Reverse transcription of the HIV-1 RNA genome involves several complex nucleic acid rearrangement steps that are catalyzed by the HIV-1 nucleocapsid protein (NC), including for example, the annealing of the transactivation response (TAR) region of the viral RNA to the complementary region (TAR DNA) in minus-strand strong-stop DNA. We report herein single-molecule fluorescence resonance energy transfer measurements on single immobilized TAR DNA hairpins and hairpin mutants complexed with NC (i.e., TAR DNA/NC). Using this approach we have explored the conformational distribution and dynamics of the hairpins in the presence and absence of NC protein. The data demonstrate that NC shifts the equilibrium secondary structure of TAR DNA hairpins from a fully "closed" conformation to essentially one specific "partially open" conformation. In this specific conformation, the two terminal stems are "open" or unwound and the other stems are closed. This partially open conformation is arguably a key TAR DNA intermediate in the NC-induced annealing mechanism of TAR DNA.

We report in situ observation of cluster growth of nanoparticles confined in an optical trapping potential by means of fluorescence correlation spectroscopy. When an optical trapping force caused by a highly focused laser beam acts on nanoparticle suspensions, the number of nanoparticles increases and an assembly can be formed at the focal spot. The decay times of fluorescence autocorrelation curves were investigated as a function of the irradiation time of the laser beam and the laser power. In the initial stage of the optical assembling, the decay time increases with the irradiation time of the laser beam. On the other hand, in the later stage, a decrease of the decay time was observed. This behavior is explained successfully by using two models of Brownian motion under weak and strong optical trapping. It was revealed that trapping and clustering of nanoparticles proceed simultaneously and clusters confined in the focal spot make larger aggregates spontaneously.

Biological network systems, such as inter- and intra-cellular signalling systems, are handled in a sophisticated manner by the transport of molecular information. Over the past few decades, there has been a growing interest in the development of synthetic molecular-transport systems. However, several key technologies have not been sufficiently realized to achieve optimum performance of transportation methods. Here we show that a new type of supramolecular system comprising of carbon nanotubes and liposomes enables the directional transport and controlled release of carrier molecules, and allows an enzymatic reaction at a desired area. The study highlights important progress that has been made towards the development of biomimetic molecular-transport systems and various lab-on-a-chip applications, such as medical diagnosis, sensors, bionic computers and artificial biological networks.

A method including surface silanization, phase transfer and self-assembly, and SiO2 shell growth has been developed to incorporate multiple hydrophobic CdSe/ZnS nanocrystals into SiO2 beads where they are well suited for bio-application due to their high brightness, less-cytotoxic, and non-blinking nature.

When a laser beam is focused into colloidal nanoparticle suspensions, a number of nanoparticles can be confined in the focal spot due to an optical gradient force. To reveal the assembling dynamics of polymer nanoparticles, the assembling process was investigated by analyzing the time evolution of the fluorescence intensity of the nanoparticles. In a dilute suspension of 100-nm-sized particles, a stepwise increase of the fluorescence intensity corresponding to a trapped single nanoparticle was observed. Statistical analysis revealed that the initial assembling rate of nanoparticles was proportional to the laser power and concentration of particle suspensions as expected from the diffusion equation. In 40-nm-sized particle suspensions, blinking profiles of fluorescence intensity were obtained, in which 2-3 particles were simultaneously trapped and then escaped from the focal point. It is considered from statistical analyses and two-dimensional Monte Carlo simulations that this assembling phenomenon is attributable to cluster formation assisted by optical trapping.