Dna Looping By Multivalent Cations

Folding DNA into a loop is a fundamental task during transcription, replication, recombination, and condensation. While the proteins that loop the DNA and the physical mechanisms for DNA looping may be different in all these scenarios, the mechanical task is the same. Here, we compare the pathways for DNA looping by multivalent cations that are known to condense DNA. Specifically, we compared the looping of DNA by protamine, hexaammine-cobalt (III), spermine, and histone H1. We used a Tethered Particle Motion (TPM) assay to investigate the real-time behavior of the folding and an Atomic Force Microscopy (AFM) assay to image the folded structures. Interestingly, all of these positively charged folding agents loop 105-nm-length DNA molecules using multiple intermediates that are long-lived (100 s), discrete (<10 s transitions), and reversible. These multiple intermediates have structures with an apparent reduction in the persistence length of the DNA. These findings suggest that the mechanism of DNA looping across various multivalent cations is similar, perhaps indicating that this mechanism is more broadly applicable to other proteins that loop DNA.