Secondary Structure of the 5′ End of Bacteriophage MS2 RNA

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Abstract
To refine the secondary structure model of the 5'' end of the bacteriophage MS2 genome, 32P-labeled MS2 RNA was partially digested with T1 RNase or with Cm-RNase and the 5''-end fragment was isolated, renatured and submitted to treatment with methoxyamine or kethoxal. The resulting modified RNA was digested with T1 RNase and the products were separated by minifingerprinting. Methoxyamine-induced modification of exposed cytidines was detected by differential mobility of modified oligonucleotides, while kethoxal-induced alteration of exposed guanosines was monitored by resistance to T1 RNase digestion. The positions of the modified residues are discussed in terms of an improved secondary structure model proposed for the 5'' end of the viral RNA. The structure itself is discussed in relation to sequence conservation and biological function.