Modified nucleotide cofactors and the interaction of the RNAome with the proteome

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DESCRIPTION (provided by applicant): We have preliminary evidence that small RNAs of the size of siRNA and miRNAs are coupled to modified nucleotides such as coenzyme A and bis-MGD. These modifications would allow small RNAs to covalently engage with the proteome to constitute nucleic acid bar codes on these proteins. We propose to use powerful nucleic acid hybridization and selection techniques to purify the proteins covalently linked to RNA and to use mass spectroscopy to identify those linked proteins. Using RNAi of these proteins we will survey for defects in small RNA function and thus an involvement of these proteins in the functions of small RNAs. Because all of the modifications are predicted to occur at the 5' end of small RNAs, most of these modified RNAs will have been systematically missed by surveys most of which demands 5' OH or 5' phosphates on the RNAs for cloning.