Fast combinatorial nanofluidic device for the dynamic study of biomolecular interactions

We present a nanofluidic device for fast combinatorial exposure of stretched and localized DNA molecules to reagents, such as DNA biding proteins, salts, and restriction enzymes. Nanofluidic devices with channel sizes close to the persistence length of DNA have long been used to stretch, visualize, and study biomolecular interactions that modify the configuration of DNA. However, there is a temporal limitation on how long you can study the interaction dynamics before the probing light photocleaves DNA and fluorescence dyes. In addition, study of the interactions among DNA and multiple reagents in different sequences needs the rapid exchange of buffers. Such studies in the nanochannels with traditional passive exchange of buffers via diffusion process is not feasible. Our device allows the simultaneous or the sequential exposure of multiple reagents with active flow of buffers. The buffers could be exchanged under 20 sec while DNA molecule still confined in the field of view. To illustrate the concept of the device, we will show the conformational change of DNA in the varying ionic concentration, restriction enzymes and DNA binding proteins.