Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA

A pentavalent branched-chain polyamine, N-4-bis(aminopropyl)spermidine 3(3)(3)4, is a unique polycation found in the hyperthermophilic archaeon Thermococcus kodakarensis, which grows at temperatures between 60 and 100 degrees C. We studied the effects of this branched-chain polyamine on DNA structure at different temperatures up to 80 degrees C. Atomic force microscopic observation revealed that 3(3)(3)4 induces a mesh-like structure on a large DNA (166kbp) at 24 degrees C. With an increase in temperature, DNA molecules tend to unwind, and multiple nano-loops with a diameter of 10-50nm are generated along the DNA strand at 80 degrees C. These results were compared to those obtained with linear-chain polyamines, homocaldopentamine 3334 and spermidine, the former of which is a structural isomer of 3(3)(3)4. These specific effects are expected to neatly concern with its role on high-temperature preference in hyperthermophiles.