Probing biopolymer conformation by metallization with noble metals

We propose a novel method for the simple visual (colorimetric) and spectroscopic monitoring of the conformational state of a biopolymer. We present an experimental example of the detection of the change in the conformation of a giant DNA molecule. This methodology is based on the difference in the manner of metallization with noble metals on a polymer scaffold depending on its conformation. Spectroscopic analysis of the metallization of DNA by metallic silver or gold provides information on the critical concentration of DNA binder, at which the folding transition from the elongated into the compact state occurs, together with the dimension and morphology of a compact DNA condensate. This method may be suitable for use in a rapid screening procedure for the high-throughput analysis of large chemical libraries to evaluate their ability to induce DNA compaction, protein folding and similar important processes

Transcription of Giant DNA Complexed with Cationic Nanoparticles as a Simple Model of Chromatin

We prepared complexes of giant double-stranded DNA with cationic nanoparticles of 10–40 nm in diameter as an artificial model of chromatin and characterized the properties of changes in their higher-order conformation. We measured the changes in transcriptional activity that accompanied the DNA conformational transitions. Complete inhibition was found at excess concentrations of nanoparticles. In contrast, at intermediate stages of DNA binding with nanoparticles, the transcription activity of DNA survived, and this strongly depended on the size of the nanoparticles. For large nanoparticles of 40 nm, a decrease in transcriptional activity can be caused by the addition of only a small amount of nanoparticles. On the other hand, there was almost no inhibition of DNA transcriptional activity with the addition of small nanoparticles (10 nm) until very high concentrations, even under conditions that induced DNA compaction as revealed by single-DNA observation. At higher concentrations of 10-nm nanoparticles, DNA transcription activity decreased abruptly until it was completely inhibited. These results are discussed in relation to the actual size of the histone core, together with the mechanism of switching of transcriptional activity in eukaryotic cells

Na+ more strongly inhibits DNA compaction by spermidine (3+) than K+

The protective effects of alkali metal ions (Li+, Na+, K+, Rb+ and Cs+) against spermidine-induced DNA compaction were studied using single-molecule observations. We found that all alkali metal salts prevent DNA compaction, where Na+ more strongly prevented DNA compaction than other alkali metal ions. We discuss our results in terms of changes in ionic radii in relation to the net translational entropy of small ions due to ionic exchange between trivalent and monovalent cations

ATP-Induced Shrinkage of DNA with MukB Protein and the MukBEF Complex of Escherichia coli▿

Fluorescence microscopic observation of individual T4 DNA molecules revealed that the MukBEF complex (bacterial condensin) and its subunit, the MukB (a member of the SMC [structural maintenance of chromosomes] superfamily) homodimer, of Escherichia coli markedly shrunk large DNA molecules in the presence of hydrolyzable ATP. In contrast, in the presence of ADP or ATP-γS, the conformation of DNA was almost not changed. This suggests that the ATPase activity of subunit MukB is essential for shrinking large DNA molecules. Stretching experiments on the shrunken DNA molecules in the presence of ATP and MukBEF indicated a cross-bridging interaction between DNA molecules

Internal motion of chromatin fibers is governed by dynamics of uncompressed linker strands

10.1016/j.bpj.2020.10.018Biophysical Journa