Intermediate DNA at low added salt: DNA bubbles slow the diffusion of short DNA fragments - Condensed Matter > Soft Condensed MatterReportar como inadecuado




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Abstract: We report a study of DNA 150 bp fragments conformations in very low addedsalt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mMbp. We found an intermediate DNA conformation in the region $0.05 < c <1$~mM, by means of fluorescence correlation spectroscopy FCS andUV-absorbance measurements. FCS detected that in this region DNA has thediffusion coefficient, $D p$ reduced below the values for both ssDNA coils andnative dsDNA helices of similar polymerization degree $N$. Thus, this DNApopulation can not be a simple mix of dsDNA and of ssDNA which results from DNAmelting. Here, melting occurs due to a reduction in screening concomitant withDNA concentration being reduced, in already very low salt conditions. Theintermediate DNA is rationalized through the well known concept offluctuational openings DNA bubbles which we postulate to form in AT-richportions of the sequence, without the strands coming apart. Within the bubbles,DNA is locally stretched, while the whole molecule remains rod-like due to verylow salt environment. Therefore, such intermediate DNA is elongated, incomparison to dsDNA, which accounts for its reduced $D p$.



Autor: Tomislav Vuletic, Sanja Dolanski Babic, Ticijana Ban, Joachim Raedler, Francoise Livolant, Silvia Tomic

Fuente: https://arxiv.org/







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