Figure 4. Chemical probing of the trans Watson-Crick GU base pair.

Various cis-acting mutants were folded in the presence of MgCl₂ and then probed in either the absence or presence of either kethoxal (A) or CMCT (B). The RNA samples were reverse transcribed and the reactions then fractionated on 8% denaturing PAGE gels. The accessibility of either G (kethoxal and CMCT) or U (CMCT) was visualized by the presence of bands that downshift one nucleotide as compared to either a G or a U ladder produced using an untreated wild-type ribozyme with either dideoxy ATP (ddA) or dideoxy CTP (ddC) during the reverse transcription step. The positions of xylene cyanol dye (XC) and of both the G and the U nucleotides of the ribozymes are indicated on both gels.