Protein assembly and DNA looping by the FokI restriction endonuclease

The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands at fixed positions upstream of the site. The sequence is contacted by a single monomer of the protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands. FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions were examined on a series of plasmids with either one recognition site or with two sites separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that site associates via a weak protein–protein interaction with a second monomer that remains detached from the recognition sequence. Nevertheless, the second monomer catalyses phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two sites, two monomers of FokI interact strongly, as a result of being tethered to the same molecule of DNA, and sequester the intervening DNA in a loop

Layer-by-layer deposition of open-pore mesoporous TiO 2- Nafion® film electrodes

The formation of variable thickness TiO2 nanoparticle-Nafion® composite films with open pores is demonstrated via a layer-by-layer deposition process. Films of about 6 nm diameter TiO2 nanoparticles grow in the presence of Nafion® by “clustering” of nanoparticles into bigger aggregates, and the resulting hierarchical structure thickens with about 25 nm per deposition cycle. Film growth is characterized by electron microscopy, atomic force microscopy, and quartz crystal microbalance techniques. Simultaneous small-angle X-ray scattering and wide-angle X-ray scattering measurements for films before and after calcination demonstrate the effect of Nafion® binder causing aggregation. Electrochemical methods are employed to characterize the electrical conductivity and diffusivity of charge through the TiO2-Nafion® composite films. Characteristic electrochemical responses are observed for cationic redox systems (diheptylviologen2+/+, Ru(NH3)3+/2+6, and ferrocenylmethyl-trimethylammonium2+/+) immobilized into the TiO2-Nafion® nanocomposite material. Charge conduction is dependent on the type of redox system and is proposed to occur either via direct conduction through the TiO2 backbone (at sufficiently negative potentials) or via redox-center-based diffusion/electron hopping (at more positive potentials)

A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease

While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the subunits, SfiI is a tetramer of identical subunits. Two of its subunits (a dimeric unit) create one DNA-binding cleft, and the other two create a second cleft on the opposite side of the protein. The two clefts bind specific DNA cooperatively to give a complex of SfiI with two recognition sites. This complex is responsible for essentially all of the DNA-cleavage reactions by SfiI: virtually none is due to the complex with one site. The communication between the DNA-binding clefts was examined by disrupting one of the very few polar interactions in the otherwise hydrophobic interface between the dimeric units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The mutant protein remained tetrameric in solution and could bind two DNA sites. But instead of being activated by binding two sites, like wild-type SfiI, it showed maximal activity when bound to a single site and had a lower activity when bound to two sites. This interaction across the dimer interface thus enforces in wild-type SfiI a cooperative transition between inactive and active states in both dimers, but without this interaction as in the mutant protein, a single dimer can undergo the transition to give a stable intermediate with one inactive dimer and one active dimer