Why is the outer circle of human mitochondrial DNA "heavy" whereas the inner circle is "light"?
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1$\begingroup$ Because their masses are different: en.m.wikipedia.org/wiki/Heavy_strand $\endgroup$ – user24284 Oct 31 '17 at 5:24
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The heavy strand is literally heavier than the light strand. The first, or at least one of the first, observations of this phenomenon was in this paper:
Corneo G, Zardi L, Polli E. 1968. Human Mitochondrial DNA. J Mol Biol 36(3):419-423.
They showed that alkaline denatured mitochondrial DNA separates into two bands upon ultracentrifugation in a cesium chloride gradient:
Human mitochondrial DNA when centrifuged in alkaline CsCl in the analytical ultracentrifuge splits into two bands displaying densities of 1.727 g/cm3 and 1.766 g/cm3, respectively. The two bands appearing in the alkaline gradient correspond to the complementary strands of human mitochondrial DNA with a different GT/CA ratio... However, when an equimolar mixture of them is renatured by heating at 65°C for five hours in 2X SSC, a single band with a density very close to that of the native DNA is obtained. The latter experiment clearly indicates that the two bands correspond to the complementary strands displaying a bias in base composition.
The difference in molar mass (M) is due to a higher purine content (Pu) in the heavy strand (which are heavier than pyrimidines). This can be seen by tabulating the base composition of the RefSeq sequence of human mitochondrial DNA:
A T G C Pu(%) M(kDa)
Light Strand 5124 4094 2169 5181 44 5063
Heavy Strand 4094 5124 5181 2169 56 5174
R script if anyone is interested:
#uses Biostrings
light = readDNAStringSet("mtDNA.fasta")
heavy = complement(light)
comp = function(seq) {
ll = as.list(alphabetFrequency(seq)[1, c("A", "T", "G", "C")])
ll["%Pu"] = with(ll, (A + G) / (A + T + G + C)) * 100
ll["M(kDa)"] = with(ll, (A * 313.2) + (T * 304.2) + (G * 329.2) + (C * 289.2) + 79.0) / 1000
return(ll)
}
comp(light)
comp(heavy)
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1$\begingroup$ Do you have actual values? I have googled in vain searching for this $\endgroup$ – David Oct 31 '17 at 10:18
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$\begingroup$ Thanks — that improves the answer greatly. Although the "heavy" strand is heavier in terms of molecular mass, it is, of course, worth emphasising that it is the buoyant density of the purines, rather than their mass, that lead to the behaviour that gave rise to the loose nomenclature. $\endgroup$ – David Oct 31 '17 at 23:43
