Mtl. Beckman et K. Kirkegaard, SITE SIZE OF COOPERATIVE SINGLE-STRANDED RNA-BINDING BY POLIOVIRUS RNA-DEPENDENT RNA-POLYMERASE, The Journal of biological chemistry, 273(12), 1998, pp. 6724-6730
The poliovirus RNA-dependent RNA polymerase binds cooperatively to sin
gle stranded RNA. We have determined the minimal RNA-binding site size
of the poliovirus polymerase using binding titration with oligonucleo
tides of increasing length. A dramatic increase in affinity was observ
ed when the length of the oligo(U) increased from 8 to 10 nucleotides
(nt), arguing that the minimal size of RNA for polymerase binding is 1
0 nt. Another increase in affinity seen as the oligo(U) reached 24 nt
suggests that a 24-nucleotide RNA can be occupied by two polymerase mo
lecules. Direct binding of wildtype polymerase to oligo(U)(12) and oli
go(U)(24) RNAs showed differences in affinity and cooperativity consis
tent with this model. The increase in binding affinity seen for oligo(
U)(10) suggests either that the RNA-binding determinants are widely sp
aced on the polymerase structure or that a substantial conformational
change in the polymerase occurs upon the filling of its RNA binding si
te.