DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.biomac.3c01435DOI Listing

Publication Analysis

Top Keywords

phase behavior
8
liquid crystal
8
crystal phases
8
simulating lyotropic
4
lyotropic phase
4
behavior partially
4
partially self-complementary
4
self-complementary dna
4
dna tetramer
4
tetramer dna
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!