Analysis, Prediction, and Design of Viral RNA Secondary Structures

Tuesday, October 30, 2007 - 2:30pm - 3:00pm
EE/CS 3-180
Christine Heitsch (Georgia Institute of Technology)
Understanding how biological sequences encode structural and functional
information is a fundamental scientific challenge. For RNA viral genomes,
the information encoded in the sequence extends well-beyond their protein
coding role to the role of intra-sequence base pairing in viral packaging,
replication, and gene expression. Working with the Pariacoto virus as a
model sequence, we investigate the compatibility of predicted base pairings
with the dodecahedral cage known from crystallographic studies.
To build a putative secondary structure, we first analyze different
possible configurations using a combinatorial model of RNA folding.
We give results on the trade-offs among types of loop structures,
the asymptotic degree of branching in typical configurations, and
the characteristics of stems in well-determined substructures.
These mathematical results yield insights into the interaction of
local and global constraints in RNA secondary structures, and suggest
new directions in understanding the folding of RNA viral genomes.