RNA-RNA Interaction Algorithms for
siRNA Design
A talk by
Saad Mneimneh
Assistant Professor
Department of Computer Science and Engineering
Southern Methodist University
Wednesday 09/22/2004
3:45 – 4:45 PM
SIC Building, Room 307
Abstract: A small interfering RNA (siRNA) can be used to silence a given gene by targeting its mRNA. The siRNA
binds to the RNA and destroys it. Although RNAs are single-stranded molecules, they usually fold. The problem of
RNA folding has been studied extensively in the literature and many efficient algorithms for determining the optimal
(minimum energy) folding of an RNA molecule have been developed. These algorithms can be used to identify
single-stranded regions (unfolded regions) of a folded RNA which are believed to be hot spots for potential siRNA
bindings and, therefore, could help in the design of effective siRNAs. However, there is no clear consensus as to
which happens first: RNA folding or siRNA binding. This motivates the RNA-RNA interaction problem where
folding and binding occur simultaneously. I will briefly show that the general problem of optimally folding two
interacting RNAs becomes NP-hard. I will also describe some preliminary approximation algorithms for the
problem. Better approximation algorithms need to be developed, however. These algorithms will be applied to fold a
target RNA with different siRNAs. The energy of the obtained structures will be used as a measure of effectiveness
of the siRNA in silencing the target RNA. The goal is to ultimately develop a better methodology by which siRNAs
are computationally designed for particular target RNAs.
Biography: Saad Mneimneh is an assistant professor in the department of computer science and engineering at
SMU. He receives his Ph.D. degree from the Massachusetts Institute of Technology in 2002. His research interests
include switching and routing algorithms, graph problems, and biology.
Everyone invited… Cookies will attend too!