakthroughs-2023-gene-therapy-crispr-cancer-fertility