Modeling of Pool Synthesis
To design RNA pools to target novel structures, we propose pools with both random and biased sequence mutations around a
specific sequence. For this purpose, we introduce the mixing matrix whose elements specify mixing (or “contamination” or
“doped”) in the four phosphoramidite (A, C, G, and U) vials; applying mixing matrices to starting sequences lead to designed
sequence pools. This representation of pool generation or synthesis using mixing matrices enables computational analysis of
pool sequences and structural diversity. The following figure shows pool design and synthesis via mixing matrix and analysis
of sequence/structure space.
Our goal is to define via computational analysis an optimal set of mixing matrices, starting sequences, and associated
weights for a given structural distribution in the pool.