Modulation of HU-DNA interactions by salt concentration and applied force.

HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.

DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA "braiding" experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements

Flat-band and multi-dimensional fermions in Pb10(PO4)6O4

Employing a combination of first-principles calculations and low-energy effective models, we present a comprehensive investigation on the electronic structure of Pb$_{10}$(PO$_{4}$)$_{6}$O$_{4}$, which exhibits remarkable quasi-one-dimensional flat-band around the Fermi level that contains novel multi-dimensional fermions. These flat bands predominantly originate from $p_x/p_y$ orbital of the oxygen molecules chain at $4e$ Wyckoff positions, and thus can be well-captured by a four-band tight-binding model. Furthermore, the abundant crystal symmetry inherent to Pb$_{10}$(PO$_{4}$)$_{6}$O$_{4}$ provides an ideal platform for the emergence of various multi-dimensional fermions, including a 0D four-fold degenerated Dirac fermion with quadratic dispersion, a 1D quadratic/linear nodal-line (QNL/LNL) fermion along symmetric $k$-paths, 1D hourglass nodal-line (HNL) fermion linked to the Dirac fermion, and a 2D symmetry-enforced nodal surface (NS) found on the $k_z$=$\pi$ plane. Moreover, when considering the weak ferromagnetic order, Pb$_{10}$(PO$_{4}$)$_{6}$O$_{4}$ transforms into a rare semi-half-metal, which is characterized by the presence of Dirac fermion and HNL fermion at the Fermi level for a single spin channel exhibiting 100$\%$ spin polarization. Our findings reveal the coexistence of flat bands, diverse topological semimetal states and ferromagnetism within in Pb$_{10}$(PO$_{4}$)$_{6}$O$_{4}$, which may provide valuable insights for further exploring intriguing interplay between superconductivity and exotic electronic states.Comment: 8 pages, 4 figure

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation

Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the force–extension measurements were in thermodynamic equilibrium. We, therefore, could use a thermodynamic Maxwell relation to deduce the change of protein number on a single DNA due to varied force. For the binding of both HU and Fis under conditions studied, numbers of bound proteins decreased as force was increased. Our experiments showed that most of the bound HU proteins were driven off the DNA at 6.3 pN for HU concentrations lower than 150 nM; our HU data were fit well by a statistical-mechanical model of protein-induced bending of DNA. In contrast, a significant amount of Fis proteins could not be forced off the DNA at forces up to 12 pN and Fis concentrations up to 20 nM. This thermodynamic approach may be applied to measure changes in numbers of a wide variety of molecules bound to DNA or other polymers. Force-dependent DNA binding by proteins suggests mechano-chemical mechanisms for gene regulation

Design monolayer iodinenes based on halogen bond and tiling theory

Xenes, two-dimensional (2D) monolayers composed of a single element, with graphene as a typical representative, have attracted widespread attention. Most of the previous Xenes, X from group-IIIA to group-VIA elements have bonding characteristics of covalent bonds. In this work, we for the first time unveil the pivotal role of a halogen bond, which is a distinctive type of bonding with interaction strength between that of a covalent bond and a van der Waals interaction, in 2D group-VIIA monolayers. Combing the ingenious non-edge-to-edge tiling theory and state-of-art ab initio method with refined local density functional M06-L, we provide a precise and effective bottom-up construction of 2D iodine monolayer sheets, iodinenes, primarily governed by halogen bonds, and successfully design a category of stable iodinenes, encompassing herringbone, Pythagorean, gyrated truncated hexagonal, i.e. diatomic-kagome, and gyrated hexagonal tiling pattern. These iodinene structures exhibit a wealth of properties, such as flat bands, nontrivial topology, and fascinating optical characteristics, offering valuable insights and guidance for future experimental investigations. Our work not only unveils the unexplored halogen bonding mechanism in 2D materials but also opens a new avenue for designing other non-covalent bonding 2D materials.Comment: 6 pages, 4 figure