Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes

Thermal denaturation is a common technique in the biophysical study of nucleic acids. These experiments are typically performed by monitoring the increase in absorbance (hyperchromism) of a sample at 260nm with temperature (Mergny & Lacroix, 2003; Puglisi & Tinoco, 1989). This wavelength is chosen as nucleic acids of mixed sequence typically exhibit their maximum absorbance here. Exceptions exist, however, some noncanonical nucleic acid structures exhibit differing spectral changes with temperature, resulting in other wavelengths being convenient reporters of secondary structure. In the case of nucleic acids that bind visible light-absorbing ligands, such as fluorogenic aptamers, another wavelength can be a convenient reporter of secondary structure stability and RNA-ligand recognition. As it can be difficult, if not impossible, to know which wavelength to employ a priori, we have developed a system for obtaining the full UV-visible spectrum of a sample at each wavelength, allowing for the subsequent extraction of the absorbance-temperature profile at the desired wavelength. Here, we describe the apparatus and software used to do so. We also describe another technique for the use of a qPCR instrument for measuring secondary structure stability of fluorescent nucleic acid-ligand complexes.

A comprehensive review of anaerobic digestion of organic solid wastes in relation to microbial community and enhancement process

Organic solid wastes (OSWs) should be regarded as valuable resources rather than dead-end landfill waste that causes public health and odor concerns. Anaerobic digestion (AD) is an ideal approach for managing organic solid waste issues and involves using a group of anaerobic microorganisms to transform OSWs into useful products. In this review, over 100 publications related to AD of OSWs have been compiled, discussed, and analyzed. A comprehensive analysis of the environmental and safety impacts of AD, its key environmental factors, co-digestion, and pretreatment, as well as the AD of OSWs by various anaerobic microbes uncovered by high throughput sequencing-based approaches, is presented. The purpose of this review is to provide an outline of the current knowledge of AD processes from a multi-angle perspective. A comprehensive understanding of AD of OSWs and genome-enabled biology development could be helpful for providing up-to-date knowledge of AD, developing it, overcoming its drawbacks and, ultimately, improving global waste control for more efficient environmental management. © 2018 Society of Chemical Industry.