seqinr (version 4.2-5)

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!

References

Lobry, J.R. (2000) The black hole of symmetric molecular evolution. Habilitation thesis, Universit<U+00E9> Claude Bernard - Lyon 1. https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf.

citation("seqinr")

Examples

# NOT RUN {
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)
# }