Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome

Abstract

AbstractA biotinyl cyclic naphthalene diimide (biotinyl cNDI) (1), in which biotin is introduced on the cyclic linker chain of cNDI with high G-quadruplex (G4) specificity, was synthesized. 1 was used for binding analysis to G4 DNAs such as c-myc, c-kit, CEGF, or TA-core. The results showed that 1 bind to G4 DNAs with high affinity and, especially, two molecules of 1 bind to c-myc DNA from top and bottom of G4 site at K = 3.9 × 10−6 M−1 without changing the G4 structure. As a pulldown assay, 1 and streptavidin magnetic beads could be used to recover a c-myc DNA or 120-mer DNA fragment having single c-myc sequence. The qPCR results for the 120-meric DNAs showed that more than 50% of genomic DNA fragments could be recovered by this pulldown assay. The results obtained here might allow the recovery of G4-containing DNA fragments from genomic DNA to analyze the true G4 present in the genome. Graphic abstract