2012/10/23 by Carsten Svaneborg, Svaneborg, Carsten, Harold Fellermann +3
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Advanced biosensing and bioanalysis techniques #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #Mesoscale and Nanoscale Physics (cond-mat.mes-hall) #Nanopore and Nanochannel Transport Studies #cond-mat.mes-hall #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1210.6156
22 pages, 7 figures. To appear in a special issue of Natural Computing
openalex publication_date 2012/10/23 · arxiv created 2012/12/28 · arxiv updated 2013/01/01 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. We observe a complex transition path from the initial state to the final state of the AND gate. This path is strongly influenced by non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the three distinct distinct DNA transitions that it is based on. We observe a exponential kinetic dependence on the toehold length of the competitive displacement operation, but that the gate operation time is only weakly dependent on both the toehold and adjacent domain length. Our gate displays excellent logical fidelity in three input states, and quite poor fidelity in the fourth input state. This illustrates how non-ideality can have very selective effects on fidelity. Simulations and detailed analysis such as those presented here provide molecular insights into strand displacement computation, that can be also be expected in chemical implementations.