Advances and opportunities in RNA structure experimental determination and computational modeling

Chemical RNA Crosslinking: Mechanisms, Computational Analysis and Biological Applications

“…10e). 14 In addition to the primary sequence and secondary structure models, experimental constraints are typically incorporated into the modeling as pseudo-energy terms: predicted conformations are penalized where the constraint is not satisfied. Compared to 2D modeling, the basic rules in 3D structure modeling have not been thoroughly studied, 117 and therefore, the modeling results are typically confounded by multiple sources of error, both computational and experimental.…”

“…1) depending on nucleotide reactivity, flexibility, or accessibility, which correlate with RNA structural constraints. 14 For example, dimethyl sulfate (DMS) selectively alkylates the N1 position of adenine and N3 position of cytosine on unpaired nucleotides 15 and the 2'-OH in flexible regions can be acylated with Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) reagents. [16][17][18] Resulting reactivity profiles have been useful to improve secondary and tertiary structure modeling, [19][20][21] however, the 1D information obtained with these experiments is not necessarily definitive evidence for specific structures.…”

“…While other recent reviews have summarized these methods, 12,14,[33][34][35] a critical analysis and evaluation of the chemical mechanisms, computational tools and applications in biology have been lacking. Simultaneous consideration of these three aspects is necessary to solve increasingly challenging problems in RNA chemistry and biology.…”

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

“…13 A variety of chemical reactions have been developed and exploited that can modify RNA at certain positions (Figure 1) depending on nucleotide reactivity, flexibility, or accessibility, which correlate with RNA structural constraints. 14 For example, dimethyl sulfate (DMS) selectively alkylates the N1 position of adenine and N3 position of cytosine on unpaired nucleotides 15 and the 2′-OH in flexible regions can be acylated with Selective 2′-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) reagents. 16−18 Resulting reactivity profiles have been useful to improve secondary and tertiary structure modeling; 19−21 recently, correlated chemical probing coupled with computational deconvolution has been used to discover potential contacts and alternative conformations in relatively short RNA regions and simple conformations.…”

“…Therefore, direct measurements of RNA structures in cells have been critical for understanding RNA behavior in various biological and pathological processes . A variety of chemical reactions have been developed and exploited that can modify RNA at certain positions (Figure ) depending on nucleotide reactivity, flexibility, or accessibility, which correlate with RNA structural constraints . For example, dimethyl sulfate (DMS) selectively alkylates the N1 position of adenine and N3 position of cytosine on unpaired nucleotides and the 2′-OH in flexible regions can be acylated with Selective 2′-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) reagents. − Resulting reactivity profiles have been useful to improve secondary and tertiary structure modeling; − however, the 1D information obtained with these experiments is not necessarily definitive evidence for specific structures.…”