| The following abstract, submitted in January 1994, illustrates the general difficulty that was experienced getting the ideas on these pages past the peer-review gate. Sometimes there were delays of several years. Editors also tend to redate revised papers which gives the impression that publication in their journals is rapid. The paper, of which this is the abstract, did not appear until late in 1995. Note reference to a paper submitted to Nucleic Acids Research which eventually had to be submitted elsewhere. The paper submitted to the Journal of Theoretical Biology did not surface until 1996. |
PERCENTAGE G+C
DETERMINES FREQUENCIES OF COMPLEMENTARY TRINUCLEOTIDE PAIRS: IMPLICATIONS FOR
SPECIATION. D. R. Forsdyke. Department of Biochemistry, Queen's University, Kingston, Ontario K7L3N6
|
To
an approximation Chargaff's rule applies to long sequences of single
stranded DNA. It follows that complementary oligonucleotides are present
in approximately equal frequencies. Thus a plot of the frequencies of 32
trinucleotides against those of their 32 complements is rectilinear with
an intercept close to the origin (Prabhu,
1993. NAR
21,2797). I
have compared the frequencies of trinucleotides in long sequences and
their shuffled counterparts. Trinucleotides fall into 4 main frequency
groups: (i) WWW, (ii) WWS+WSW+SWW, (iii) SSW+SWS+WSS, and (iv) SSS.
Among the 32 complementary trinucleotide pairs there is a hierarchy of
frequencies which is influenced both by percentage G+C (not affected by
shuffling the order of bases) and by primary sequence. It is proposed
that evolutionary pressures select for sequences with complementary
oligonucleotides in close proximity, thus creating the potential to form
stem-loops. These are dispersed throughout genomes and are rate-limiting
in recombination (Tomizawa,1984.
Cell
38, 861; Forsdyke,
J.
Mol. Evol.
submitted).
Individual species have fine-tuned their stem-loop forming potential to
avoid recombination with other species. As a consequence we see today
that similar species in similar environments may differ greatly in G+C
percentages (Forsdyke,
J. Theor.
Biol. and
Nucleic
Acids Res.
submitted).
Supported by the MRC of Canada. |
Return to: Hierarchy paper 1995 (Click Here)
Return to: Bioinformatics (Genomics) Index (Click Here)
Return to: HomePage (Click Here)
This
page was established circa 2000 and was last edited
03 Feb 2013
by Donald Forsdyke