Artificial DNA cutters for DNA manipulation and genome engineering

This tutorial review provides recent developments in artificial cutters for site-selective scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for molecular biology and biotechnology, since their site-selectivity of scission is much higher than that of naturally occurring restriction enzymes and also their scission site is freely chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an artificial restriction DNA cutter, prepared from Ce(iv)/EDTA and pseudo-complementary peptide nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and scission specificity are determined simply in terms of the Watson-Crick rule so that even the whole genome of human beings was selectively cut at one predetermined site. Consistently, homologous recombination in human cells was successfully promoted by this tool. For the purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also briefly described. The potential applications of these cutters and their future aspects are discussed.     

Electron transport and shell structures of single InAs quantum dots probed by nanogap electrodes

We have investigated electron transport and electron filling in single InAs quantum dots (QDs) using nanogap electrodes. Elliptic InAs QDs with diameter of 60/80 nm exhibited clear shell filling up to 12 electrons. Shell-dependent charging energies and level quantization energies for the s, p, and d states were determined from the addition energy spectra. Furthermore, it is found that the charging energies and the tunneling conductances strongly depend on the shell, reflecting that the electron wave functions for higher shells are more extended in space.     

The staining efficiency of cyanine dyes for single‐stranded DNA is enormously dependent on nucleotide composition

The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson‐Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.     

Efficient Preparation of Large‐Sized Rings of Single‐Stranded DNA through One‐Pot Ligation of Multiple Fragments

Circular single‐stranded DNA (c‐ssDNA) has significant applications in DNA detection, the development of nucleic acid medicine, and DNA nanotechnology because it shows highly unique features in mobility, dynamics, and topology. However, in most cases, the efficiency of c‐ssDNA preparation is very low because polymeric byproducts are easily formed due to intermolecular reaction. Herein, we report a one‐pot ligation method to efficiently prepare large c‐ssDNA. By ligating several short fragments of linear single‐stranded DNA (l‐ssDNA) in one‐pot by using T4 DNA ligase, longer l‐ssDNAs intermediates are formed and then rapidly consumed by the cyclization. Since the intramolecular cyclization reaction is much faster than intermolecular polymerization, the formation of polymeric products is suppressed and the dominance of intramolecular cyclization is promoted. With this simple approach, large‐sized single‐stranded c‐ssDNAs (e.g., 200‐nt) were successfully synthesized in high selectivity and yield.     

Two-photon photochromism of two simple chromene derivatives

Two kinds of typical chromene derivatives, 5a,9-dimethyl-5aH-benzo[b]chromene (1) and 7a,11-dimethyl-7aH-dibenzo[b,f]chromene (2), were synthesized to understand the relationship between molecular structures and two-photon photochromism for chromene derivatives. The photochromic performances of 1 and 2 in hexane were investigated by measuring ultraviolet (UV)–visible absorption and ¹H nuclear magnetic resonance spectral changes upon UV irradiation. The results indicate that 1 showed the two-photon photochromic reaction, whereas the main photochemical reaction of 2 was the isomerization between the open-E and open-Z isomers. Density functional theory (DFT) calculations suggest that these different photochromic performances are attributed to the differences in relative stabilities of closed, open-Z and open-E isomers for 1 and 2. Combined with DFT calculations for 12aH-12a-methyl-naphtho[3,2]chromene (3), the most typical chromene derivative well exhibiting two-photon photochromism, we conclude that chromene derivatives show the best two-photon photochromic performances only if closed isomers are more stable than open-Z and open-E isomers.     

Breakdown of the quantum Hall effect due to electron heating

The breakdown of the Quantum Hall effect observed on GaAs-AlGaAs samples is quantitatively explained in terms of peculiar electron-heating characteristic to the Quantum Hall regime. The current instability originates from an S-shaped current-voltage characteristic. Further, exponential dependence of the dissipative conductivity on the electric field, observed in the lower field range, is interpreted as a consequence of the finite size of the wave function of localized states in the presence of potential gradient.     

Synthesis and optical properties of coated nanoparticle composites

The synthesis of coated nanoparticles is a new direction in engineering, specifically in the study of physical properties of materials. We examine semiconductor coated semiconductor particles, CdS/PbS, and metal coated particles, Au₂S/Au, and the theoretical basis for their unique properties. Coated self-assembled nanoparticles are also studied and recent progress is reported.