Dna Folding By Multivalent Cations

Folding short lengths of DNA into loops is a fundamental area of research in the field of nanoengineering. While physical mechanisms of DNA folding may differ according to the multivalent cations involved in folding, the mechanical task is the same. Here, we compare the folding pathways and resulting loops for DNA folding by multivalent cations that are known to condense DNA. Specifically, we compared the looping of DNA by protamine (+21 and 5 kDA), hexaammine-cobalt (III) (+3 and 0.3 kDa), spermine (+4 and 0.2 kDa), and histone H1 (+42 and 20 kDA). 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 findings suggest that the mechanism of DNA folding across various multivalent cations is similar, perhaps indicating that this mechanism is more broadly applicable to other proteins that fold DNA.