Probing transient protein-mediated DNA linkages using nanoconfinement

We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configurationthat makes loops appear as folds whose size can easily be quantified. Using this technique, we studythe interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particularpersistence length and effective width. We find that the rate of DNA fold unrolling is significantly reducedwhen T4 DNA ligase and ATPare applied to bare DNA.Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligasecan transiently stabilize foldedDNA configurations by coordinating genetically distant DNA stretches.