Precise localization of several covalent RNA‐RNA cross‐link in Escherichia coli 16S RNA

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Abstract
The RNA-RNA cross-linking reagent N-acetyl-N''-(p-glyoxylyl-benzoyl)cystamine, which reacts via its glyoxal residue with guanines not involved in G .cntdot. C base pairs, was used to introduce reversible RNA-RNA cross-links into E. coli 16S rRNA. A 2-dimensional gel method was devised for the separation of the cross-linked oligonucleotides and the precise location of guanines involved in 4 of these cross-links was determined by sequencing the oligonucleotides. One cross-link involves guanosines 1315 and 1360 situated in 2 hairpin end loops of domain III. The other cross-links involve pairs of guanosine situated with the same hairpin end loops.