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We directly visualize the weak and slow interactions between specific unwinding sites on supercoiled DNA, and site-specific probes designed to bind to these sites, as a function of DNA supercoiling and temperature. We use Convex Lens-induced Confinement microscopy to confine the DNA molecules within a sealed, glass array of nanoscale pits, embedded in a coverslip. Throughout our wide-field observations of single-molecule binding and diffusive trajectories, which extend over several seconds to minutes, the DNA molecules are free to explore all possible configurations, which we show has crucial influence over the observed dynamics. The increase in binding rate that we observe, with both temperature and supercoiling, is consistent with Z-DNA formation playing a key role in governing DNA dynamics. This alternate structure suppresses supercoil-induced DNA unwinding in DNA at low temperatures, for a wide range of negative superhelicities. The new single-molecule methodology that we present may be used to visualize a wide range of molecular interactions that are challenging or impossible to access with other methods such as optical or magnetic tweezers. These include interactions that are highly dependent on molecular topology, proceed over many seconds to minutes, or are rare.