Preferential adsorption of a 'kinked' DNA to a neutral curved surface: Comparisons to and implications for nonspecific DNA-protein interactions

We have examined the adsorption of different DNA sequences to mercaptoethanol-capped CdS quantum dots, ~40 Å diameter, as a minimalist model for nonspecific protein-DNA interactions, and compared these results to what we have previously found for Cd²⁺-surface-rich dots of the same size (Mahtab, R.; Rogers, J.P.; Murphy, C.J. J. Am. Chem. Soc. 1995, 117, 9099). We find that neutralization of the surface leads to no detectable binding, based on our luminescence assay, for 'straight' and A-tract oligonucleotides, while a crystallographically 'kinked' sequence does still bind, but by a factor of 4 less than that observed for a divalent metal ion-rich surface. The binding constants for both surfaces are within the range of nonspecific protein-DNA interactions. The kinetics of binding are also monitored and are compared to nonspecific protein-DNA interactions for large DNA fragments. Issues of biopolymer static bending vs flexibility are also addressed with fluorescence resonance energy transfer experiments.