Accepted_test

In our study we investigate the structure and dynamics of DNA-DNA kissing loop (KL) complexes, with the aim of creating molecular switches with distinct properties for controlling gene expression. The motivation stems from the need for precise and effective methods to regulate gene expression in the context of rapid advancements in genetic engineering. The study highlights the potential utility of DNA-based tools, given the chemical stability of DNA polymers compared to RNA analogues. The authors utilize both theoretical and experimental methods to delve into the structure and kinetics of DNA-DNA KL complexes.

The methods employed include molecular modeling using a coarse-grained oxDNA model, NUPACK software for verification of secondary structures, and experimental techniques such as electrophoretic mobility shift assays, UV-Vis, and fluorescent spectroscopy. The study explores the influence of loop size and nucleotide distribution on the structural and kinetic properties of the forming complex, leading to the compilation of a library of sequences capable of assembling into pseudoknot complexes with specified geometry.

The results demonstrate control over the temperature boundary between linear duplex (LD) and KL, as well as the influence of nucleotide distribution and loop size on the structural and kinetic properties of the forming complex. The study suggests potential modifications to promote a more open and less stable complex for improved functionality, with further exploration and refinement holding promise for diverse applications.