"Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy.

Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to occur on similar timescales as one-dimensional (1D) diffusion of proteins on DNA if effective in stalling these proteins as they scan DNA. We examined the flexibility and dynamics of DNA oligomers containing 3 base pair (bp) mismatched sites specifically recognized in vitro by nucleotide excision repair protein Rad4 (yeast ortholog of mammalian XPC). A previous Forster resonance energy transfer (FRET) study mapped DNA conformational distributions with cytosine analog FRET pair primarily sensitive to DNA twisting/unwinding deformations (Chakraborty et al. Nucleic Acids Res. 46: 1240-1255 (2018)). These studies revealed B-DNA conformations for nonspecific (matched) constructs but significant unwinding for mismatched constructs specifically recognized by Rad4, even in the absence of Rad4. The timescales of these unwinding fluctuations, however, remained elusive. Here, we labeled DNA with Atto550/Atto647N FRET dyes suitable for fluorescence correlation spectroscopy (FCS). With these probes, we detected higher FRET in specific, mismatched DNA compared with matched DNA, reaffirming unwinding/bending deformations in mismatched DNA. FCS unveiled the dynamics of these spontaneous deformations at ~ 300 µs with no fluctuations detected for matched DNA within the ~ 600 ns-10 ms FCS time window. These studies are the first to visualize anomalous unwinding/bending fluctuations in mismatched DNA on timescales that overlap with the < 500 µs "stepping" times of repair proteins on DNA. Such "flexible hinge" dynamics at lesion sites could arrest a diffusing protein to facilitate damage interrogation and recognition.

Momentum distribution and contact of the unitary Fermi gas.

We calculate the momentum distribution n(k) of the unitary Fermi gas by using quantum Monte Carlo calculations at finite temperature T/ϵ(F) as well as in the ground state. At large momenta k/k(F), we find that n(k) falls off as C/k4, in agreement with the Tan relations. From the asymptotics of n(k), we determine the contact C as a function of T/ϵ(F) and present a comparison with theory. At low T/ϵ(F), we find that C increases with temperature, and we tentatively identify a maximum around T/ϵ(F) ≃ 0.4. Our calculations are performed on lattices of spatial extent up to N(x) = 14 with a particle number per unit volume of ≃ 0.03-0.07.