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Author(s)

     X.Luo , M.McKeague, S.Pitre, M.Dumontier, J.Green, A.Golshani, M.C.DeRosa, F.Dehne

Title

     Computational Approaches Towards the Design of Pools for the In Vitro Selection of Complex Aptamers

Publication Name

     RNA

Publication Type

     Journal
Publisher
     
Place
     
Editor(s)
     
Number
      16
School
     
Volume
      12
Chapter
     
Pages
      2252-2262
Other Publication Information
     
Publication Year
     2010
Abstract
     It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structural complexity and can be used to increase the overall structural diversity of initial pools for in vitro selection experiments. Random Filtering selectively increases the number of five-way junctions in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure distribution, whether uniform or otherwise. We show that using our computationally designed DNA pool greatly improves access to highly complex sequence structures for SELEX experiments (without losing our ability to select for common one-way and two-way junction sequences).
Keywords
     in vitro selection, random pool, aptamer pool design, RNA/DNA secondary structure, genetic algorithm, ATP aptamer
Website
     http://rnajournal.cshlp.org/search?submit=yes&pubdate_year=&volume=&firstpage=&doi=&author1=&author2=&title=Computational+Approaches+Towards+the+Design+of+Pools+for+the+In+Vitro+Selection+of+Complex+Aptamers&andorexacttitle=or&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=&fyear=&tmonth=&tyear=&format=standard&hits=10&sortspec=relevance&submit=yes&submit=Submit
Paper Status
     Published
DOI / Publication ID
     10.1261/rna.2102210



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