Fig. 2: Computational investigations reveal contact modes and frequency of interactions in peptide/nucleic acid coacervates.
a Representative atomistic force-field simulation snapshot of the R4/RNA8 mixture, showing a cluster of RNA and peptide, and unbound peptide in excess. Inset shows the interaction modes, e.g., hydrogen bonding, ionic interactions, and cation-π/π-π stacking. The simulations were performed with OpenMM 8.1.2, leveraging the CUDA platform in mixed precision mode, using the Amber14SB force field for peptides, OL3 parameters for RNA, and bsc1 for DNA. See Supplementary Information for more details. b Comparison between the number of DNA and RNA interactions with arginine peptides (per frame, per nucleotide), separated into three categories: hydrogen bonding, ionic interactions and stacking. c Simplified rendering of R4/DNA8 (blue) and R4/RNA8 (purple) clusters, showing the helical, structured conformation acquired by DNA strands and the more disordered folding acquired by RNA strands, which leaves ribonucleotides exposed to interact with peptides. d Number of peptide/oligonucleotide contacts (all modes of interaction), which represents the total number of intermolecular contacts that one molecule of RNA8 or DNA8 forms with R3 or R4. e Excess peptide remaining in the simulation box at equilibrium for RNA8 or DNA8 coacervates with R3 or R4. R = Arginine, DNA8 = 8-deoxyribonucleotide-long mixed sequence ((ACTG)2), RNA8 = 8-ribonucleotide-long mixed-sequence oligonucleotide ((ACUG)2). n = 5 for data in (b), (d) and (e); mean and SD values are provided. All plotted values can be found in Supplementary Tables S7–S10. Source data are provided as a Source Data file.
