Impact of Flanking Nucleotides on G-quadruplex Topology

Nucleic acid sequences rich in guanine (G) bases tend to form non-canonical structures called G-quadruplex (G4). G4s hold promise in the treatment of many diseases, including cancer, so understanding the structure and the factors affecting it will shed light on future studies. With this motivation, the effect of flanking bases at the ends of the G4-forming DNA sequences from human telomere was investigated. The results indicate that the flanking sequences did not show significant change upon insertion of flanking bases however the effect dramatically increased with each Adenine base insertion. In addition, no considerable change was observed upon insertion of single thymine (T). According to the MD simulation analysis, the deletion of the flanking T base increased the kinetic energy of the system while decreased the potential energy of the system, however, overall structure did not show significant change.