Effects of Polyethylene Glycol on the Hydrogen Bonds and Stacking Interactions of DNA/DNA, DNA/RNA, and RNA/RNA Calculated by a Mesoscopic Model

The addition of polyethylene glycol (PEG) to the buffer of oligonucleotide melting experiments is a way to simulate the cellular crowding. PEG reduces the water activity, but how this affects the hydrogen bonding and base stacking is mostly unknown. Here, we use published melting temperature data for DNA/DNA (DD), DNA/RNA (DR), and RNA/RNA (RR) to calculate how the hydrogen bonds and stacking interactions change upon the addition of PEG. For this, we used a mesoscopic model that describes the helical stability in terms of the intramolecular interactions. For the hydrogen bonds, we find that PEG has almost no effect on DD and a moderate effect on CG in DR. However, for RR, hydrogen bonds become much stronger for CG but much weaker for AU. Changes in stacking interactions were also found to be strongest for RR.