Theoretical studies on binding modes of copper-based nucleases with DNA

One-Pot Aqueous Synthesis of Nucleoside-Templated Fluorescent Copper Nanoclusters and Their Application for Discrimination of Nucleosides

“…The fluorescence quantum yield (QY) of A-CuNCs, C-CuNCs, and G-CuNCs at 300 nm excitation was respectively measured to be 1.34%, 0.44%, and 0.27% by using the comparative approach with quinine sulfate in 0.1 mol L –1 H 2 SO 4 aqueous solution (QY = 0.546) . Therefore, the order of the fluorescence QY of CuNCs templated by the four nucleosides was A > C > G ≫ T. On the basis of earlier literature, ,,, we suppose that this result can be caused by the affinity of nucleoside for Cu 2+ and the donating capability of nucleoside, as well as the nucleoside quenching efficiency. Moreover, it was worth noting that thymidine as a template failed to generate fluorescent CuNCs in this work.…”

Recent Developments and Applications of the MMPBSA Method

“…For DNA-protein interactions, there were mechanistic studies involving proteins such as HU, one of the major nucleoid-associated proteins for stabilizing DNA bending (Kim et al, 2014 ), highly conserved chromatin protein Cren7 for cellular processes such as transcription, replication, and repair (Chen L. et al, 2015 ), MutS, which recognizes mismatched DNA in DNA repair using ATP (Ishida and Matsumoto, 2016 ), copper nucleases for predicting electrostatic interactions with B-DNA (Liu C. M. et al, 2016 ), and metallopeptides binding to the Drew-Dickerson dodecamer (Galindo-Murillo and Cheatham, 2014 ). For RNA-protein interactions, the binding of toll-like receptor 3 and 22 was studied in relation to fish viral diseases (Sahoo et al, 2015 ), and the RNA-recognition motif of RNA-binding protein was analyzed for anti-cancer actitivies (Chang et al, 2016 ).…”