Kunjin virus (KUN) C is a typical flavivirus core protein which is tru
ncated in vivo to a mature form of 105 residues enriched in lysine and
arginine. In order to study the possible association of KUN C with RN
A in vitro, we prepared several recombinant C proteins with specific d
eletions, each fused at the amino-terminus to glutathione-S-transferas
e (GST) and expressed in E. coli. They were reacted with KUN RNA probe
s transcribed in vitro from cDNA representing the 5' untranslated regi
on (5' UTR, 93 of 96 nucleotides), the 3' UTR (624 nucleotides), and t
he 5' UTR plus most of the C coding region (5' core, 440 nucleotides).
Fusion protein C107 (incorporating mature C) bound strongly to all KU
N RNA probes with apparent specificity, being completely resistant to
inhibition by 800 mM NaCl, and to competition by a large excess of tRN
A. In reactions with labelled KUN RNA probes putative binding sites we
re identified in the isolated amino-terminal (32 residues) and carboxy
terminal (26 residues) basic amino acid domains; this binding was stro
ngly competed by unlabelled KUN UTR probes but weakly or not at all by
tRNA. These small domains probably acted co-operatively in binding of
mature C to KUN RNA probes. The KUN RNA-core protein binding reaction
s are similar to those reported with other viral coat or capsid protei
ns and viral RNAs.