The Decoding Code in mRNA 
secondary and tertiary structures are crucial. In 
the handful of known cases of proteins having the 
unusual amino acid selenocysteine, a UGA stop 
codon is reprogrammed to be decoded as this 
21st amino acid. The decoding code clearly in- 
cludes structural elements that are downstream, 
in one case 150 nucleotides away in the non- 
translated part of the message. 
An emerging theme of the decoding code is 
mRNA secondary and tertiary structural elements. 
Stem-loop structures can often be identified by 
inspection of sequence, and evidence for their 
participation can be obtained by making disrup- 
tive and restorative mutations. The functional 
stems can be short in some contexts, long in 
others, and can be near the site of action or well 
downstream. 
In an increasing number of cases, the crucial 
structure is more complicated, involving a pseu- 
doknot where a sequence downstream of a stem- 
loop folds back to pair with the loop of the 
stem, resulting in two stems and two loops that 
are intertwined. Physical-chemical properties of 
model pseudoknots show that the two stems are 
coaxial, with considerable stability coming from 
the extended base stacking that is achieved. 
To test the biological importance of each of the 
bases of these complicated structures requires 
construction of a very large number of mutants, 
and analysis of the resulting structural changes is 
so far minimal. In some cases the actual sequence 
of the proposed stems is unimportant so long as 
base-pairing is maintained and the sequence of 
the loops is not crucial. In fact, these criteria are 
used to define the importance of a stem or pscu- 
doknot. In at least one case (MuLV stop codon 
read-through) , a few bases in the loop region of a 
pseudoknot are crucially important. 
Structures in ribosomal RNA are beginning to 
be delineated clearly, largely from evolutionary 
comparisons of sequence. We are still quite igno- 
rant, however, about the complexity of structures 
in mRNA. At least for the elements involved in the 
decoding code, there is a biological assay for 
function. 
We are even less clear about how these struc- 
tures in mRNA alter the decoding process. The 
simplest view — that mRNA structures merely 
cause a ribosomal pause allowing alternative reac- 
tions — is almost certainly naive. But whether the 
structures bind protein factors, interact with ribo- 
somal proteins, pair with ribosomal RNA, or even 
interact with other parts of mRNA is completely 
untested. Investigation of these possibilities in 
the context of the decoding code will be 
revealing. 
Ribosome Interaction Sequence 
GGA UAG ^ J- GGA UUA- 
■ -STOP ■ \ 
Coding Gap 
GLY LEU 
u 
UCA AAA AAC UUG 
Decoding of the genetic code. Top: Model of a 
ribosome traversing the 50-nucleotide coding 
gap in mRNA of bacteriophage T4 's gene 60, 
illustrating the involvement of upstream pep- 
tide sequences and sequences in the gap. 
Bottom: Model of a ribosome reading a stop 
codon in mRNA of a murine leukemia virus, 
stimulated by a downstream pseudoknot 
structure. 
Research of Norma Wills, Robert Weiss, 
Dianne Dunn, and fohn Atkins in the labora- 
tory of Raymond Gesteland. 
UC AAA AAA CUU C 
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