Secondary Structure Analysis of an RNA Interacting with Guanine-rich Sequence

摘要

RNA structure has sometimes been analyzed by biophysical method such as NMR (nuclear magnetic resonance), which has not been popular because the RNA with small size only is available and a large amount of RNA is required for the structural analysis with NMR. So biochemical methods using structure specific enzymes and chemicals have widely been used for the analysis of RNA structure. Enzymes which have mainly been used for probing RNA structure in solution, are double-strand-specific RNase V1, single-strand-specific nuclease S1 and RNase T1 which has the specificity for a guanine in single strand region. Chemicals used for probing RNA structure, are DMS (dimethyl sulfate) which methylates position N-1 of adenines and, to a lower extent, N-3 of cytosines, CMCT (l-cyclohexyl-3-(2-morpho-linoethyl)carbodiimide metho-p-toluene sulfonate) which modifies position N-3 of uridine and, to a weaker degree, N-1 of guanines and kethoxal (3-ethoxy-l,l-dihydroxy-2-buta-none) which modifies position N-l and N-2 of guanine in the single strand.