Re: Symmetry of DNA replication

On Mon, 21 Jan 2008 23:52:18 -0500 (EST), "Graham Jones" <x@xxx>
wrote:

[...snip]

"EvolveAGene 3: A DNA coding sequence evolution simulation program" by Barry
G. Hall.
http://precedings.nature.com/documents/1230/version/1/files/npre20071230-1.pdf

"Comparison of the Accuracies of Several Phylogenetic Methods
Using Protein and DNA Sequences" Barry G. Hall
http://mbe.oxfordjournals.org/cgi/reprint/msi066v1.pdf

No mention is made of whether it matters if a base pair such as AT is
replicated with A on the leading strand, and T on the lagging strand, or
vice-versa. I am trying to figure out whether it does matter. To rephrase
my original question: if you are looking at the replication of a particular
gene, is it equally likely that the antisense strand is the leading strand
or the lagging strand? From your answer, I think it depends on where the
sequences that act as origins of DNA replication are in relation to the
gene.

Just thinking out loud here... If you have a unicellular organism, and a
particular gene which always gets the antisense strand as the leading
strand, and assume the leading and lagging strands make very different
numbers of errors, then presumably, focussing on this gene, you get a
"lagging daughter cell" and a "leading daughter cell". Even this assymmetry
wouldn't matter at the population level, except that selection acts on the
two daughter cells, so it might...


Graham


For point mutations, whether you use a 2,4.5 or 6 parameter model,
the two strands are treated as symmetrical, having no different
mutational bias. For Hall's purposes and probably for your purposes
this is OK.
But the strands are expected to be mutationally biased. Strand
asymmetries in mutations may result in skewed strand nucleotide
frequencies. For instance, if mutation to an A is more frequent than
mutation to a T, then a strand portion having more mutations than its
paired portion (the lagging strand portion) should have more A's than
T's. Similarly expect an asymmetry with G's and C's on the two
strands. This property has been used to identify DNA bidirectional
replication origins since here the strand will switch from leading to
lagging.
A gene coding sequence then gets overweighted for A's or T's (and G's
or C's) depending upon the particular strand it is found.
William L Hunt


.

Relevant Pages

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  • Re: Richard Dawkins - amusing quote
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    (talk.origins)
  • Re: Richard Dawkins - amusing quote
    ... specified in the DNA for coiling. ... but also on which side of the double helix is being ... the railing has a pattern. ... and each copy remains with the strand that it was ...
    (talk.origins)