RNA folding simulation

RNA Folding
by Giff Ransom
Scientific Background
• RNA molecules are single
stranded copies of a segment
of a gene in the DNA.
• Though a DNA strand is locked
in a double helix with its
partner, making their three
dimensional structure
predictable and stable, RNA
molecules have no such
complementary strand.
• Rather than staying stretched
out in a line, RNA molecules
tend to fold back on
themselves, and the threedimensional shape formed by
a given strand is important for
studying its interaction with
other molecules.
Scientific Background
As an RNA molecule folds, its
bases bond with other
complementary bases in the
strand, similar to DNA. However,
since the sequence isn't
symmetrical, it will not match
perfectly and form a double helix.
Exactly which bases line up with
their pair determines the most
stable structure of the RNA
Most biologists use twodimensional simulations when
they need to find the ideal
configuration for a given RNA
molecule. However, these do not
provide an accurate
representation of the threedimensional dynamics and
emerging structure.
3D Simulation
molecular dynamic
simulations give a much
better glimpse of the RNA
molecule's structure, as
well as a more accurate
prediction of the actual
Ideally, each atom of the
molecule would be
modeled, but this limits the
size and scope of the
Kurt Grunberger, 2002
The molecular structure can be simplified
while still fairly accurately predicting
the RNA tertiary structure
My Model
• I intend to create a 3D
RNA folding simulation
accurate enough to
reproduce experimental
configurations for small
RNA molecules.
• Rather than implementing
an atomic-level molecular
dynamics engine, my
model will operate on the
higher level of bases and
sugars. I aim to achieve
computational simplicity
while retaining the basic
forces and angles
between key elements.
So Far…
• Created a basic
simulation using the DNA
double helix structure as
the resting point for my
spring constants
• Implemented bond length
and bond angle springs
• Verlet integration
• Electrostatic attraction
and repulsion in bases
• Very basic rigid body (i.e.
angular forces) dynamics
on bases
Yet to Do…
• It just doesn’t look
right yet – needs a
good bit of
• Use constraints
rather than springs
on the bondlengths
• Implement
torsional potential if