In this dissertation, the procedure outlined by the MARTINI papers, were utilized, specifically the methodology to parameterize the bonded interactions between the CG beads and the corresponding AA of single stranded DNA. As explained in references, the authors developed a single set of Martini bonded parameters, determined from the average of all the systems they modeled. Figure (SI) shows examples of the distributions determined for different DNA sequences. More details can be found in the supporting information within References. Simulation Parameters