Another Realization of Aqueous Computing with Peptide Nucleic Acid
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
A PNA-mediated Whiplash PCR-based Program for In Vitro Protein Evolution
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
A Formal Language Analysis of DNA Hairpin Structures
Fundamenta Informaticae
Autonomous programmable DNA nanorobotic devices using DNAzymes
Theoretical Computer Science
Isothermal reactivating Whiplash PCR for locally programmable molecular computation
Natural Computing: an international journal
Autonomous programmable nanorobotic devices using DNAzymes
DNA13'07 Proceedings of the 13th international conference on DNA computing
Design of a biomolecular device that executes process algebra
Natural Computing: an international journal
Hairpin structures in DNA words
DNA'05 Proceedings of the 11th international conference on DNA Computing
On hairpin-free words and languages
DLT'05 Proceedings of the 9th international conference on Developments in Language Theory
A Formal Language Analysis of DNA Hairpin Structures
Fundamenta Informaticae
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In Whiplash PCR( WPCR), autonomous molecular computation is achieved by the recursive, self-directed polymerase extension of a mixture of DNA hairpins. A barrier confronting efficient implementation, however, is a systematic tendency for encoded molecules towards backhybridization, a simple form of self-inhibition. In order to examine this effect, the length distribution of extended strands over the course of the reaction is examined by modeling the process of recursive extension as a Markov chain. The extension efficiency per polymerase encounter of WPCR is then discussed within the framework of a statistical thermodynamic model. The efficiency predicted by this model is consistent with the premature halting of computation reported in a recent in vitro WPCR implementation. The predicted scaling behavior also indicates that completion times are long enough to render WPCR-based massive parallelism infeasible. A modified architecture, PNA-mediated WPCR (PWPCR) is then proposed in which the formation of backhybridized structures is inhibited by targeted PNA2/DNA triplex formation. The efficiency of PWPCR is discussed, using a modified form of the model developed for WPCR. Application of PWPCR is predicted to result in an increase in computational efficiency sufficient to allow the implementation of autonomous molecular computation on a massive scale.