Engineered Oligonucleotides for G-Quadruplex Study

Synthetic oligonucleotides were purchased from Sigma-Aldrich and diluted with ultrapure water to a final concentration of 100 μM (Table 1). The PUMA sequence was derived from the BBC3 (PUMA) P53 target gene; oligonucleotide sequences with different G4 formation potential were designed to decrease the chance of intramolecular G4 formation by mutating the KSHV G-quadruplex sequence [25 (link)]. KSHV-Mut2.0 and KSHV-Mut1.5 sequences were designed by the G4 Killer program [27 (link)] to change G4 Hunter score below 2.0 and 1.5, respectively; the sequences of KSHV-1NO, KSHV-2NO and KSHV-3NO were designed by sequential substitution of G bases in guanine repeats. The propensities of G4 formation were predicted for these sequences by the G4 Hunter program and measured as G4 Hunter scores (Table 1) [28 (link)].