Intermediate DNA at low added salt: DNA bubbles slow the diffusion of short DNA fragments

TL;DR

This study reveals an intermediate DNA conformation in very low salt conditions, characterized by DNA bubbles that slow diffusion, detected through fluorescence correlation spectroscopy and UV measurements, highlighting a novel DNA state.

Contribution

The paper identifies and characterizes an intermediate DNA conformation caused by bubbles in low salt conditions, a state not previously well understood or documented.

Findings

DNA exhibits reduced diffusion coefficient in low salt, indicating a distinct intermediate state.

Intermediate DNA involves bubbles in AT-rich regions, elongating the molecule without strand separation.

This conformation affects DNA mobility, providing insights into DNA behavior in extreme ionic environments.

Abstract

We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~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, $D_p$ 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 $D_p$.