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

Anal Sci. 2024 Apr 12. doi: 10.1007/s44211-024-00551-5. Online ahead of print.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.PMID:38609708 | DOI:10.1007/s44211-024-00551-5
Source: Analytical Sciences : the international journal of the Japan Society for Analytical Chemistry - Category: Chemistry Authors: Source Type: research