Home Tutorials In Vitro Selection Use of RNA Pool Designer

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.

Mixing Matrix
Starting Sequence
RNA Motif Distributions
Measures of Sequence/Structure Similarity
Algorithm for Structured Pool Designs