Chemistry, the missing link in “The Double Helix”

Last week there was a celebration of the 60^th anniversary of the publication of the papers (sometimes it seems as if there was only one but, actually there were three) on the structure of DNA. The occasion invited recollection and reflection and, perhaps for the last time, allowed some of the protagonists to tell the world famous events in Cambridge, UK.  Much ink has been poured over this to the point that some times it does not feel like Science but rather like a fairy tale, a legend about a girl in the midst of boys chasing a structure which only she could get at the time but which only they could interpret. There is a holy grail (the structure contained the secret of life), there is a race for it, there are goodies and baddies, magicians, traitors, there is ambition, frustration…….the stuff of great stories and great movies, and a movie was made by the BBC called ‘Life Story’. It is not commercially available, which is a shame, but it was screened during the events last week. It is a great movie and if you have a chance to see it: enjoy.

History is written by those who can write it for those that want to read it, often without asking questions. Scientists, particularly life scientists, rarely become chroniclers of their own fields so, it was somewhat surprising to all involved when James Watson produced “The double helix”, his iconoclastic account of events in Cambridge and London in 1952-1953. It is a riveting account that sweeps you into the story at the expense of the science which is, as they would say today, dumbed down. The undoubted significance of its conclusion and the manner in which this unfolds makes you not think that there is something missing.

The story, as perceived from the multiple re-tales of Watson, is more an adventure than actual History or Science, and this is perhaps the reason why it feels as if a vial with DNA had been gathering dust in some cupboard in Kings College since 1869, when F. Miescher purified it from the leukocytes in pus bandages of a hospital in Tübingen (Germany), waiting for Watson and Crick to reveal its secrets from their astute interpretation of the photo 51 of Rosalind Franklin. However: how did they know what to fit the photograph to? How did they know the structure of the nucleotides? How did they know that DNA was a polymer? This bit of the story is never told and the fairy tale aspect of the account makes it sound unimportant, a given. After all, was it not in the picture, Watson’s drive and the brilliant mind of Crick that conjured up the helix? But if you think about it, the X ray photograph did not tell them the components they had to fit (a sugar, a phosphate and a base in each unit of the polymer), it did not tell them how they were linked, nor what were the molecular dimensions and forms they were looking for. This was Chemistry and Chemistry always plays little cameos (if at all) in the accounts of Watson, and always as a distraction from the main plot. And yet, model building was derived from Linus Pauling’s insights into the chemical bond but, more significantly, there are two instances in the story at which Chemistry makes significant contributions. The first one through the famous Chargaff rules, central for the determination of the structure. The second one in the suggestion of Jerry Donahue (a biochemist who shared an office with them) to use the right tautomeric forms of the bases when trying to build the model; this proved crucial. Both contributions were significant and are always underplayed. However, even before this, the discovery of the components of DNA, the clarification of the differences between DNA and RNA, the discovery of the structure of the nucleotides, all this were major pieces of Science without which Photo 51 would not have a reason to be and it certainly would not have been possible to read. But these findings, their history and their role in the double helix have been relegated to ‘specialized books”, if not to obscurity,  by the trailblazing account of the race to get the structure of the DNA.

Chemistry is the great important missing character in the story and this, in a way, has had a price; more on this below. First, a brief account of what is placed, literally, under the carpet, as dust that might contaminate the racy account of the race for the double helix by James Watson with the help of Francis Crick. If you want to read about this in a context I suggest you look at “The path to the double helix” by R. Olby (University of Washington Press 1974) and “A century of DNA” by FH Portugal and J. Cohen (MIT Press 1977).

DNA was not dormant since 1869, and one can weave a good account of how it revealed its secrets slowly from the chemical and the biological angles, through the first half of the XX century. The biological one, largely centered on Griffith in London and Avery and his team at Rockefeller in New York, is well known and there is little need to recount it here. In fact it was Watson’s knowledge of the experiments of O. Avery that drove his quest for the Holy Grail and made him want to know the structure (at all costs) so that he could interpret this work. The importance of this intuition, which fuelled the race, cannot be underestimated. But, on the other hand the Chemistry, is less known, and without it nobody would have known where to start in 1952.

DNA was thought to be important because it made up so much of the nuclei of animal cells, where the chromosomes resided, and where increasingly people thought the material basis of heredity resided. Miescher already knew that there was phosphorus in nuclein and that phosphorous was not present in proteins, which were a component of nuclein. By 1878 Albrech Kossel isolated (to some degree of purity) the non protein component of nuclein and showed that, in addition to phosphorous, it contained five organic compounds, the bases as we know them today: A, C, T, G and U. Thus at the dawn of the XX century elements are in need of a global structure and this task befell to Phoebe Levene  (1869-1940) a Russian émigré medical doctor, turned brilliant biochemist at the Rockefeller research Institute in New York, who pursued the fundamental structure of the units of nucleic acids. He found and characterized the sugars in DNA and RNA –which at the time were thought to divide themselves between animals (DNA) and plants (RNA), and found the basic unit of these acids: the nucleotide. He uncovered the bonds and thereby the structure between the different elements: the familiar P-sugar-base, the nucleotide. Needless to say that this a central piece in the puzzle and the key element in the interpretation of Photo 51. It was also a piece of structural work, chemical structural work, and had its little dramas and certainly its toilings, but nobody wrote a best seller about it. There are many reasons one can think why this is left out of the story: lack of glamour, a time dilution effect, the tediousness of Chemistry……but there is something that perhaps made a major contribution to this. Levene, using data that was not correct, suggested that the basic unit of DNA was a tetranucleotide (ATCG each with their P and sugar bound in an uncomfortable ring) and that nuclein was a sum, of these molecules. This was wrong but nevertheless is said to have influenced much of the functional thinking about DNA at the time. Such a molecule did not have the ‘informational content’ , as we would say today, to code for heredity and favoured the hypothesis, widely spread at the time, that the keeper of heredity was the protein in the nuclein. Everybody? Well, in one of those little jokes of historical fate, as Levene was moving away from DNA as the basis for heredity, a few meters away in Rockefeller Avery and his team were toiling away on their experiments on Pneumoccocus which established DNA as the ‘transforming principle”. Also, paradoxically, Levene showed that DNA was a large polymer with a MW above 10⁶, something that would question the tetranucleotide hypothesis and which had been seen before and would be confirmed later. The coming together of the notion that DNA is a polymer with the detailed structure of the monomer is, as one can imagine, the essential seed for the X-ray structures, which were being undertaken before R. Franklin is charged with getting the structure at Kings.

