RNA-ligand interactions

Volume 317. RNA-Ligand Interactions (Part A Structural Biology Methods) Edited by Daniel W. Celander and John N. Abelson... 

The well-resolved imino proton resonances from base-paired uracil and guanine resonances serve as powerful probes to characterize RNA-ligand interaction by NMR. The chemical shift of imino proton resonances is responsive to perturbations in the local chemical environment that result from RNA conformational... 

Figure 13 Relaxation parameters of protein-RNA-ligand interactions of the L11 system. Free L11 (blue), L11, and RNA (red) and L11, RNA, and Thiostrepton (green). RNA binding shows effects on all parameters, pronounced for certain residues in the C-terminal domain (arrows), whereas the additional Thiostrepton binding leads to an increase in Ti of the N-terminal domain. Binding of RNA locks the two domains in a fixed orientation relative to each other and strongly restricts the motion of the C-terminal domain, Thiostrepton then locks the N-terminal in place. See color insert.

Chow CS, Bogdan IM. A structural basis for RNA-ligand interactions. Chem. Rev. 1997 97 1489-1513. 

Site-specifically modified RNAs have been used in many applications to examine RNA stmcture-function relationships, RNA-protein interactions, RNA-ligand interactions, and RNA-catalysis mechanisms. Some earlier studies demonstrated the use of synthetic oligonucleotides to probe the roles of specific functional groups and detailed mechanisms in ribozyme catalysis (55). The synthesis of nucleoside analogs allows for a full-range of chemical diversity (e.g., inductive effects, space-filling capacity, etc.) to be explored, such that quantitative stmcture activity relationships can be determined for RNA enzymes and other biologically important RNAs (56). 

Pfeffer, P., Gohlke, H. DrugScoreRNA-knowledge-based scoring function to predict RNA-ligand interactions. J. Chem. Inf. Model 2007, 47(5), 1868. 

Keyvrords CW EPR spectroscopy Dynamics ENDOR ESEEM Hyperfine spectroscopy In-cell EPR Nucleic acids PELDOR RNA-ligand interactions RNA-protein interactions Stmcture... 

Computational techniques such as SAR are now addressing the dearth of information on DNA or RNA-ligand interactions in qualitative and quantitative ways. When the structure of the receptor is unknown, SARs can be derived empirically a... 

The aim of this article is to provide an overview of the range of methodologies that can be used to build qualitative and quantitative models of DNA or RNA-ligand interactions. The construction of such models may resort to computational methods that go beyond 3D-SAR and 3E>-QSAR, and recent reviews of these techniques are available (see Free Energy Calculations Methods and Applications Free Energy Per-turbation Calculations Free Energy Simulations and Solvation Modeling). ... 

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