Non-Watson-Crick base pairs that you won't find in the textbooks and Wikipedia

(Continued from previous blog). Yesterday, I found 'officially forbidden' non-Watson-Crick CA and TG base pairs on the website of Nature Scitable. The standard Watson-Crick base pairs are AT and CG. They are in all the textbooks. But, you won't find the non-Watson-Crick base-pairs in the textbooks. Certainly not in this detail. The first figure (a) gives the 4 bases and their rare (tautomeric) forms. They are not in the textbooks. They are apparently in a chemical equilibrium (see arrows). The rare forms are indeed rare, but apparently they do exist. So, we should know about them.

Left: common, Right: rare tautomeric forms of the 4 bases
©Nature Scitable

Standard Watson-Crick base pairs
©Nature Scitable

All 4 bases A, T, C, G have rare forms. But only rare-C and rare-G participate in base pairs, see figure (c). The pairs consists of a common and a rare base. Note that rare-A and rare-T do not participate in rare base pairs:

Rare matching base pairs CA and TG
©Nature Scitable [1]

If this is not confusing enough, on the same webpage Nature shows aberrant base pairing of the bases in their 'normal' form:

Non-Watson-Crick base pairs TG and CA.
©Nature Scitable

My conclusion is that Evolution textbooks and Wikipedia [6] give an incomplete picture of which base pairs are possible in DNA. They do tell about mutation and base pair mismatch, but never show non-Watson-Crick base pairs. I think they should do so. This is an extremely important point: how can you explain mutation to students, if rare base forms and rare base pairs do not exist? Then, show them! If DNA would replicate exclusively on the basis of the standard Watson-Crick base pair rule, then DNA would be copied with 100% reliability eternally. I think, one cannot blame polymerase for copying errors, because polymerase can't enforce chemically impossible base pairing.

Secondly, students get the wrong impression that DNA is a perfect molecule, that bases always follow the Watson-Crick rule, and that DNA is fine-tuned for life. It is an intrinsic property of the bases that they have rare (tautomeric) forms and that they can pair in a non-standard way. 

Hubert Yockey 1992

The question remains: How often do non-Watson-Crick base pairs occur in DNA?  Surprisingly, I found in an aside on page 300 of Hubert Yockey [2] that "the probability that adenine will mispair to cytosine is about 10^-4 x 10^-4 = 10^-8." (AC pair). That is very small. About the CG pair he writes: "...the base selected has a probability of about 10^-4 of being in the imino or enol tautometirc form that leads to mispairing." 

He doesn't do anything with these calculations. However, if I understand him correctly, this means that there is a 1 in 10,000 probability that the C or G base is in the wrong form. This would mean that at every replication round of our genome of 3.2 billion bases, 320,000 C or G bases would mispair. Considering that the human body starting from a zygote experiences about 10 quadrillion (10¹⁵) cell divisions in a lifetime [3] then the unimaginable number of 3,2 x 10²⁰ C or G base mismatches would occur [4]. The proofreading and repair system has the task to repair these mutations...

Anyhow, it is clear by now that DNA as a carrier of hereditary information is far from perfect [5]. A perfectly intelligently designed DNA would be stable, have bases without tautomers, 100% replication fidelity, didn't need proofreading and repair and didn't have accumulation of DNA damage during aging. No cancer and no genetic diseases as a result! Mutations would only be positive and introduced deliberately as an adaptation to changing environmental conditions.

In the next blog I will return to Kondrashov!

Correction

I was informed that on the Dutch wikipedia page Kwantumbiologie tautomerism is mentioned and illustrated with AT base pair mutating in to an AC base pair. On that page one finds interesting references to the English literature! [24 Jan 2023]

Notes

1. This illustration is also present in H F Judson The Eighth Day of Creation, page 434 (not a textbook!)
2. Hubert Yockey (1992) Information theory and molecular biology, hardback Cambridge University Press, page 300. (not an evolution textbook). I have a review of the book on my WDW website.
   
3. Wikipedia article cell division (13 Jan 23), but the meaning of quadrillion differs!
4. In fact 3,2 billion base pairs is the haploid number, but our body cells are diploid so the number should be 6,4 billion! That is the amount of DNA that has to be replicated! And both C and G could be in the wrong tautomeric form, so multiply the number by two.
   
