Biology Reference
In-Depth Information
sequences and aligning them is continued until it is possible to produce a con-
tinuous DNA sequence for the DNA of interest.
A variety of questions can be asked after the sequences are obtained.
Sequences can be searched for all known restriction endonuclease target sites,
and the computer can generate a comprehensive and precise restriction map.
The sequences can be searched for interesting structures such as
tandem repeats
and
inverted repeats
, which would indicate the insertion of transposable ele-
ments (TEs). The sequences can predict which proteins are coded for based on
the sequences in the possible open reading frame (ORF) on each of the two
strands. An ORF is a segment of DNA that does not include a termination codon
and that may indicate that a polypeptide-coding region exists. Both strands
must be interpreted because it is not known in advance which is the coding and
which is the noncoding strand.
The DNA sequence, or the deduced polypeptide sequence, may be compared
with sequences in data banks. Often, because of the degeneracy of the DNA
code, similarities are found when two polypeptide sequences are compared;
these sequence similarities might not have been apparent if the comparison had
been carried out only at the DNA-sequence level. DNA-sequence similarities may
be present because of
convergent evolution
or through homology. Convergent
evolution implies that the two sequences did not have a common ancestral
sequence but that selection for a particular function in two different lineages
has converged on a particular structure or related structures.
The term
homology
has become controversial because it has multiple defi-
nitions. Traditionally, similar structures in different organisms have been
called homologous if the organisms have descended from a common ancestor.
However, some molecular biologists have used the term “per cent homology”
when they mean there is
similarity
in DNA sequence, which may not be due to
descent from a common ancestor.
A search of the DNA or protein sequence banks for
similarities
with any newly
discovered sequence might turn up amazing degrees of similarity. For example,
homeotic
genes, genes that direct cells in different segments to develop in par-
ticular patterns, have been cloned from
D. melanogaster
. The
homeobox
, a seg-
ment of
≈
180bp, is characteristic of the homeotic class, and probes using the
homeo-box sequence have been used to isolate previously unknown homeotic
genes in other insects. Sequences homologous to the homeobox have been iso-
lated from mice and humans, indicating that similar genetic mechanisms control
aspects of development in higher organisms. The high degree of conservation
between the homeobox sequences of
Drosophila
, frogs, mice, and humans
