Webb16 okt. 2012 · Chemical and enzymatic footprinting experiments, such as shape (selective 2′-hydroxyl acylation analyzed by primer extension), yield important information about RNA secondary structure. Indeed, since the -hydroxyl is reactive at flexible (loop) regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA … Webb10 okt. 2024 · Objective: Childhood trauma is linked to the dysregulation of physiological responses to stress, particularly lower cardiovascular reactivity (CVR) to acute stress. The mechanisms that explain this association, however, are not yet fully understood. Method: Using secondary data from the Midlife in the United States (MIDUS) Biomarker Project (N …
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Webb1 jan. 2024 · SHAPE was designed as a method providing a sequence-independent and time-effective analysis of RNAs with single nucleotide resolution. 7, 8 Chemically, 2′-hydroxyl (2′-OH) groups are modified by electrophilic molecules (SHAPE reagents) during the acylation reaction, resulting in adducts that are subsequently detected as stops in … WebbSHAPE reactivities are converted into pseudo free energy contributions by using the approach from Deigan et al., 2009: ΔG SHAPE ( i) = slope · ln [Reactivity ( i) + 1] + … great lake tasmania accommodation
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Webb6 dec. 2024 · To facilitate understanding of the relationship between nucleotide flexibility, SHAPE reactivity, and RNA 3D structure, we developed an analytical 3D Structure-SHAPE Relationship (3DSSR) method and a predictive convolutional neural network (CNN) model that predict the SHAPE reactivity from RNA 3D structures. Webb28 feb. 2024 · Here, SHAPE(i) refers to the SHAPE reactivity score at position i of the sequence. The slope and intercept parameters must be determined empirically [ 44 ] for … Webb9 sep. 2024 · SHAPE reactivity can be incorporated as restraints in RNA modeling algorithms to generate RNA secondary structure models with high accuracies ( Figure 1B, C) ( 37, 59, 60) and to detect regions that form well-determined structures or that are likely to sample multiple conformations ( Figure 1C ). great lake tasmania fishing