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

• Published in: Chemphyschem Vol. 19; no. 18; pp. 2299 - 2304
• Main Authors: Nishio, Takashi, Yoshikawa, Yuko, Fukuda, Wakao, Umezawa, Naoki, Higuchi, Tsunehiko, Fujiwara, Shinsuke, Imanaka, Tadayuki, Yoshikawa, Kenichi
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 18.09.2018; John Wiley and Sons Inc
• Subjects: Animals; archaea; Atomic force microscopy; Bacteriophage T4 - genetics; branched polyamine; Cattle; Chain branching; Chains; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; Genome; high temperature; higher-order structure of DNA; Hot Temperature; Microscopy, Atomic Force; nano-loop; Nucleic Acid Conformation; Polyamines; Polyamines - chemistry; Polyelectrolytes; Spermidine - analogs & derivatives; Spermidine - chemical synthesis; Spermidine - chemistry; Temperature; Temperature dependence; Thermococcus - chemistry; nano-loop; higher-order structure of DNA; branched polyamine; high temperature; archaea
• ISSN: 1439-4235; 1439-7641
• DOI: 10.1002/cphc.201800396

A pentavalent branched‐chain polyamine, N4‐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 °C. We studied the effects of this branched‐chain polyamine on DNA structure at different temperatures up to 80 °C. Atomic force microscopic observation revealed that 3(3)(3)4 induces a mesh‐like structure on a large DNA (166 kbp) at 24 °C. With an increase in temperature, DNA molecules tend to unwind, and multiple nano‐loops with a diameter of 10–50 nm are generated along the DNA strand at 80 °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. Structural change in genome‐size DNA: Branched‐chain polyamine induces a randomly oriented mesh‐like structure for a single DNA (166 kbp), as revealed by AFM observations. With an increase in temperature up to 80 °C, multiple nanoloops are generated along the DNA strand. These effects are markedly different from those of linear‐chain polyamines (the scale bar in the Figures is 1 μm).