chargaff
Base composition in ssDNA for 7 bacterial DNA
Description
Long before the genomic era, it was possible to get some data for the global composition of single-stranded DNA chromosomes by direct chemical analyses. These data are from Chargaff's lab and give the base composition of the L (Ligth) strand for 7 bacterial chromosomes.
Usage
data(chargaff)
Format
A data frame with 7 observations on the following 4 variables.
- [A]
-
frequencies of A bases in percent
- [G]
-
frequencies of G bases in percent
- [C]
-
frequencies of C bases in percent
- [T]
-
frequencies of T bases in percent
Details
Data are from Table 2 in Rudner et al. (1969) for the
L-strand. Data for Bacillus subtilis were taken from
a previous paper: Rudner et al. (1968). This is in
fact the average value observed for two different strains
of B. subtilis: strain W23 and strain Mu8u5u16.
Denaturated chromosomes can be separated by a technique of
intermitent gradient elution from a column of methylated
albumin kieselguhr (MAK), into two fractions, designated,
by virtue of their buoyant densities, as L (light) and H
(heavy). The fractions can be hydrolyzed and subjected to
chromatography to determined their global base composition.
The surprising result is that we have almost exactly A=T
and C=G in single stranded-DNAs. The second paragraph page
157 in Rudner et al. (1969) says: "Our previous
work on the complementary strands of B. subtilis DNA
suggested an additional, entirely unexpected regularity,
namely, the equality in either strand of 6-amino and 6-keto
nucleotides ( A + C = G + T). This relationship, which
would normally have been regarded merely as the consequence
of base-pairing in DNA duplex and would not have been predicted
as a likely property of a single strand, is shown here to
apply to all strand specimens isolated from denaturated DNA
of the AT type (Table 2, preps. 1-4). It cannot yet be said
to be established for the DNA specimens from the equimolar
and GC types (nos. 5-7)."
Try example(chargaff) to mimic figure page 17 in Lobry
(2000) :
Note that example(chargaff) gives more details:
the red areas correspond to non-allowed values beause the sum
of the four bases frequencies cannot exceed 100%.
The white areas correspond to possible values (more exactly
to the projection from R^4 to the corresponding R^2 planes
of the region of allowed values).
The blue lines correspond to the very small subset of allowed
values for which we have in addition PR2 state, that is
[A]=[T] and [C]=[G]. Remember, these data are for ssDNA!
Source
Rudner, R., Karkas, J.D., Chargaff, E. (1968) Separation of
B. subtilis DNA into complementary strands, III. Direct
Analysis. Proceedings of the National Academy of Sciences of the United States of America, 60:921-922.
Rudner, R., Karkas, J.D., Chargaff, E. (1969) Separation of microbial deoxyribonucleic acids into complementary strands. Proceedings of the National Academy of Sciences of the United States of America, 63:152-159.
References
Lobry, J.R. (2000) The black hole of symmetric molecular evolution. Habilitation thesis, Université Claude Bernard - Lyon 1. https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf.
citation("seqinr")
Examples
data(chargaff)
op <- par(no.readonly = TRUE)
par(mfrow = c(4,4), mai = rep(0,4), xaxs = "i", yaxs = "i")
xlim <- ylim <- c(0, 100)
for( i in 1:4 )
{
for( j in 1:4 )
{
if( i == j )
{
plot(chargaff[,i], chargaff[,j],t = "n", xlim = xlim, ylim = ylim,
xlab = "", ylab = "", xaxt = "n", yaxt = "n")
polygon(x = c(0, 0, 100, 100), y = c(0, 100, 100, 0), col = "lightgrey")
for( k in seq(from = 0, to = 100, by = 10) )
{
lseg <- 3
segments(k, 0, k, lseg)
segments(k, 100 - lseg, k, 100)
segments(0, k, lseg, k)
segments(100 - lseg, k, 100, k)
}
string <- paste(names(chargaff)[i],"\n\n",xlim[1],"% -",xlim[2],"%")
text(x=mean(xlim),y=mean(ylim), string, cex = 1.5)
}
else
{
plot(chargaff[,i], chargaff[,j], pch = 1, xlim = xlim, ylim = ylim,
xlab = "", ylab = "", xaxt = "n", yaxt = "n", cex = 2)
iname <- names(chargaff)[i]
jname <- names(chargaff)[j]
direct <- function() segments(0, 0, 50, 50, col="blue")
invers <- function() segments(0, 50, 50, 0, col="blue")
PR2 <- function()
{
if( iname == "[A]" & jname == "[T]" ) { direct(); return() }
if( iname == "[T]" & jname == "[A]" ) { direct(); return() }
if( iname == "[C]" & jname == "[G]" ) { direct(); return() }
if( iname == "[G]" & jname == "[C]" ) { direct(); return() }
invers()
}
PR2()
polygon(x = c(0, 100, 100), y = c(100, 100, 0), col = "pink4")
polygon(x = c(0, 0, 100), y = c(0, 100, 0))
}
}
}
# Clean up
par(op)