Top-down coarse-grained model for single stranded nucleic acids.

Abstract

Though there exist several coarse-grained (CG) models for nucleic acids describing a range of resolutions, these generally give a poor reproduction of single-stranded nucleic acid properties, particularly RNA, and do not allow sequence specificity to be easily incorporated. Models that do tend to be higher in resolution and more computationally expensive to use. Since recent work has revealed the importance of both RNA and DNA in the formation of complex coacervates, as well as the role of proteins in forming a scaffold for DNA condensation in chromatin and spermatogenesis, we therefore adapt our existing 3-site model of nucleic acids to include sequence-specificity.