Translocation of DNA or RNA is a ubiquitous phenomenon.
One intricate translocation process is viral DNA packaging.
During maturation, the lengthy genome of dsDNA viruses
is translocated with remarkable velocity into a limited
space within the procapsid. We have revealed that φ29
DNA packaging is accomplished by a mechanism similar to
driving a bolt with a hex nut, which consists of six DNA-packaging
pRNAs. Four bases in each of the two pRNA loops are involved
in RNA/RNA interactions to form a hexagonal complex that
gears the DNA translocating machine. Without considering
the tertiary interaction, in some cases only two G/C pairs
between the interacting loops could provide certain pRNAs
with activity. When all four bases were paired, at least
one G/C pair was required for DNA packaging. The maximum
number of base pairings between the two loops to allow
pRNA to retain wild-type activity was five, whereas the
minimum number was five for one loop and three for the
other. The findings were supported by phylogenetic analysis
of seven pRNAs from different phages. A 75-base RNA segment,
bases 23–97, was able to form dimer, to interlock
into the hexamer, to compete with full-length pRNA for
procapsid binding, and therefore to inhibit φ29 assembly
in vitro. Our result suggests that segment 23–97
is a self-folded, independent domain involved in procapsid
binding and RNA/RNA interaction in dimer and hexamer formation,
whereas bases 1–22 and 98–120 are involved
in DNA translocation but dispensable for RNA/RNA interaction.
Therefore, this 75-base RNA could be a model for structural
studies in RNA dimerization.