Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Combining Biophysical Methods for Structure-Function Analyses of RNA in Solution

RNA-level regulation by riboswitches relies on the specific binding of small metabolites to the aptamer domain to trigger substantial conformational changes that affect transcription or translation. Although several biophysical methods have been employed to study such RNAs, the utility of any one single method is limited. Hybrid approaches, therefore, are essential to better characterize these intrinsically dynamic molecules and elucidate their regulatory mechanisms driven by ligand-induced conformational changes. This chapter outlines procedures for biochemical and biophysical characterization of RNA that employs a combination of solution-based methods: isothermal titration calorimetry (ITC), small-angle X-ray scattering (SAXS), and atomic force microscopy (AFM). Collectively, these tools provide a semi-quantitative assessment of the thermodynamics associated with ligand binding and subsequent conformational changes.

Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs

Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.

Facile Fabrication of High-Performance Thin Film Nanocomposite Desalination Membranes Imbedded with Alkyl Group-Capped Silica Nanoparticles

The advantages of thin film nanocomposite reverse osmosis (TFN-RO) membranes have been demonstrated by numerous studies within the last decade. This study proposes a facile and novel method to tune the microscale and nanoscale structures, which has good potential to fabricate high-performance TFN-RO membranes. This method involves the addition of alkyl capped silica nanoparticles (alkyl-silica NPs) into the organic phase during interfacial polymerization (IP). We discovered for the first time that the high concentration alkyl-silica NPs in organic solvent isopar-G can limit the diffusion of MPD molecules at the interface, therefore shaping the intrinsic thickness and microstructures of the PA layer. Moreover, the alkyl group modification greatly reduces the NPs agglomeration and increases the compatibility between the NPs and the PA matrix. We further demonstrate that the doping of alkyl-silica NPs impacts the performance of the TFN-RO membrane by affecting intrinsic thickness, higher surface area, hydrophobic plugging effect, and higher surface charge by a series of characterization. At brackish water desalination conditions (2000 ppm NaCl, 1.55 MPa), the optimal brackish water flux was 55.3 L/m²∙h, and the rejection was maintained at 99.6%, or even exceeded this baseline. At seawater desalination conditions (32,000 ppm NaCl, 5.5 MPa), the optimized seawater flux reached 67.7 L/m²∙h, and the rejection was sustained at 99.4%. Moreover, the boron rejection was elevated by 11%, which benefits from a hydrophobic plugging effect of the alkyl groups.

Microscopy and Spectroscopy Techniques for Characterization of Polymeric Membranes

Polymeric membrane is a proven technology for water purification and wastewater treatment. The membrane is also commercialized for gas separation, mainly for carbon dioxide removal and hydrogen recovery. Characterization techniques are excellent tools for exploring the membrane structure and the chemical properties. This information can be then optimized to improve the membrane for better performance. In this paper, characterization techniques for studying the physical structure such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM) are discussed. Techniques for investigating the crystal structure such as X-ray diffraction (XRD), small-angle X-ray scattering (SAXS), and wide-angle X-ray scattering (WAXS) are also considered. Other tools for determining the functional groups such Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and nuclear magnetic resonance (NMR) are reviewed. Methods for determining the elemental composition such as energy-dispersion X-ray spectroscopy (EDS), X-ray fluorescent (XRF), and X-ray photoelectron spectroscopy (XPS) are explored. The paper also gives general guidelines for sample preparation and data interpretation for each characterization technique.