DNA motion capture assay and protein-induced fluorescence enhancement (PIFE). (A) Under laminar flow, DNA experiences differential tension. Thus, different parts of the DNA exhibit different degrees of stretching. (B) In the DNA motion capture assay, five quantum dots are labeled at specific positions on λ-DNA. Upon flowing proteins, DNA bridgers and benders show different DNA compaction patterns. (C) When a protein is located in the vicinity of Cy3 dye, the fluorescence intensity increases. This phenomenon is called protein-induced fluorescence enhancement (PIFE). (D) PIFE can be combined with a single-molecule DNA flow-stretching assay. Here, Cy3 dyes are sparsely labeled on a DNA and proteins are introduced by flow. The example graph represents changes in DNA end-to-end length and integrated Cy3 intensity on the DNA over time.
