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Additional info for Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding:, Part 1
7 Cytosine analogs. The chemical modification of each analog is highlighted with a box. 8 Uridine analogs. The chemical modification of each analog is highlighted with a box. Nucleotide Analog Interference Mapping 23 20 -deoxy-20 -fluoro modifications (FAaS, FUaS), and 2 -deoxy-2 -thio modifications (SHAaS, SHGaS, SHCaS, SHUaS). 1). , 1998). Interferences observed with dNaS substitutions identify those 20 -OH groups required for function, while the interference patterns observed with OMeNaS and FNaS analogs help define the functional role of these 20 -OH groups.
1). Each of the nucleobase analogs provides specific information on the role of adenosine functional groups in RNA activity. , 1998b). PuraS and 2APaS remove the amine, leading to interference at any site where this functional group is required for activity. m6AaS replaces one proton of the amine with a methyl group. Interference with this analog indicates either that both N6 protons are required for function or that there is insufficient space in the local structure to accommodate the additional methyl group.
3. 4. 5. Quantitating sites of interference 4. 1. 2. Base modifications 5. Nucleotide Analog Interference Suppression 6. Conclusions References 9 12 15 16 18 19 21 23 25 26 27 Abstract Nucleotide analog interference mapping (NAIM) is a powerful chemogenetic technique that rapidly identifies chemical groups essential for RNA function. Using a series of phosphorothioate-tagged nucleotide analogs, each carrying different modifications of nucleobase or backbone functionalities, it is possible to simultaneously, yet individually, assess the contribution of particular functional groups to an RNA’s activity at every position within the molecule.