Two Bond-Exchange modes in sodium silicate liquids

Because of their network structure, the diffusion mechanism of network-forming elements, namely silicon and oxygen, remains unclear. Several diffusion mechanisms have been proposed based on molecular dynamics simulations; however, the bond-exchange motion has not been quantitatively analyzed. This study introduces the concept of bond-breaking/forming particles. By treating the bond-breaking/forming events as instant particles, the bond-exchange event can be interpreted as a pair-correlation function of these particles. Here, examples of sodium silicate liquids at various pressures are presented using the results of force-field molecular dynamics simulations. Analyses of the pair correlation of bond-breaking/forming particles revealed two distinct bond-exchange modes. Only the short mode contributed to the diffusion of the network-forming elements based on comparative analysis of the pressure dependence of the integrated peaks of the pair-correlation functions and the self-diffusion coefficients of silicon

スピンラベル法によるタンパク質の比較研究<総説 マイレビュー>

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Observation of B+→pΛ̅γ

journal articl

Near-Complete Suppression of Quantum Dot Blinking in Ambient Conditions

Colloidal semiconductor quantum dots are attractive fluorophores for multicolor imaging because of broad absorption and narrow emission spectra, and they are brighter and far more photostable than organic dyes. However, severe intermittence in emission (also known as blinking) has been universally observed from single dots and has been considered an intrinsic limitation difficult to overcome. This is unfortunate because growing applications in spectroscopy of single biological molecules and quantum information processing using single photon sources could greatly benefit from long-lasting and nonblinking single-molecule emitters. For instance, in a recent application of single-dot imaging, the tracking of membrane receptors was interrupted frequently due to the stroboscopic nature of recording. Blinking can also reduce the brightness in ensemble imaging via signal saturation. Here we show that the quantum dot blinking can be suppressed with the emission duty cycle approaching 100% while maintaining biocompatibility

An Optical Trap Combined with Three-Color FRET

We developed a hybrid technique combining optical tweezers and single-molecule three-color fluorescence resonance energy transfer (FRET). In demonstrative experiments, we observed the force-sensitive correlated motion of three helical arms of a Holliday junction and identified the independent unfolding/folding dynamics of two DNA hairpins of the same length. With 3 times the number of observable elements of single-molecule FRET, this new instrument will enable the measurement of the complex, multidimensional effects of mechanical forces in various biomolecular systems, such as RNA and proteins

Additional file 1: of Accelerated FRET-PAINT microscopy

Accelerated FRET-PAINT Microscopy. Figure S1. Excitation spectra of Cy5 (black) and CF660R (red). Figure S2. A cross-sectional histogram of microtubules. Figure S3. Photo-induced damage of DNA probes. (DOCX 538 kb

ウズベキスタンにおける行政法改革

2008-07-25福家俊朗教授退職記念論文集　第三部：比較公法学の論点departmental bulletin pape

Intrinsic Z-DNA Is Stabilized by the Conformational Selection Mechanism of Z-DNA-Binding Proteins

Z-DNA, a left-handed isoform of Watson and Crick’s B-DNA, is rarely formed without the help of high salt concentrations or negative supercoiling. However, Z-DNA-binding proteins can efficiently convert specific sequences of the B conformation into the Z conformation in relaxed DNA under physiological salt conditions. As in the case of many other specific interactions coupled with structural rearrangements in biology, it has been an intriguing question whether the proteins actively induce Z-DNAs or passively trap transiently preformed Z-DNAs. In this study, we used single-molecule fluorescence assays to observe intrinsic B-to-Z transitions, protein association/dissociation events, and accompanying B-to-Z transitions. The results reveal that intrinsic Z-DNAs are dynamically formed and effectively stabilized by Z-DNA-binding proteins through efficient trapping of the Z conformation rather than being actively induced by them. Our study provides, for the first time, detailed pictures of the intrinsic B-to-Z transition dynamics and protein-induced B-to-Z conversion mechanism at the single-molecule level

Dynamic Anchoring of the 3′-End of the Guide Strand Controls the Target Dissociation of Argonaute–Guide Complex

Argonaute (Ago) is the catalytic core of small RNA-based gene regulation. Despite plenty of mechanistic studies on Ago, the dynamical aspects and the mechanistic determinants of target mRNA binding and dissociation of Ago–guide strand remain unclear. Here, by using single-molecule fluorescence resonance energy transfer (FRET) assays and <i>Thermus thermophilus</i> Ago (<i>Tt</i>Ago), we reveal that the 3′-end of the guide strand dynamically anchors at and releases from the PAZ domain of Ago, and that the 3′-end anchoring of the guide strand greatly accelerates the target dissociation by destabilizing the guide–target duplex. Our results indicate that the target binding/dissociation of Ago–guide is executed through the dynamic interplays among Ago, guide, and target

Energetics of Z‑DNA Binding Protein-Mediated Helicity Reversals in DNA, RNA, and DNA–RNA Duplexes

Z-DNA binding proteins (ZBPs) specifically recognize and stabilize left-handed double helices, including Z-DNA and Z-RNA. However, the energetics of Z-form stabilization by ZBPs have never been characterized due to the technical limitations of bulk studies, resulting in an unclear understanding of the ZBP operational mechanism at the molecular level. Here, we use single-molecule fluorescence resonance energy transfer (FRET) to determine the energetics of Z-form stabilization by ZBP for DNA, RNA, and DNA–RNA duplexes, revealing that the formation of B–Z or A–Z junctions dominates the thermodynamics and kinetics of Z-form stabilization. Furthermore, in contrast to general assumptions, the Z-form is most efficiently and most rapidly formed in the DNA–RNA hybrid duplex due to the greatly reduced junction energy in the DNA–RNA hybrid