Fig. 4
Biophysical analyses of KSHV-GQ and HCMV-GQ. (a) KSHV and HCMV PQS oligonucleotide sequences and their positions with respect to respective precursor miRNAs. The wild-type (Wt) oligonucleotide possesses the intact G-quadruplex motif while the mutant (Mut) oligonucleotide contains G-quadruplex disrupting mutations. (b) The CD spectra shows formation of parallel G-quadruplex structures for oligonucleotides Wt-KSHV-GQ and Wt-HCMV-GQ. (c) Native polyacrylamide gel electrophoresis indicates intramolecular G-quadruplex structure formation as depicted by higher mobility of both the wild-type oligonucleotides (Wt-KSHV-GQ and Wt-HCMV-GQ) compared to that of the mutant oligonucleotides (Mut-KSHV-GQ and Mut-HCMV-GQ) and C (length-matched controls: 27mer and 18mer sequences that do not form DNA secondary structures). On the other hand, denaturing polyacrylamide gel electrophoresis shows comparable migration rate for the wild-type, mutant and the length-matched controls in presence of 7 M urea (denaturant). (d) 1D 1H NMR spectra of Wt-KSHV-GQ and Wt-HCMV-GQ oligonucleotide show imino proton peaks in the range of 10.5–12 ppm; these peaks were not observed in case of mutants