Analysis and Re-engineering of Whiplash PCR: Simulations of Fidelity and Efficiency, and an Improved Architecture Based on Targeted Strand Displacement (小特集 DNAコンピューティングの応用とシミュレーション)

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概要

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• In Whiplash PCR (WPCR), autonomous biomolecular computation is implemented in vitro by the recursive, self-directed polymerase extension of a mixture of DNA hairpins. In this work, the statistical thermodynamic formalism for modeling and simulation of two related processes, mis-hybridization and back-hybridization, which are known to compromise the computational fidelity and efficiency of both WPCR and PNA-mediated WPCR (PWPCR) is reviewed and expanded. Illustrative simulations of the predicted impact of each effect are provided, and their relative effects on overall WPCR feasibility are compared, along with a discussion of existing strategies to improve efficiency. A novel re-engineered architecture, Displacement WPCR (DWPCR) is then proposed, which eliminates back-hybridization, via targeted protection by primer annealing, polymerase extension, and DNA strand displacement.

• 日本シミュレーション学会の論文
• 2005-12-15

著者

• Rose John

  Department Of Computer Science And Undergraduate Program In Bioinformatics And Systems Biology The U

関連論文

• Analysis and Re-engineering of Whiplash PCR: Simulations of Fidelity and Efficiency, and an Improved Architecture Based on Targeted Strand Displacement (小特集 DNAコンピューティングの応用とシミュレーション)
• Enhanced Condensation Heat Transfer

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