Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA

Abstract

We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.

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

“…In other words, DNA segments are aligned parallel to each other in the presence of a linear‐chain polyamine but are randomly‐oriented in the presence of a branched‐chain polyamine. This difference between linear‐ and branched‐chain polyamines is in good agreement with our previous result . To compare the frequency of crossings in the presence of linear‐ and branched‐chain polyamines, we calculated the number of crossings per 1 μm, ξ , from AFM images based on the method of analysis depicted in Table .…”

“…Spermidine SPD was purchased from Nacalai Tesque (Kyoto, Japan). Homocaldopentamine 3334 and N 4 ‐bis(aminopropyl)spermidine 3(3)(3)4 were synthesized according to a previous report . Calf Thymus DNA (CT DNA: 8–15 kbp) was purchased from Wako Pure Chemical Industries (Osaka, Japan).…”

“…We found that branched‐chain polyamines tend to induce a meshwork assembly of randomly oriented DNA fibers, whereas linear‐chain polyamines cause a parallel alignment between DNA segments . Circular dichroism (CD) measurements revealed that branched‐chain polyamines induce the A‐like form in the secondary structure of DNA, while linear‐chain polyamines have only a minimal effect …”

“…We previously investigated the effects of branched‐ and linear‐chain polyamines on the higher‐order structure of genome‐size DNA at room temperature by the use of fluorescence microscopy and atomic force microscopy (AFM) . We found that branched‐chain polyamines tend to induce a meshwork assembly of randomly oriented DNA fibers, whereas linear‐chain polyamines cause a parallel alignment between DNA segments . Circular dichroism (CD) measurements revealed that branched‐chain polyamines induce the A‐like form in the secondary structure of DNA, while linear‐chain polyamines have only a minimal effect …”

Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile‐specific branched‐chain polyamine

“…Therefore, polyamines play an important role, especially in translation. N 4 -Bis(aminopropyl)spermidine has a stronger effect for DNA compaction because of the greater basicity of the quaternary ammonium group [10]. One comprises long linear-chain polyamines such as caldopentamine and caldohexamine, while the other comprises branchedchain polyamines such as N 4 -aminopropylnorspermidine (tris(3-aminopropyl)amine), N 4 -aminopropylspermidine, tetrakis-(3-aminopropyl)ammonium, and N 4 -bis(aminopropyl)spermidine.…”