A PCR-based Protocol for In Vitro Selection of Non-crosshybridizing Oligonucleotides

Authors:
Russell Deaton;Junghuei Chen;Hong Bi;Max Garzon;Harvey Rubin;David Harlan Wood
Affiliations:
-;-;-;-;-;-
Venue:
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Year:
2002

Citing 1
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Abstract

DNA computing often requires oligonucleotides that do not produce erroneous cross-hybridizations. By using in vitro evolution, huge libraries of non-crosshybridizing oligonucleotides might be evolved in the test tube. As a first step, a fitness function that corresponds to noncrosshybridization has to be implemented in an experimental protocol. Therefore, a modified version of PCR that selects non-crosshybridizing oligonucleotides was designed and tested. Experiments confirmed that the PCR-based protocol did amplify maximally mismatched oligonucleotides selectively over those that were more closely matched. In addition, a reaction temperature window was identified in which discrimination between matched and mismatched might be obtained. These results are a first step toward practical manufacture of very large libraries of non-crosshybridizing oligonucleotides in the test tube.