Biology Reference
In-Depth Information
Fig. 6.
Solution structure of the HIV-1 nucleocapsid domain zinc knuckles
(1AAF).
that this internal flexibility is important for binding of the NC protein
to its nucleic acid targets, also known as adaptive binding.
The HIV-1 RNA Packaging Signal
Genome recognition and packaging in retroviruses is mediated by
interactions between the NC protein and a long stretch of nucleotides
in the unspliced viral genome (about 120 nucleotides in the case of
HIV-1). This sequence has become known as the
-site and is gener-
ally located between the 5´-long terminal repeat and the gag initiation
codon.
46,55,56
Ψ
-sites overlap with the RNA
dimer initiation elements that ensure packaging of two copies of
the unspliced genomic RNA (see below).
57
In all known cases the
Ψ
The secondary structures
of the
-site RNAs of HIV-1 and MMLV (Fig. 1) have been studied
extensively by molecular biology and computational approaches.
58-65
The motifs contain several stem-loop structures, four in the case of
HIV-1 (termed SL1 to SL4) and three for MMLV, connected by short,
single-stranded linkers of 4-15 nucleotides. Several high-resolution
structures have been obtained for RNA constructs based on these
secondary structures.
66
Ψ
