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New approaches for determining functional siRNA

New approaches for determining functional siRNA. Liyang Diao Dr. Stanley Dunn, advisor. mRNA. protein. DNA. 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

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New approaches for determining functional siRNA

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  1. New approaches for determining functional siRNA Liyang Diao Dr. Stanley Dunn, advisor

  2. mRNA protein DNA 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 http://nobelprize.org/educational_games/medicine/dna/index.html

  3. 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

  4. 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

  5. T A G C Previous Model Pancoska’s Eulerian graph model • Represent a string of siRNA by a directed digraph first • Construct a weighted undirected Eulerian graph • Compare graphs for functional and non functional siRNA • For these two sets of siRNA, compute graph properties that reflect sequence structure.

  6. T A G C Issues with Pancoska’s Algorithm • Uniqueness • Complex pattern recognition Other Ideas • Number of nucleotide mutations • Levenshtein distance: A T T C G T G G A C G G A T T C G T G G A C C G A T T C G T G G A … Measures the minimum number of substitutions/insertions required to go from one string to another.

  7. Current/Future Progress • 420 total number of possible siRNA strands of length 20. • How many are potentially functional? • Combinatorics!

  8. 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:

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