Eukaryotic translation initiation factor 4A (eIF4A)
has been proposed to use the energy of ATP hydrolysis to
remove RNA structure in the 5′ untranslated region
(UTR) of mRNAs, helping the 43S ribosomal complex bind
to an mRNA and scan to find the 5′-most AUG initiator
codon. We have examined the effect of changing the atomic
composition and length of single-stranded oligonucleotides
on binding to eIF4A and on stimulation of its ATPase activity
once bound. Substitution of 2′-OH groups with 2′-H
or 2′-OCH3 groups reduces ATPase stimulation
at least 100-fold, to background levels, without significantly
affecting oligonucleotide affinity. These effects suggest
that 2′-OH groups participate in an eIF4A conformational
change that occurs subsequent to oligonucleotide binding
and is required for ATPase stimulation. Replacing nonbridging
oxygen atoms in phosphodiester linkages with sulfur atoms
to make phosphorothioate linkages has no significant effect
on stimulation, while substantially increasing affinity.
Extending the length of an RNA oligonucleotide from 4 to
∼15 nt gradually increases oligonucleotide affinity
and ATPase stimulation. Consistent with this observation,
the increase in affinity and stimulation provided by phosphorothioate
linkages and 2′-OH groups is proportional to the
number of these groups present within larger oligonucleotides.
Further, changing the position of blocks of phosphorothioate
linkages or 2′-OH groups within a larger oligonucleotide
does not affect affinity and has only a small effect on
stimulation. These observations suggest that numerous interactions
between the oligonucleotide and eIF4A contribute individually
to binding and ATPase stimulation. Nevertheless, significant
stimulation is observed with as few as four RNA residues.
These properties may allow eIF4A to operate within regions
of 5′ UTRs containing only short stretches of exposed
single-stranded RNA. As stimulation increases when longer
stretches of single-stranded RNA are available, it is possible
that the accessibility of single-stranded RNA in a 5′
UTR influences translation efficiency.