Site-directed insertion of photoreagents into the inner parts of RNA molecules

New methods of constructing RNA molecules with photoreagents at predetermin ed sites are described. The merits and demerits of different methods of ins erting photoreagents into RNA molecules are discussed. A combination of RNA engineering and photoactivated cross-linking methods allows identification of the nucleotide-nucleotide and nucleotide-protein contacts in ribonucleo protein complexes. The methods are successfully applied in the studies of s uch complex structures as ribosomes, spliceosomes, and functional complexes of RNA polymerase.