One coda to the chemistry of DNA, and an important one. Chemical structures are abstractions from the sorcery of the chemical laboratory. The proof of the structure lies in synthesizing it de novo. In the case of the nucleotides this was achieved by Alexander Todd, curiously working not far away from the Cavendish. He and his group synthesized ATP in the 1950s and later a dinucleotide, crucial in interpreting the polymer in the proposed structure.

Together the work of Kossel, particularly Levene and later Todd, provide the elements that need to be modelled from Photo 51. Levene and Todd must have had their Eureka moments, but never told any one or we have not been told about them.  For all that we hear about Watson’s, the photograph and the rest, where would all this be without knowing that a nucleotide was made of a phosphate, a sugar and a base and that one had to use the correct chemical form of the bases? One has to separate two things in the ‘discovery’ and, unfortunately, this is not done often enough. On the one hand there is the structure. This is what chemists worried about, this is what Franklin was interested in and this is what has gone down in history as the prize. It has been argued, probably correctly, that chemistry failed to deliver the structure. In many ways, it could not have done this but nothing should be taken out from the fact that it did its job, to deliver the elements needed to interpret the biophysical data. On the other hand there was the meaning of the structure. This is more subtle but this is the really important contribution of Watson and Crick. Sure, this cannot be gauged without the structure but this bit, the function, might have gone unnoticed by most of the biophysicists of the time and who knows how much time it would have taken for people to notice once someone produced the double helix; and there is little doubt that this would have happened because DNA, as we have seen, had its own momentum with what journals would call today ‘incremental advances in knowledge”……..For Watson, the structure was the gamble. He and Crick were able to read genetics into it and this is their major and unique contribution, not the structure which was a culmination of almost 100 years of work. Reading and listening (on the web) to Crick one gets the impression that he is extremely well aware of this (remember that he was not overjoyed when he read “the double helix”).

So, Watson’s account is biased to highlight the role of Watson and of Watson and Crick in the structure, on the race, on the goal; we all know that. In doing so he sidesteps the contribution of Chemistry to the story. It leaves a blank between Miescher and London and Cambridge in the early 50s. It is done, I am sure, inadvertently, maybe a literary license in the fantasy he made up of an interesting piece of History, but it has consequences- though I am not sure that Watson’s account is the main reason for this. It proposes a way of doing Science that was alien to most people at the time. More importantly, leaving gaps like that in Science, could be important.

Biology is Chemistry, and much of the molecular underpinning of the cell is chemical. The fantastic contributions of Genetics to our understanding of the workings of the cell have overshadowed this and today the interplay between Genetics and Molecular Biology dominates as the main tool of discovery. If the sequence of a gene shows a kinase like domain, it must code for a kinase that works like a kinase; we rarely check. If the sequence of a protein says it has to be in the nucleus and, when we look for the protein, sometimes we find it outside the nucleus, it must be an artefact and thereby wrong. We trust the homology. Biochemistry is, for the most part, associated with structural biology and the chemical underpinning of the cell has been relegated to a second plane that we can extract from the sequences. There are, of course, counterexamples and the discovery that cytochrome c plays in apoptosis is one of these but, in general, we have forgotten that much of our knowledge about the cell comes from Biochemistry, real Bio-Chemistry. We would do well in revising this because at this moment there are too many things that do not fit the picture provided by the Genetics. We understand well replication, transcription and translation but beyond this, as we are starting to measure (to be quantitative), there are too many questions: interactions between components generate carefully controlled quantitative outputs e,g those associated with the homeostasis of tissues, temperature adaptable circadian clocks or periodic patterns of gene expression. One of the best understood cellular processes, the cell cycle, is a good example of the insights that a combination of Genetics and Biochemistry can produce.

Structure encodes function but sometimes, the details of function lie in…. function itself…..we would do well in reflecting on how much Photo 51 owes to Chemistry and see if we can find a way to sort out questions of cellular dynamics from a reinvention of Bio-Chemistry which today, I would say, needs to be a Bio-Physical Chemistry to understand rates and compartmentalization and the dynamics of the structural biology of the cell. Maybe this kind of Chemistry is a way towards the much needed Physiology of the Cell.

Note: I owe the idea to jottle these lines to my colleague Christian Schroeter who, in attending the Crick Symposium in Cambridge (UK) last week, remarked to me that a most interesting part of the Symposium was an acknowledgment by Jack Dunitz of the chemical background of the history of DNA. He like many did not know very much about this.