5. Fazale Rana (2022) DNA’s Fine-Tuned Structure Minimizes Harmful Tautomers,  Reasons to Believe. This is a perfect example of a christian/Intelligent designer who claims that DNA’s optimized structure is evidence for the intelligent design of DNA. He does not show any mismatch base pairs such as the Nature Scitable page does. He does not  deny that base tautomers exist, and that tautomeric forms are harmful and trigger mutations, but claims that it could be worse! Read the article, and draw your own conclusion!
6. The Wikipedia article Base pair doesn't mention tautomerism, let alone showing illustrations of base mispairs. The Wikipedia article DNA doesn't mention tautomerism. On the page Tautomer DNA is not mentioned at all, although "nucleobases guanine, thymine, and cytosine" are present, but strangely adenine is absent on that page! Wikipedia is really incomplete in this respect. Later I found the Wikipedia article Non-canonical base pairing, ... but the DNA article does not contain a link to this article. The DNA article however, does contain a paragraph 'Non-canonical bases', but that is not the same as non-canonical base pairing! Wikipedia is like loose sand:  a badly-integrated, disjointed system. There is no supervisor who takes care of the coherence of the whole system. This can be expected from a multi-author encyclopedia. [15 Jan 2023] [23 Jan 2023]
   

Two Nobel Prizes contradicting each other: Watson and Crick versus Tomas Lindahl

In 1962 Watson, Crick and Wilkins received the Nobel Prize for the discovery of the structure of DNA. In 2015, Tomas Lindahl received the Nobel Prize for the discovery of DNA repair. The first prize symbolizes the beauty of the DNA molecule. The second Nobel Prize symbolizes the weaknesses of the same molecule. So, in a sense, these prizes contradict each other.

Watson-Crick versus Lindahl

How the beauty of DNA (and the Nobel Prize?) blinded scientists for the weaknesses of DNA. Surprise: later those weaknesses were awarded a Nobel Prize!

Why is DNA perfect? Because DNA structure has been proven chemically correct and because the structure gives for the first time a satisfactory explanation of heredity in the biological world. Two problems solved at once. Heredity requires a a stable structure. Since all life forms from bacteria to humans are based on DNA, and life is some 3 billion years old, DNA simply must be a stable structure.

But then came Swedish scientist Tomas Lindahl. He showed that the apparent stability of DNA is not based on its structure, but –totally unexpected – on enzymatic repair and proofreading! So, DNA only seemed stable. But when he started his research, repair-enzymes were unknown. Clearly, his idea contradicted known facts. To see how it could be that all biologists were blinded by the beauty and the logic of DNA, we must first look at some details of DNA structure. Here, I follow the description of Francis Crick in What Mad Pursuit (1988).

In 1950, three years before the discovery of the structure of DNA, chemist Chargaff had found in DNA from many different species the amount of base A equaled the amount of T and the amount of C equaled the amount of G. The relative amounts of AT and CG in species differ. Chargaff did not conclude anything from his data about the structure of DNA. For Watson and Crick it was crucial evidence for AT and CG base pairing. Furthermore, AT and CG base pairs have equal dimensions. So they fit perfectly in a regular double helix. This is important for a very long molecule. Furthermore, to fit in the double helix the four bases have to be in the correct tautomeric form [1]. The beauty of the DNA model is that the specificity of base pairing gives a mechanism for replication (making a copy of DNA). This is a crucial function in biology (cell division, heredity!). Base pairing guaranties an exact copy of a DNA string. So, a crucial biological property is explained with an elegant chemical structure and its properties. "This base pairing is the key feature of the structure [of DNA]" (Crick, 1988, p.166).

One problem remains: a mutation implies that a wrong base is incorporated, but how can mutations occur if base-pairing is always correct? In their second paper in Nature, Watson and Crick wrote: 

"We believe that the bases will be present almost entirely in their most probable tautomeric forms." ... "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." [2]

So, they explained mutation theoretically and in principle, but had no data about how often the bases were in the 'correct' or 'wrong' tautomeric form [4], [6]. Consequently, they had no idea how often spontaneous mutation occurs. Neither did they seem to care. They simply assumed it occurs in negligible frequencies. They ignored the problem. It apparently did not invalidate the structure as a carrier of hereditary information.

In the years after 1953 scientists were busy with experimental validation of the double helix model. This took some time. Furthermore, solving the genetic code (how the DNA code is translated into proteins) took some hard work too. The solution of these two problems created a solid foundation of molecular biology. It was a tremendous breakthrough. In fact it was a solid foundation for the whole of biological science including evolutionary biology. It seemed no important problems remained. Crick wanted to move on to other fields of research! 

But, than came Lindahl: 

"It was at the time a far-fetched idea that DNA might be unstable in the cellular environment. (Lindahl Nobel lecture )

Tomas Lindahl discovered the intrinsic fragility of DNA. This constituted no less than a paradigm shift. For example: could anyone predict on the basis of the structure of DNA that Uracil could be present in DNA? (it normally occurs only in RNA!). That specific enzymes exist that continuously scan DNA for the presence of Uracil? Also: oxidative damage (see Lindahl Nobel Prize lecture). Water is a damaging agent for DNA! For a complete overview see the Wikipedia article about the endogenous causes of DNA damage.

