A DNA motif is a nucleic acid or amino acid sequence pattern that has, or is conjectured to have, some biological significance. Normally, the pattern is fairly short and is known to recur in different genes or several times within a gene. DNA motifs are often associated with structural motifs found in proteins.
An example is the N-glycosylation site motif:
- Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro
This pattern may be written as N{P}[ST]{P}
where N=Asn, P=Pro, S=Ser, T=Thr
and {X} means any amino acid except X; and [XY] means either X or Y.
The notation [XY] does not give any indication of the probability of X or Y occurring in the pattern. Sometimes patterns are defined in terms of a probabilistic model such as a hidden Markov model.
Table of contents |
2 Discovery of DNA motifs 3 Pattern Description Notations 4 See also 5 References |
The notation [XYZ] means X or Y or Z, but does not indicate the likelihood of
any particular match. For this reason, two or more patterns are often associated with a single DNA motif - the defining pattern, and various typical patterns.
For example, the defining sequence for the IQ motif may be taken to be:
Usually, however, the first letter is I, and both [RK] choices resolve to R.
Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes
equated with the IQ motif itself, but a more accurate description would
be a consensus sequence for the IQ motif.
There are software programs which, given multiple input sequences, attempt to identify one or more candidate motifs. One example is MEME (see References below), which generates statistical information for each candidate.
DNA motifs have been discovered by studying similar genes in different species.
For example, by aligning the amino acid sequences specified by
the GCM (glial cells missing) gene in man, mouse and D. melanogaster,
Akiyama and others discovered a pattern which they called the GCM motif.
It spans about 150 amino acid residues, and begins as follows:
The authors were able to show that the motif has DNA binding activity.
Several notations for describing motifs are in use but
most of them are variants of standard notations for regular expressions
and use these conventions:
Different pattern description notations have other ways of forming pattern elements. One of these notations is the PROSITE notation, described in the following subsection.
The PROSITE notation uses the IUPAC one-letter codes and conforms to
the above description with the exception that a concatenation symbol, '-', is used between pattern elements, but it is often dropped between letters of the pattern alphabet.
PROSITE allows the following pattern elements in addition to those described previously:
Motifs and consensus sequences
where x signifies any amino acid, and the square brackets indicate an alternative (see below for further details about notation).Discovery of DNA motifs
Software
Discovery through evolutionary conservation
Here each . signifies a single amino acid or a gap, and each * indicates
one member of a closely-related family of amino acids.Pattern Description Notations
The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation:
Thus the pattern [AB] [CDE] F matches the six amino acid sequences corresponding to ACF, ADF, AEF, BCF, BDF, and BEF.PROSITE Pattern Notation
Some examples:
The signature of the C2H2-type zinc finger domain is:
See also
References