Our enhanced-sampling simulations indicated that end-to-end association of DNA fragments is associated with a very large free energy well. To ensure that our predictions were indeed correct, we performed a brute-force simulation of 458 DNA fragments in a cubic volume 23.8 Å on each side. The DNA fragments, which were not in contact initially, aggregated into chains containing up to 11 DNA fragments in length during the 260 ns simulation. Initially, the unit cell containing all the DNA fragments is depicted. Subsequently, the assembly of the longest 10 aggregates is animated. Since aggregates can span across the periodic boundary of the system, neighboring periodic images of the unit cell are shown.
The simulation confirmed that the free energy associated with end-to-end association of DNA fragments is very large.