Thirty five years after the discovery of the double helix and twenty six years after the Nobel Prize, Francis Crick published What Mad Pursuit (1988). By that time Lindahl had already published several papers demonstrating DNA-repair enzymes, his first in 1974. Surprisingly, I found only 1 page about DNA error-correction [3] in What Mad Pursuit. Not important enough? It did not fit in his DNA-is-perfect-paradigm? Yes, Crick knew very well mutations exist. He did experimental work with phage mutants. The mutations he studied were created with chemical mutagens (acridine, proflavin). So, the damage came from outside DNA, not from the inside. It wasn't spontaneous damage. Those mutations were not a threat to the DNA-is-perfect-paradigm. But Lindahl showed that DNA is inherently unstable in its normal cellular environment. Certainly a revolutionary idea. The reason must be clear by now: DNA must be reliable to function as a carrier of genetic information. Evolution produced complex beings such as humans. How much evidence do you need?

Summary 

Life exists - so DNA must be stable

Life exists - so DNA must be repairable

Watson, Crick, and Wilkins received the Nobel Prize for the structure of DNA. Although they did not explicitly claim DNA is stable, it is implicit in the statement that DNA is the carrier of hereditary information and the structure explains why this is the case. The Nobel Prize in Chemistry 2015 was awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for DNA repair. Repair implies DNA on its own is not a stable molecule. Although the Watson-Crick model is not refuted, its assumed stability certainly has been refuted. I didn't find this contradiction clearly in the literature [5]. I wrote this blog because it is worth pointing out.

In a next blog I will reveal important consequences of the stability/instability of DNA. This blog resulted from shocking remarks in Kondrashov (2017) Crumbling Genome (see previous blog).

 

Notes

1. Tautomerism is a dynamic equilibrium between two compounds with same molecular formula. Crick did not elaborate on the frequency of right/wrong tautomeric forms of the bases. In his What Mad Pursuit he writes that "Jerry Donohue, who shared an office with us, told us that some of the textbook formulas were erroneous and that each base occurred almost exclusively in one particular form." (p.65). (Which from?). Please note: "almost exclusively"!
2. Watson, Crick (1953) Genetical Implications of the Structure of Deoxyribonucleic Acid, Nature, May 1953. This is the second publication of Watson and Crick.
3. and a rough estimate about error-rate. I will return to that in a next blog. 
4. It seems there are no data and there is no theory to predict the frequency of wrong base tautomeres after 70 years! See:  "calculating the position of tautomeric equilibria in nucleobases is certainly within the grasp of contemporary quantum chemistry, and semi-empirical parameters on which the positions of these equilibria might most sensitively depend could presumably be identified." page 354 in Fitness of the Cosmos for Life. CUP 2008 [added: 9 Jan 2023] 
   
5. Intelligent Design theorist Michael Denton (1998) triumphantly claims that DNA is a remarkably stable structure! I added a paragraph to my review of his Nature's Destiny. How the Laws of Biology reveal Purpose in the Universe on my DWD website. [added: 10 Jan 2023]
6. Hubert Yockey (1992) is the first author where I found a probability of mispairing of the AT and CG base pairs. In an aside on page 300 he calculates that "the probability that adenine will mispair to cytosine is about 10^-4 x 10^-4 = 10^-8." About the CG pair he writes: "...the base selected has a probability of about 10^-4 of being in the imino or enol tautometirc form that leads to mispairing."  (see: keto–enol tautomerism). [added: 11 Jan 2023]

 

 

Further Reading

• Nobelprize.org: DNA repair – providing chemical stability for life, 2015. This gives a popular explanation of DNA repair. Recommended.
• Watson, Crick (1953) Genetical Implications of the Structure of Deoxyribonucleic Acid, Nature, May 1953. This is the second publication of Watson and Crick. The first (the most famous) was published April 25.
• Francis Crick (1988) What Mad Pursuit, paperback. Is a popular account of the discovery of DNA in Crick's own words. Recommended.
• Tomas Lindahl (1993) Instability and decay of the primary structure of DNA, Nature, 1993. (Abstract). "Although DNA is the carrier of genetic information, it has limited chemical stability. Hydrolysis, oxidation and nonenzymatic methylation of DNA occur at significant rates in vivo." (free pdf).
• Deborah E Barnes, Tomas Lindahl (2004)  Repair and genetic consequences of endogenous DNA base damage in mammalian cells, Annu Rev Genet. (full text) (makes clear that oxygen, water and metabolites damage DNA in rest).
  
• Blog page with list of DNA blogs of the past 10 years (2012-2022). 

Happy New Year 2023 for all my blog followers!

 

Happy 2023 for all blog visitors!