Tonau Nakai | Searcharxiv

arXiv2004

Phase Transition in Reconstituted Chromatin

By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed states in reconstituted chromatin. Based on an analysis of the spatial distribution of nucleosome cores, we deduced an effective thermodynamic potential as a function of the nucleosome-nucleosome distance. This enabled us to interpret the folding transition of chromatin in terms of a first-order phase transition. This mechanism for the condensation of chromatin is discussed in terms of its biological significance.

q-bio.SC↗

arXiv2004

All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition

Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the addition of various kinds of chemical species that usually induce DNA condensation. In this study, we performed a single-molecule observation on a large DNA, Lambda ZAP II DNA (ca. 41 kbp), in a solution containing RNA polymerase and substrates along with spermine, a tetravalent cation, at different concentrations, by use of fluorescence staining of both DNA and RNA. We found that transcription, or RNA production, is completely inhibited in the compact state, but is actively performed in the unfolded coil state. Such an all-or-none effect on transcriptional activity induced by the discrete conformational transition of single DNA molecules is discussed in relation to the mechanism of the regulation of large-scale genetic activity.

q-bio.BM↗