Huangpruitt4909

Fourier transform infrared (FTIR) spectroscopy has been widely used for the analysis of both protein and nucleic acid secondary structure. This is one of the vibration spectroscopy methods that are extremely sensitive to any change in molecular structure. While numerous reports describe how to proceed to analyze protein and deoxyribonucleic acid (DNA) structures using FTIR, reports related to the analyses of ribonucleic acids (RNAs) are few. Nevertheless, RNAs are versatile molecules involved in a multitude of roles in the cell. In this chapter, we present applications of FTIR for the structural analysis of RNA, including the analysis of helical parameters and noncanonical base pairing, often found in RNA. The effect of temperature pretreatment, which has a great impact on RNA folding, will also be discussed.Native electrospray ionization mass spectrometry (native ESI-MS) is a powerful tool to investigate non-covalent biomolecular interactions. It has been widely used to study protein complexes, but only few examples are described for the analysis of complexes involving RNA-RNA interactions. Here, we provide a detailed protocol for native ESI-MS analysis of RNA complexes. As an example, we present the analysis of the HIV-1 genomic RNA dimerization initiation site (DIS) extended duplex dimer bound to the aminoglycoside antibiotic lividomycin.RNA modification mapping by mass spectrometry (MS) is based on the use of specific ribonucleases (RNases) that generate short oligonucleotide digestion products which are further separated by nano-liquid chromatography and analyzed by MS and MS/MS. Recent developments in MS instrumentation allow the possibility to deeply explore posttranscriptional modifications. Notably, development of nano-liquid chromatography and nano-electrospray drastically increases the detection sensitivity and allows the identification and sequencing of RNA digested fragments separated and extracted from two-dimensional polyacrylamide gels, as long as the mapping and characterization of ribonucleotide modifications.We have previously described (Geffroy et al. Methods Mol Biol 166525-40, 2018) how to unfold (or fold) a single RNA molecule under force using a dual-beam optical trap setup. In this chapter, we complementarily describe how to analyze the corresponding data and how to interpret it in terms of RNA three-dimensional structure. As with all single-molecule methods, single RNA molecule force data often exhibit several discrete states where state-to-state transitions are blurred in a noisy signal. In order to cope with this limitation, we have implemented a novel strategy to analyze the data, which uses a hidden Markov modeling procedure. A representative example of such an analysis is presented.Surface plasmon resonance (SPR)-based instruments have become gold-standard tools for investigating molecular interactions involving macromolecules. The major advantage is that the measured signal is sensitive to changes in mass. Therefore, all kinds of complexes can be analyzed including those with compounds as small as cations. CHQ inhibitor SPR is mainly used to determine the dissociation equilibrium constant and the binding rates of a reaction if slow enough. SPR is well suited for analysis molecular interactions with nucleic acids because these negatively charged macromolecules do not have a tendency to stick to the sensor chip surface as some proteins can do. To illustrate the use of SPR with RNA molecules, we describe methods that we used for monitoring the interaction between the protein Rop from E. coli and two RNA-RNA loop-loop complexes. One is derived from the natural target of Rop, RNAI-RNAII. The other one is an RNA-RNA complex formed between a shortened version of the TAR element of HIV-1 and a structured RNA, TAR* rationally designed to interact with TAR through loop-loop interactions. These methods can be easily adapted to other complexes involving RNA molecules and to other SPR instruments.Data from fluorescence-based methods that measure in vivo hybridization efficacy of unique RNA regions can be used to infer regulatory activity and to identify novel RNA RNA interactions. Here, we document the step-by-step analysis of fluorescence data collected using an in vivo regional RNA structural sensing system (iRS3) for the purpose of identifying potential functional sites that are likely to be involved in regulatory interactions. We also detail a step-by-step protocol that couples this in vivo accessibility data with computational mRNA target predictions to inform the selection of potentially true targets from long lists of thermodynamic predictions.Dynamic light scattering represents an accurate, robust, and reliable technique to analyze molecule size in solution and monitor their interactions in real time. Here, we describe how to analyze by DLS an RNA-protein interaction. In our frame, we studied complexes formed between RNA fragments derived from the genome of HIV-1 in association with the viral precursor Pr55Gag. These interactions are crucial for the specific selection of the viral genomic RNA (gRNA) from the bulk of the viral spliced and cellular RNAs. This chapter displays how DLS allows to characterize the interactions that regulate the early steps of viral assembly.Colocalization single-molecule spectroscopy (CoSMoS) allows studying RNA-protein complexes in the full complexity of their cellular environment at single-molecule resolution. Conventionally, the interaction between a single RNA species and multiple proteins is monitored in real time. However, comparing interactions of the same proteins with different RNA species in the same cell extract promises unique insights into RNA biology. Here, we describe an approach to monitor