Biology Reference
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-site RNAs. Shown are the kissing hairpin
structure formed by two SL1 RNAs (A), the monomeric form of SL1 (B) and
the structure of SL2 with its AUA triplet (C) (1N8X, 1ESY).
Fig. 7.
Structure of the HIV-1
Ψ
-site contains the dimer
initiation element, and it has been found that this portion of the
RNA can self-associate to form either “kissing hairpin” structures or
duplexes depending on the solution conditions.
67,68
The duplex struc-
ture consists of an extended A-form helix with two bulged adenines
(Fig. 7) and indicates the capability of SL1 to adopt an alternate
duplex structure rather that the expected stem-loop structure. This
structural feature is likely to be crucial for packaging of the dimeric
genome. The structure of the upper part of SL1 has been shown to
form kissing hairpin dimers via base pairing of the six base palin-
dromes GCGCGC and a distinctive pattern of inter-strand base stack-
ing interactions of nucleotides in the stem-loop junctions (Fig. 7).
A solution structure of the complete stem and bulge segment of SL1
was obtained by substituting the wild-type loop with an extra stable
tetraloop (GAGA) and thus preventing dimer formation.
69
The result-
ing structure shows two helical regions separated by a bulge that
results in an angle of approximately 25
The stem-loop I (SL1) of the HIV-1
Ψ
between the upper and lower
stem. The bulge consists of a G:A mismatch that stacks with the upper
stem and two guanines that stack between the mismatch and the
lower stem (Fig. 7).
°
