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Chargaff's rules states that DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine.

Statistics of different organism

As in the table $A \ne T$ and $C \ne G$. So I was wondering if Chargaff's rule is really applicable?

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BTW did you try reading Chargaff's papers? This was way before the discovery of DNA structure. Even their method (at that time) of DNA extraction and analysis was not as refined as the ones that we have now. You may not find Chargaff's paper that easily but have a look at one of my answers in Chemistry.SE. – WYSIWYG Feb 23 at 5:08
up vote 15 down vote accepted

In addition to Remi.b's answer, it should be noted that the phage Phi X 174 is the only organism in your list which significantly deviates from Chargaff's Rule (by more than 1-2 percentage points for the A-T pair). While sampling errors are indeed more likely in organisms with small genomes, there is in fact another factor in play here.

This is because Chargaff's Rule only applies to double-stranded DNA, due to the complementary base pairing that occurs between A-T and C-G. Since Phi X 174 is in fact a single-stranded + sense bacteriophage, Chargaff's Rule is inapplicable to it, since it does not obey the standard Watson-Crick base pairing that is the molecular basis of Chargaff's Rule. In fact, the Wikipedia article from which you obtained the chart states this as well:

The following table is a representative sample of Erwin Chargaff's 1952 data, listing the base composition of DNA from various organisms and support both of Chargaff's rules. An organism such as φX174 with significant variation from A/T and G/C equal to one, is indicative of single stranded DNA.

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Oh... how did I miss that?! Very good point! +1 – Remi.b Feb 22 at 15:18
@Remi.b because OP should have read about dsDNA – aaaaaa Feb 22 at 16:30

Does Chargaff's rule hold true on these data?

From the table:

  • Ratios A/T and G/C are close to 1 with extreme at 0.77 and 1.05.

  • Ratios A/G and T/C are quite far away from 1, with several extremes around 2 or 0.5.

So, yes Chargaff's rule seem to apply quite nicely.

Why isn't the ratio A/T exactly 1?

The question of why the ratios A/T and G/C are not closer to 1 is interesting though. To fully answer this question I would need to go back into the primary literature who produced those numbers.

It appears that the three species of the list that have the smallest genome size ($\phi X174$, E. coli and yeast) are also the three species that show the greatest deviation from unity. The two species that have the largest genome size (maize and wheat) have the smallest deviation from unity. Overall, this suggests that this deviation is only a consequence of sampling error.

Did you say Sampling error?

This is just a small stat reminder

From wiki

In statistics, sampling error is incurred when the statistical characteristics of a population are estimated from a subset, or sample, of that population. Since the sample does not include all members of the population, statistics on the sample, such as means and quantiles, generally differ from statistics on the entire population

Sampling error is not an error that a researcher does but an intrinsic property of the sampling process. Expected deviation from the true value is decreasing as the sample size increases, i.e. small sample size will show greater deviations (on average) from the true value than larger sample size.

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I would put it down to straightforward experimental error rather than sampling error. The methods used to obtain the numbers are relatively crude chemical methods. – Jack Aidley Feb 22 at 17:11
Not sure if you mean "measurement error" or "bias" when talking about "experimental error". In any case, I am personally not be able to give my opinion on this matter as I haven't read these papers. – Remi.b Feb 22 at 18:01

March Ho's answer is correct. However the important thing to learn from this is that biology is not physics, and there are no rules — only observations and explanations. What Chargaff made was an observation for which he had no explanation. It was only when Crick and Watson postulated AT,GC base-pairing in double-stranded DNA that the observation was rationalized. More important, those DNAs that were exceptions to the 'rule' could be rationalized as differing from the Crick/Watson model. In the case of phiX 174 it was because it had a single-stranded genomic DNA, but one can envisage other (incorrect as it turns out) explanations in terms of modified bases that were not detected in the assay. Biology is a science of exceptions rather than rules.

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While the answer is otherwise good, I don't understand what you mean by "biology is not physics and there are no rules". As far as I know, rules are violated rather often (relativity vs Newtonian mechanics for example) in physics as well. – March Ho Feb 22 at 15:05
Rules (indeed Laws) in physics tend to involve equations based on a conceptual framework. Deviations of observations from equations (one can stick to Newtonian mechanics and look at deviations from Boyle's Law, I seem to remember) lead to modified equations based on additional assumptions rather than fudge factors. I don't see any equations or theory in biology, except at the very basic chemical level. It seems to me more that Nature finds one solution to a problem, we observe it, but it isn't a rule as somewhere else she solves the problem with a black swan. – David Feb 22 at 17:25
Did you just say I don't see any equations or theory in biology?? You should read some primary literature then. I am a theoretician working in the field of population genetics (subfield of evolutionary biology) btw. – Remi.b Feb 22 at 17:59
Well I'm molecular biologist turned bioinformatician with a first degree in chemistry. Sure there's a role for maths and theory in your sort of biology, but it doesn't underpin the subject like it does physics. And my answer was intended to help the questioner in a wider sense. Namely that she should not be looking to learn or lean on apparent rules, but to look for the pattern behind observations and prepare herself for Nature's variety of patterns. Shine and Dalgarno, won't prepare her for Kozak, and Kozak won't prepare her for internal initiation. Nor Mendel's 'laws' for McClintock. – David Feb 22 at 19:03
@David biology has not been classically employing mathematics which the field of physics has been since ages ago. This is changing as more and more mathematicians (and even physicists) are applying mathematical models to explain biological systems. The issue is that biological systems are way more complex than a bouncing ball (or even space rockets). People like Remi and me and many others are working in this interfacial area where mathematical principles are combined with biological observations. – WYSIWYG Feb 23 at 5:04

protected by Mad Scientist Feb 22 at 17:11

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