multiple RNA species simultaneously to enable direct comparison. This approach represents a technological development to avoid conventional inter-experiment comparisons.The SNAPf-tag is a chemical tag that allows rapid and highly specific covalent labeling of proteins even in the full complexity of the cellular environment. The SNAPf-tag has been instrumental to study native RNA-protein complexes at single-molecule resolution in their cellular environment as efficient labeling of the RNAs and proteins of interest is essential for this colocalization single-molecule spectroscopy (CoSMoS) technique. However, removal of excessive benzylguanine dye after the labeling reaction has remained challenging. Here, we describe a strategy to remove excessive benzylguanine dye using SNAPf-tag coated beads as sponges.Imaging fluorescently labeled biomolecules on a single-molecule level is a well-established technique to follow intra- and intermolecular processes in time, usually hidden in the ensemble average. The classical approach comprises surface immobilization of the molecule of interest, which increases the risk of restricting the natural behavior due to surface interactions. Encapsulation of such biomolecules into surface-tethered phospholipid vesicles enables to follow one molecule at a time, freely diffusing and without disturbing surface interactions. Further, the encapsulation allows to keep reaction partners (reactants and products) in close proximity and enables higher temperatures otherwise leading to desorption of the direct immobilized biomolecules.Here, we describe a detailed protocol for the encapsulation of a catalytically active RNA starting from surface passivation over RNA encapsulation to data evaluation of single-molecule FRET experiments in TIRF microscopy. We present an optimized procedure that preserves RNA functionality and applies to investigations of, e.g., large ribozymes and RNAs, where direct immobilization is structurally not possible.The Work and Social Adjustment Scale (WSAS) is a brief global measure of functional impairment that is widely used in adult health. We have adapted the WSAS for its use in youth, the WSAS-Youth version (WSAS-Y) and WSAS-Parent version (WSAS-P). This study evaluated the psychometric properties of the scale. The internal consistency, factor structure, convergent and divergent validity, test-retest reliability and sensitivity to change of the WSAS-Y/P were studied in 525 children and adolescents with obsessive-compulsive disorder and related disorders receiving treatment. The internal consistency of the WSAS-Y/P was excellent across diagnostic groups and time-points. link2 Exploratory factor analysis extracted a single-factor of functional impairment, explaining in excess of 85% of the variance. link3 The test-retest reliability was adequate. The WSAS-Y/P correlated more strongly with other measures of functional impairment than with measures of symptom severity, indicating good convergent/divergent validity. Finally, the WSAS-Y/P was highly sensitive to change after treatment.PURPOSE OF REVIEW Recent advances the genomic profiling of patients with Waldenström macroglobulinemia (WM) have led to the identification of novel therapeutic targets in these patients. In this review, we cover the current standard of care and the recently evaluated novel approaches with high potential to be incorporated in the therapeutic armamentarium against WM. RECENT FINDINGS The MYD88L265P mutation is the most common genomic abnormality in WM, and is encountered in 80-95% of patients, making it an important target for drug development. The success of the first-generation Bruton tyrosine kinase (BTK) inhibitor, ibrutinib, has generated tremendous interest in the study of more selective and potent BTK inhibitors. Additionally, the identification of CXCR4WHIM mutations in up to approximately 40% of patients with WM has fueled research regarding their implication on systemic therapy in WM. In a rapidly advancing field of targeted therapies, the treatment options for patients with WM are expanding as researchers continue to uncover and harness the survival pathways active in this hematologic malignancy.This study investigated whether maternal perceptions of child body mass status would predict child body mass index (BMI) z-score via two sets of sequential mediators (1) four maternal practices promoting child energy expenditure and (2) children's energy expenditure behaviors. The data of N = 729 mother-child dyads were collected at baseline [T1; n = 495 at 7- to 8-month follow-up (T2)]. Mothers reported perceptions of child body mass status and maternal practices (T1); children reported sedentary screen use and physical activity (T1, T2). Child body mass was assessed objectively (T1, T2). Higher stimulation to be active (T1) was related to a lower child BMI z-score (T2) via higher levels of child physical activity (T2). Higher levels of monitoring of screen use (T1) were associated with higher child BMI z-score (T2) via lower levels of child physical activity (T2). Encouraging parents to stimulate their children to be active may be beneficial for children's weight maintenance.This mini-review covers 25 fully functionalized facial calix[4]arene-based symmetrical and conical cyclic tetramers with significant (comparable to established therapeutic agents) anticancer and anti-infective activities. The main role of the calixarene scaffold in these calix[4]arene-based active pharmaceutical ingredients (calix[4]API-s) is to replicate embedded phenolic units in the cyclic tetramers. So, probably owing to the multivalency, facial, conical structures of calix[4]API-s and synergistic effect of their four replicated units, they can be considered as effective bioactive agents.