RNA-DNA triplexes: molecular mechanisms and functional relevance

Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.

A new flexible monochromator setup for quick scanning x-ray absorption spectroscopy

A new monochromator setup for quick scanning x-ray absorption spectroscopy in the subsecond time regime is presented. Novel driving mechanics allow changing the energy range of the acquired spectra by remote control during data acquisition for the first time, thus dramatically increasing the flexibility and convenience of this method. Completely new experiments are feasible due to the fact that time resolution, edge energy, and energy range of the acquired spectra can be changed continuously within seconds without breaking the vacuum of the monochromator vessel and even without interrupting the measurements. The advanced mechanics are explained in detail and the performance is characterized with x-ray absorption spectra of pure metal foils. The energy scale was determined by a fast and accurate angular encoder system measuring the Bragg angle of the monochromator crystal with subarcsecond resolution. The Bragg angle range covered by the oscillating crystal can currently be changed from 0 degrees to 3.0 degrees within 20 s, while the mechanics are capable to move with frequencies of up to ca. 35 Hz, leading to ca. 14 ms/spectrum time resolution. A new software package allows performing programmed scan sequences, which enable the user to measure stepwise with alternating parameters in predefined time segments. Thus, e.g., switching between edges scanned with the same energy range is possible within one in situ experiment, while also the time resolution can be varied simultaneously. This progress makes the new system extremely user friendly and efficient to use for time resolved x-ray absorption spectroscopy at synchrotron radiation beamlines.

Novel angular encoder for a quick-extended x-ray absorption fine structure monochromator

New concepts for time-resolved x-ray absorption spectroscopy using the quick-extended x-ray absorption fine structure (QEXAFS) method are presented. QEXAFS is a powerful tool to gain structural information about, e.g., fast chemical reactions or phase transitions on a subsecond scale. This can be achieved with a monochromator design that employs a channel-cut crystal on a cam driven tilt table for rapid angular oscillations of the Bragg angle. A new angular encoder system and a new data acquisition were described and characterized that were applied to a QEXAFS monochromator to get spectra with a directly measured accurate energy scale. New electronics were designed to allow a fast acquisition of the Bragg angle values and the absorption data during the measurements simultaneously.