Proc. Natl. Acad. Sci. USA
Vol. 96, pp. 3584–3589, March 1999
Biochemistry
Engineering precision RNA molecular switches
GARRETT A. SOUKUP AND RONALD R. BREAKER*
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
Edited by Larry Gold, NeXstar Pharmaceuticals, Inc., Boulder, CO, and approved January 15, 1999 (received for review September 29, 1998)
ABSTRACT
Ligand-specific molecular switches com-
posed of RNA were created by coupling preexisting catalytic
and receptor domains via structural bridges. Binding of ligand
to the receptor triggers a conformational change within the
bridge, and this structural reorganization dictates the activity
of the adjoining ribozyme. The modular nature of these
tripartite constructs makes possible the rapid construction of
precision RNA molecular switches that trigger only in the
presence of their corresponding ligand. By using similar
enzyme engineering strategies, new RNA switches can be
made to operate as designer molecular sensors or as a new
class of genetic control elements.
Mastery of the molecular forces that dictate biopolymer
folding and function would allow molecular engineers to
participate in the design of enzymes—a task that to date has
been managed largely by the random processes of evolution.
The reward for acquiring this capability is substantial, consid-
ering that many applications in medicine, industry, and bio-
technology demand high-speed enzymes with precisely tai-
lored catalytic functions. ‘‘Modular rational design’’ has
proven to be an effective means for conferring additional
chemical and kinetic complexity on existing protein (1–4) and
RNA enzymes (5–9). This engineering strategy takes advan-
tage of the modular nature of many protein (10) and RNA
subdomains (11–13), which can be judiciously integrated to
form new multifunctional constructs. The recent discoveries of
new catalytic RNA motifs (14, 15) and new ligand-binding
motifs (16, 17) have considerably expanded the opportunities
for ribozyme engineer