Nonequilibrium replication and selection from reactive nucleotides using hyperexponential RNA polymerization in a thermal trap

• Applicants: Professor Dr. Dieter Braun; Professor Dr. Ulrich Gerland
• Subject Area: Statistical Physics, Nonlinear Dynamics, Complex Systems, Soft and Fluid Matter, Biological Physics ; Biophysics
• Term: from 2014 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 265469975

• Final Report Year: 2024

Final Report Abstract

This project pursued three objectives, (i) experimentally establishing enhanced polymerization within a thermal trap, (ii) experimentally creating a codon-replicator based on tRNA-like molecules, and (iii) theoretically describing and exploring the interplay between the nonequilibrium physics of the thermal trap and the molecular binding and reaction processes within it. Despite technical challenges and resulting delays, all three objectives were eventually reached. For (i), nucleotide polymerization within a thermal trap was implemented using aminoimidazole-activated DNA nucleotides and 2′,3′-cyclic RNA nucleotides as building blocks. This closed pore system displayed an up-concentration for single nucleotides of more than thousand-fold at the bottom of the pore compared to the top after 24 hours. We detected enhanced polymerization for both of the used chemistries. Suprisingly, the copolymerization of 2′,3′-cGMP and 2′,3′-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. For (ii), we used a pool of oligonucleotides that was adapted with minor mutations from tRNA. We showed that this pool spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The metastable hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. For (iii), we first considered the coupling between physical and chemical non-equilibria as a driving force, which could potentially kickstart primitive evolutionary processes. We explored the question of the coupling efficiency within a theoretical model inspired by the flow-through thermophoretic trap of the Braun lab. Our analysis showed that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. We believe that this result will be useful for a better understanding of the conditions, for which nonequilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting. We then started to model the kinetic self-assembly of RNA strands via template-directed ligation. Within this model, we found a surprisingly rich behavior that depends on the interplay between the different kinetic timescales in the system.

Publications

• Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length. Nature Chemistry, 7(3), 203-208.
  Kreysing, Moritz; Keil, Lorenz; Lanzmich, Simon & Braun, Dieter
  
• The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled. Physical Chemistry Chemical Physics, 18(30), 20135-20143.
  Göppel, Tobias; Palyulin, Vladimir V. & Gerland, Ulrich
  
• Toward living nanomachines. Oxford Scholarship Online.
  Mast, Christof; Möller, Friederike; Kreysing, Moritz; Schink, Severin; Obermayer, Benedikt; Gerland, Ulrich & Braun, Dieter
  
• tRNA sequences can assemble into a replicator. eLife, 10.
  Kühnlein, Alexandra; Lanzmich, Simon A & Braun, Dieter
  
• A heated rock crack captures and polymerizes primordial DNA and RNA. Physical Chemistry Chemical Physics, 25(4), 3375-3386.
  Dirscherl, Christina F.; Ianeselli, Alan; Tetiker, Damla; Matreux, Thomas; Queener, Robbin M.; Mast, Christof B. & Braun, Dieter