Datasheet

Table 1-2 (continued)
1-Letter Code Nucleotide Base Name Category
R A or G Purine
Y C or U Pyrimidine
-- ------- None (gap)
Some programs automatically handle the U-instead-of-T conversion — and
many don’t even distinguish between the two classes of nucleic acids. So
don’t be surprised if a database entry displays RNA sequences (such as mes-
senger RNA) with a T instead of a U. In fact, like proteins, RNA sequences are
encoded in the DNA. For this reason, people have adopted the habit of work-
ing with the sequences of the RNA
genes (written in DNA) rather than with
RNA sequences.
RNA structures: Playing with sticky strands
Even though RNA molecules consist of single strands of nucleotides, their
natural urge for pairing with complementary sequences is still there. Think of
each such single strand as a free-floating piece of Scotch tape: You know that
it won’t take long for that tape to become a messy ball, until no sticky part
remains exposed. This is exactly what happens to the single-stranded RNA
molecule — more or less (for the sake of poetic license) — although Figure
1-8 shows more precisely how the stickiness works.
Now you understand why we insisted on the notion of strand complementarity
(refer to Figure 1-6). Single-stranded RNA molecules pair different regions of
their sequences to form stable double-helical structures — admittedly less
regular than (but quite similar to) the double-helical structure of DNA. Once
synthesized, each RNA molecule quickly adopts a compact fold — trying to
pair as many nucleotides as possible, while keeping the chain not only flexi-
ble but true to its own geometry. Hairpin shapes, as shown in Figure 1-8, are
U G
5'
3'
A C
ACUG
C
U
A
U
Figure 1-8:
How RNA
turns itself
into a
double-
stranded
structure.
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Part I: Getting Started in Bioinformatics
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