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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)



Roberto Takata <rmtakata@gmail.com> wrote:


> Other possibility is to analyze the DNA sequences of extant organisms
> with homologous peptide sequences.
>
> For example, the alpha-2 collagen fragment from T-rex was sequenced as:
> G L P G E S G A V G P A G P I G S R
>
> It would correspond to a DNA sequence:
> GGN YTN CCN GGN GAR WSN GGN GCN GTN GGN CCN GCN GGN CCN ATH GGN WSN MGN
>
> The correspondent chicken DNA sequence is:
> GGT CTT CCT GGT GAA AGC GGT GCT GTT GGT CCT GCT GGT CCT ATT GGA AGC CGT
>
> That comparison allow us to have some improved knowledge about T-rex's
> DNA sequence.


Sadly no, this is simply not correct.  We can't use the chicken's DNA
sequence to fill in the blanks in the inferred _Tyrannosaurus rex_ DNA
sequence.  It cannot be assumed that _T. rex_ has the exact same codon
for each amino acid residue as the chicken.  As David says, the best
we can do is use the degenerate sequence (i.e., with those "extra
symbols" reflecting an unknown base position), because we cannot know,
and will probably never know, what the DNA sequence is for _T. rex_.


BTW, the sequence you provide for _T. rex_ alpha-2 collagen (above) is
exactly the same as that for the chicken (GLPGESGAVGPAGPIGSR).  It is
not one of the six _T. rex_ collagen sequences deposited by Asara et
al. (2007) in GenBank.


Of course, all this assumes that the peptide sequence actually comes
from _T. rex_.  Check out: Bern et al. (2009) Reanalysis of
_Tyrannosaurus rex_ mass spectra.  J. Proteome Res. 8: 4328–4332.


I can personally attest to the sensitivity of mass spectrometry (MS)
analysis, and its unfortunate ability to pick up contaminants present
at extremely low levels.  In a seawater sample I analyzed from
freezing waters off the coast of Antarctica, the MS picked up a
peptide belong to a protein from the tropical rubber tree _Hevea
brasiliensis_.  I inferred that this protein actually come from our
latex gloves, which we wear during collection and processing of the
seawater samples.


> If we had the crocodile or alligator or caiman sequence the comparison
> could be improved.


No, it would make no difference at all.






Cheers

Tim