Improving the odds: Influence of starting pools on in vitro selection outcomes.
As with any outcome of an evolutionary process, the success of in vitro selection experiments depends critically on the starting population. In vitro selections isolate functional nucleic acids that fold into specific structures and form unique binding and catalytic sites. The selection outcomes therefore depend on the molecular and structural diversity of the initial pools. In addition, the experiments are strongly influenced by the length of the starting pool. Longer randomized regions support the formation of more complex structures and presumably allow formation of more intricate tertiary interactions, but they also tend to misfold and aggregate, whereas shorter pools are sufficient to yield simpler motifs. Furthermore, introducing a sequence bias that promotes secondary structure formation appears to prejudice the population towards more functional macromolecules. We review the literature on the influence of the starting pools on the predicted and actual outcomes of laboratory evolution experiments.
Department of Chemistry, University of California, Irvine, CA 92697, USA.
Kelsey
K
Pobanz
Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. Electronic address: aluptak@uci.edu.
Andrej
A
Lupták
D019020:Directed Molecular Evolution; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D052156:SELEX Aptamer Technique / Q000379:methods*
D011506:Proteins; D012313:RNA
Aptamer; Genotype; In vitro selection; Molecular evolution; Phenotype; Ribozyme; SELEX