New approaches for
determining functional siRNA
Liyang Diao
Dr. Stanley Dunn, advisor
Protein Production
• Production of proteins starts with DNA
• DNA is in the nucleus
• Requires mRNA to finish protein production
mRNA: messenger RNA
RNAi: RNA interference
• Suppresses gene expression
• Affects mRNA
DNA
mRNA
http://nobelprize.org/educational_games/medicine/dna/index.html
protein
More on RNAi
siRNA: short-interfering RNA
• Typically 20-25 nucleotides long
• Double-stranded
• Participates in RNAi by degrading
mRNA
Potential for effective gene therapy
Issues
• Some genes are more effectively
suppressed than others
• Mechanism is poorly understood
Diagram: http://www.ambion.com/techlib/append/RNAi_mechanism.html
Question
How do we know which siRNA are functional?
Some ideal properties:
GC content between 30-55%
 Low level of secondary structure
 Differential between thermodynamic stability
of 5’ and 3’ ends: A/U content
 Specific positional nucleotide preferences
 Avoid long GC stretches

http://bioinf.man.ac.uk/resources/phase/manual/RNAMolecule.png
Previous Model
Pancoska’s Eulerian graph model
• Represent a string of siRNA by a directed digraph first
• Construct a weighted undirected Eulerian graph
A
T
G
C
• Compare graphs for functional and non functional siRNA
• For these two sets of siRNA, compute graph properties that
reflect sequence structure.
Issues with Pancoska’s Algorithm
A
T
G
C
ATTCGTGGACG
GATTCGTGGAC
CGATTCGTGGA
…
• Uniqueness
• Complex pattern recognition
Other Ideas
• Number of nucleotide mutations
• Levenshtein distance:
Measures the minimum number of
substitutions/insertions required to go
from one string to another.
Current/Future Progress
• 420 total number of possible siRNA
strands of length 20.
• How many are potentially functional?
• Combinatorics!
Math
• Let H(n,i,j) be the number of potential positions of A/U, G/C pairs.
•
•
•
•
Thus, the total number of potential strings is 220 * H(n,i,j).
n the total number of G or C nucleotides
i the total number of A or U nucleotides at 5’ end
j the total number of A or U nucleotides at 3’ end
Quantity desired: