2010/10/04 by Tomislav Vuletić, Vuletic, Tomislav, Babic, Sanja Dolanski +4
Biochemistry, Genetics and Molecular Biology · Engineering · #Advanced biosensing and bioanalysis techniques #DNA and Nucleic Acid Chemistry #FOS: Physical sciences #Nanopore and Nanochannel Transport Studies #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.1010.0731
openalex publication_date 2010/10/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We report a study of DNA (150 bp fragments) conformations in very low added salt <0.05mM, across wide DNA concentration range 0.0015≤ c ≤ 8~mM (bp). We found an intermediate DNA conformation in the region 0.05 < c < 1~mM, by means of fluorescence correlation spectroscopy (FCS) and UV-absorbance measurements. FCS detected that in this region DNA has the diffusion coefficient, Dp reduced below the values for both ssDNA coils and native dsDNA helices of similar polymerization degree N. Thus, this DNA population can not be a simple mix of dsDNA and of ssDNA which results from DNA melting. Here, melting occurs due to a reduction in screening concomitant with DNA concentration being reduced, in already very low salt conditions. The intermediate DNA is rationalized through the well known concept of fluctuational openings (DNA bubbles) which we postulate to form in AT-rich portions of the sequence, without the strands coming apart. Within the bubbles, DNA is locally stretched, while the whole molecule remains rod-like due to very low salt environment. Therefore, such intermediate DNA is elongated, in comparison to dsDNA, which accounts for its reduced Dp.