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Analysis of Shuffled Gene Libraries John M. Joern, Peter Meinhold and Frances H. Arnold*
 

Summary: Analysis of Shuffled Gene Libraries
John M. Joern, Peter Meinhold and Frances H. Arnold*
Division of Chemistry and
Chemical Engineering 210-41
California Institute of
Technology, Pasadena
CA 91125, USA
In vitro recombination of homologous genes (family shuf»ing) has been
proposed as an effective search strategy for laboratory evolution of genes
and proteins. Few data are available, however, on the composition of
shuf»ed gene libraries, from which one could assess the ef«ciency of
recombination and optimize protocols. Here, probe hybridization is used
in a macroarray format to analyze chimeric DNA libraries created by
DNA shuf»ing. Characterization of hundreds of shuf»ed genes encoding
dioxygenases has elucidated important biases in the shuf»ing reaction.
As expected, crossovers are favored in regions of high sequence identity.
A sequence-based model of homologous recombination that captures this
observed bias was formulated using the experimental results. The chi-
meric genes were found to show biases in the incorporation of sequences
from certain parents, even before selection. Statistically different patterns

  

Source: Arnold, Frances H. - Division of Chemistry and Chemical Engineering, California Institute of Technology

 

Collections: Chemistry; Biology and Medicine