Datasheet

Such sequences are called palindromes, after the term for a phrase or sen-
tence that reads the same in both directions (such as “Madam, I’m Adam” or
“A man, a plan, a canal: Panama.”)
Palindromic sequences aren’t merely a
curiosity; they play important biological roles. For instance, most DNA cut-
ting enzymes (so-called
restriction enzymes) have palindromic target
sequences. Other palindromic sequences serve as
binding sites, where regula-
tory proteins stick so they can turn genes on and off. Palindromic sequences
also have a strong influence on the 3-D structure of DNA molecules. (And not
just DNA. See the next section for more on palindromic sequences in RNA.)
Looking for exact or approximate palindromes in DNA sequences is a classic
bioinformatic exercise.
Analyzing RNA Sequences
DNA (deoxyribonucleic acid) is the most dignified member of the nucleic acid
family of macromolecules. Its sole and only task is to ensure — forever — the
conservation of the genetic information for its organism. It is thus very stable
and resistant, and lies well-protected in the nucleus of each cell.
Ribonucleic
acid
(RNA) is a much more active member of the nucleic acid family; it’s syn-
thesized and degraded constantly as it makes copies of genes available to the
cell factory.
In the context of bioinformatics, there are only two important differences
between RNA and DNA:
 RNA differs from DNA by one nucleotide.
 RNA comes as a single strand, not a helix.
The one-letter IUPAC codes for RNA sequences are shown in Table 1-2.
Table 1-2 Most Common Letters Used for
RNA Nucleotide Sequences
1-Letter Code Nucleotide Base Name Category
A Adenine Purine
C Cytosine Pyrimidine
G Guanine Purine
U Uracil Pyrimidine
N Any nucleotide Purine or Pyrimidine
(continued)
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Chapter 1: Finding Out What Bioinformatics Can Do for You
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