Analysis of Shuffled Libraries by Oligonucleotide Probe Hybridization

  • Peter Meinhold
  • John M. Joern
  • Jonathan J. Silberg
Part of the Methods in Molecular Biology™ book series (MIMB, volume 231)


In vitro recombination is often used to generate genetic diversity for directed evolution. Recombination techniques that rely on fragment hybridization yield libraries with preferred crossover positions and, in some cases, a bias toward incorporation of one parent over the others. This limits the diversity, and thus the utility of the library. These biases vary depending on the technique used for recombination, the distribution of sequence similarities within the parental genes, and the efficiency by which the different parental genes are PCR amplified. To assess the diversity generated in a library of chimeras, sequences of a large number of chimeras are required. While DNA sequencing can yield this information, sequencing these genes is prohibitively expensive, especially when the genes being recombined are large. Oligonucleotide probe hybridization, in contrast, offers a cost-effective approach for obtaining information about library biases that allows for optimization of shuffling procedures. When coupled with functional information, this technique can provide information about the relationship between sequence and function (1,2).


Sodium Dodecyl Sulfate Probe Site Identical Region Hybridization Oven Terminal Transferase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Humana Press Inc., Totowa, NJ 2003

Authors and Affiliations

  • Peter Meinhold
    • 1
  • John M. Joern
    • 1
  • Jonathan J. Silberg
    • 1
  1. 1.Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadena

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