No abstract

R-loops are functional structures in chromatin comprising one single-stranded DNA and a DNA:RNA hybrid. Here, we report ssDRIP-seq, a single-strand DNA ligation-based library preparation technique for genome-wide identification of R-loops. When applied in Arabidopsis, ssDRIP-seq exhibits high efficiency, low bias and strand specificity. We found that Arabidopsis R-loops are enriched by both AT and GC skews, and are formed in the sense and antisense orientations. R-loops are strongly enriched in gene promoters and gene bodies, and are highly associated with noncoding RNA and repetitive genomic regions. Furthermore, R-loops are negatively correlated with CG DNA hypermethylation, and are prevalent in regions with multiple chromatin modifications, showing strong correlations with the activated and repressed gene loci. Our analyses indicate that R-loops are common features in the Arabidopsis genome and suggest that the R-loops play diverse roles in genome organization and gene regulation, thereby providing insights into plant nuclear genome formation and function.

Photoconductivity in individual semiconducting single-wall carbon nanotubes was investigated using a confocal scanning optical microscope. The magnitude of the photocurrent was found to increase linearly with the laser intensity, and to be maximum for parallel orientation between the light polarization and the tube axis. Larger currents were obtained upon illuminating the tubes at 514.5 nm in comparison to those at 647.1 nm, consistent with the semiconducting tubes having a resonant absorption energy at the former wavelength. Moreover, the determination of the photoresponse as a function of position along single nanotubes has proven to be a useful tool to monitor local electronic structure effects.

Single-walled carbon nanotubes (SWCNTs), due to their excellent structural and electronic properties, [1] have emerged as an attractive material for various applications including molecular electronics [2,3] and field emission devices. [4] A variety of devices have been realized with SWCNTs, such as single electron transistors (SETs) operating at very low temperatures, [5] field-effect transistors (FETs), [6] chemical sensors, [7] and logic circuits. [8] Besides the use of pristine SWCNTs, it has been shown that SWCNTs can be chemically modified, [9±11] a process which, for example, allowed the fabrication of SETs [12] and memory devices [13] operating at room temperature. Electrochemistry is a well-suited tool for controlled modification of SWCNTs. [14] This approach has been followed using both reductive and oxidative coupling schemes, resulting in thin layers of molecules around the SWCNTs.[15] However, little is known about the nature of chemical coupling between the grafted layers and the carbon framework of an individual nanotube, and also about the effect of chemical modification on its electronic properties. Towards this objective, we report in this communication the detailed investigation of individual electrochemically modified SWCNTs. The characterization methods include electrical transport measurements and confocal Raman spectroscopy, both of which can address selected single SWCNTs or bundles. While transport measurements give information about the electronic properties of an individual SWCNT, confocal Raman spectroscopy on individual nanotubes [16] can detect changes of the vibrational properties and hence the disturbances in the lattice structure of an isolated nanotube. These studies were performed separately on metallic and semiconducting SWCNTs, in both cases comparing the effect of the oxidative and reductive coupling schemes. The electrochemical modification (ECM) of individual SWCNTs was performed with 4-aminobenzylamine (A) using the oxidative scheme and with 4-nitrobenzene diazonium tetrafluoroborate (B) employing the reductive scheme. The transport measurements were carried out on the same SWCNTs before and after ECM. Before ECM, the gate dependence of the 2-probe resistance was used to identify a given individual SWCNT as metallic or semiconducting. At room temperature, the unmodified metallic SWCNTs showed a 2-probe resistance in the range 10±25 kX, while the resistance of the semiconducting nanotubes was found to vary between 200 kX and 100 MX among different samples. As control experiments, ECM was performed on selected SWCNTs in the pure electrolyte solution in the absence of A or B. In both cases, neither an increase in height nor a change in the resistance could be detected after modification. Figure 1 summarizes a typical observation made on metallic SWCNTs after oxidative ECM. The SWCNTs were investigated by atomic force microscopy (AFM) before and after ECM to determine the thickness of the grafted layers. The AFM image in Figure 1a shows an individual metallic nanotube contact...