| chargaff {seqinr} | R Documentation |
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.
data(chargaff)
A data frame with 7 observations on the following 4 variables.
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)."
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.
Try example(chargaff) to mimic figure page 17 in
http://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf.
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 !
citation("seqinr")
data(chargaff)
op <- par(no.readonly = TRUE)
par(mfrow=c(4,4))
xlim <- c(0,100)
ylim <- xlim
par(mai=rep(0,4))
par(c(0.01, 0.99, 0.01, 0.99))
par(xaxs="i")
par(yaxs="i")
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(0,100,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=20, xlim=xlim, ylim=ylim,
xlab="",ylab="", xaxt="n", yaxt="n")
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="lightpink")
polygon(x=c(0,0,100), y=c(0,100,0))
}
}
}
# Clean up
par(op)