2026-09-30T03:37:33Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:23856 2026-09-23T22:27:22Z ddc:004 open_access

Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics Evans, Constantine G. Cervera Roldan, Angel Rogers, Trent Woods, Damien Self-assembly kinetic model kinetic simulation thermodynamic prediction A fundamental problem in crystallisation, and in molecular tile-based self-assembly in particular, is how to simultaneously control its two main constituent processes: seeded growth and spontaneous nucleation. Often, we desire out-of-equilibrium growth without spontaneous nucleation, which can be achieved through careful calibration of temperature, concentration and experimental time-scale a laborious and overly-sensitive approach. Another technique is to find alternative nucleation-resistant tile designs [Minev et al, 2001]. Rogers, Evans and Woods [In prep] propose blockers: short DNA strands designed to dynamically block DNA tile sides, altering self-assembly dynamics. Experiments showed independent and tunable control on nucleation and growth rates. Here, we provide a theoretical explanation for these surprising results. We formally define the kBlock model where blockers bind to tiles at thermodynamic equilibrium in solution and stochastic kinetics allow self-assembly of a tiled structure. In an intentionally simplified mathematical setting we show that blockers permit reasonable seeded growth rates, akin to a non-blocked tile system at lower tile concentration, crucially giving nucleation rates that are exponentially suppressed. We then implement the kBlock model in a stochastic simulator, with results showing remarkable alignment with oversimplified theory. We provide evidence of blocker-induced tile buffering, where a large reservoir of blocked tiles slowly feeds a small unblocked tile subpopulation which acts like a regular, non-blocked, low tile concentration system, yet is capable of long-term buffered assembly. Finally, and perhaps most satisfyingly, theory and simulations align remarkably well with DNA self-assembly experiments over a wide range of concentrations and temperatures, matching the size of growth temperature windows to within 12%. Blockers are a straightforward solution to the challenging problem of simultaneously and independently controlling growth and nucleation, using a motif compatible with many DNA tile systems. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Constantine G. Evans and Angel Cervera Roldan and Trent Rogers and Damien Woods 2025 Is Part Of LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.31.7 urn:nbn:de:0030-drops-238564 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.7 eng https://creativecommons.org/licenses/by/4.0/legalcode