The aggregation/deaggregation of chlorin p6 with the surfactants CTAB, SDS, and TX 100 have been studied by using absorption, fluorescence, and light scattering techniques. The ionic surfactants are found to cause aggregation of fluorophore at submicellar concentrations. The aggregates dissolve at higher surfactant concentrations to yield micellized monomers. This is rationalized by the interplay of electrostatic and hydrophobic effects. A prominent pH effect is observed in the ionic surfactant induced aggregation process as the charge on the fluorophore is controlled by the pH of the medium. Interestingly, the neutral TX-100 also induces aggregation of chlorin p6 at low concentrations, indicating that hydrophobic effects by themselves can cause aggregation unless there is a hindrance by repulsive electrostatic effects.

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In ensemble and single-molecule experiments using the yeast proliferating cell nuclear antigen (PCNA, clamp) and replication factor C (RFC, clamp loader), we have examined the assembly of the RFC · PCNA · DNA complex and its progression to holoenzyme upon addition of polymerase δ (polδ). We obtained data that indicate (i) PCNA loading on DNA proceeds through multiple conformational intermediates and is successful after several failed attempts; (ii) RFC does not act catalytically on a primed 45-mer templated fork; (iii) the RFC · PCNA · DNA complex formed in the presence of ATP is derived from at least two kinetically distinguishable species; (iv) these species disassemble through either unloading of RFC · PCNA from DNA or dissociation of PCNA into its component subunits; and (v) in the presence of polδ only one species converts to the RFC · PCNA · DNA · polδ holoenzyme. These findings redefine and deepen our understanding of the clamp-loading process and reveal that it is surprisingly one of trial and error to arrive at a heuristic solution.DNA replication | replication factor C | single-molecule FRET D NA replication is carried out by effective coordination of the activities of many proteins at the replication fork. Given the complex nature of DNA synthesis, a structural and functional conservation of the accessory proteins apparently has evolved across diverse organisms (1-3). However, eukaryotic DNA replication has diverged and become more complicated than its prokaryotic counterpart due in part to the multisubunit composition of several proteins. In yeast, lagging strand DNA synthesis requires the coordinated actions of polymerase δ (polδ), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) (4). Eukaryotic PCNA, a ring-shaped trimer of identical subunits, plays a pivotal role in both DNA replication and repair by tethering the DNA polymerase to significantly enhance the processivity of DNA synthesis (5-10). The productive assembly of a polymerase-PCNA complex bound to DNA requires loading of the PCNA clamp by RFC (11). RFC, an ATP-driven motor, is composed of a large subunit (RFC-A, 95 kDa) and four small subunits (RFC-B-RFC-E, 36-40 kDa) and forms a RFC · PCNA · ATP complex that binds specifically to primed DNA (12).The clamp-loading process occurs via multiple steps (13-16). X-ray crystallographic and electron microscopic studies of the clamp loader complexed with the clamp revealed that PCNA was either in a closed or slightly open conformation that perhaps represents the structure of an intermediate step in PCNA loading (13,17). PCNA, in solution, has a closed conformation and must be opened for loading on DNA and further reclosed to be retained on the DNA possibly through a specific single interface (18).The structure of the yeast RFC · PCNA complex (13) provided the coordinates for introducing a fluorescent donor-acceptor pair within the PCNA to probe the FRET efficiencies distance information on the conformation of the PCNA subunit interface (19). In the presence of ATP, the PCNA...

We report a novel type of inorganic membranelike structure formed by the self-assembly of hydrophilic polyoxometalate macroanions. Such nanoscaled, water-soluble macroions tend to form stable, uniform, single-layer “blackberry” structures (20−1000 nm in size) in dilute solutions via noncovalent bond interactions. Two interesting features of “Keplerate” {Mo72Fe30} blackberries are found from fluorescence studies:  (1) They create a microscaled, relatively isolated water environment (containing over 3 million water molecules) which possesses different properties from the bulk water. (2) The blackberry membrane is permeable to small cations, but not to anions. The passive transport of cations across the blackberry membrane is relatively slow but does not need any carrier or additional energy.

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