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.

Optical trapping and manipulation techniques have attracted significant attention in various research fields. Optical forces divided into two terms, such as a scattering force and gradient one, work to push forward and attract objects, respectively. This is a typical property of optical forces. In particular, a tool known as optical tweezers can be created when a laser beam is converged at a focal point, causing strong forces to be generated so as to trap and manipulate small objects. In this study, we propose a novel method to build up assembled structures of polystyrene particles by using optical trapping techniques. Recording trajectories of single particles, the optical forces are quantitatively evaluated using particle tracking velocimetry. Herein, we treat various particle sizes whose diameters range from 1 to 4 μm and expose them to a converged laser beam of 1064 nm wavelength. As a result, both experimental and theoretical results are in good agreement. The behavior of particles is understood in the framework of Ashkin’s ray optics. This finding clarifies optical force fields of microparticles distributed in a slit-like microfluidic channel and will be applicable for effectively forming ordered structures in liquids.

We propose and demonstrate the enhancement of the biased diffusion of dye-doped nanoparticles using resonance and nonresonance laser beams. The Brownian motion of nanoparticles in a laser focus is investigated by fluorescence correlation spectroscopy (FCS) and the time variation in fluorescence intensity. From the analysis of autocorrelation functions, it is demonstrated that the difference between the transit times of nanoparticles in the focal spot with and without resonance laser irradiation increases $7-fold by the simultaneous irradiation of a near-infrared laser. This method is applicable to the selective optical manipulation of dye-stained nanomaterials and biomolecules in solution.

There is currently substantial interest in creating bioelectronic devices that can be implanted in and attached to humans for sensing and control of organs and internal systems in order to prolong and improve the quality of life.[1-4] Herein we report a new type of implantable bioelectronic device that is operated by laser irradiation from outside the body. Carbon nanotubes (CNTs), which absorb laser light and transform it to thermal energy with high efficiency, are key in the design of this device; the thermal energy is further converted into electrical power with a Seebeck device. The CNT-based photo-thermal-electrical (PTE) converter is unique and has potential in practical use as it can be simply operated by laser irradiation, and can be easily removed or replaced as it is embedded near the skin.Among several photothermally active nanomaterials, CNTs are of particular interest because of their extraordinarily high efficiency of photothermal energy conversion and high light-absorption cross-section in a wavelength range that can be transmitted through living tissue (diagnostic window: 650-1100 nm).[5] The photothermal energy conversion of CNTs is effective in various biological applications. [6][7][8][9][10][11][12][13][14][15][16][17][18][19] It is well known that gold nanoparticles also have photothermal properties, but CNTs can be more effectively heated at various wavelengths because of their strong absorbance over a wide wavelength range.[6] Thermal energy can be converted into electricity by using thermoelectric (TE) conversion devices that utilize the Seebeck effect. [18][19][20] A PTE energy conversion system that combines TE elements and CNTs is available and can be used in the diagnostic window of living tissues. PTE converters are promising devices for electrical power supply to embedded implantable medical devices. We recently fabricated a PTE converter using CNT gels exposed to 1064 nm laser light, and demonstrated that it generated sufficient electrical energy to power a motor and lightemitting diodes. [18,19] However, the applications of our previous PTE converters were limited to ex vivo electrical power generation. Herein, we demonstrate that 1) a well-dispersed single-walled CNT/poly(dimethylsiloxane) (SWNT-PDMS) composite can be formed, and a novel PTE converter fabricated with a CNT polymer composite can effectively convert the photothermal energy of CNTs into electricity; 2) the PTE converter can supply electrical power for stimulation of electrical activity in physiological tissues, such as a heart muscle of zebrafish (Danio rerio) and a sciatic nerve of a frog (Xenopus laevis); and 3) the PTE converter was effective in the body of a rat. These results dramatically extend the concept of a PTE converter into new areas and applications.To prepare the CNT-based PTE converter, we first prepared CNT polymer sheets. We wrapped noncovalent SWNTs with poly(3-hexylthiophene) (P3HT) and dispersed them in PDMS sheets (P3HT-SWNT-PDMS; see Methods in the Supporting Information). The strong tendency of...