Structure of helix 18. (A) In vivo DMS modification of helix 18 (H18) of rRNA. The 4TU labeling was performed for 2, 4, and 6 min. Lane C is an additional control with 6 min of 4TU labeling without DMS addition. The results from one experiment are visualized on two autoradiograms. Primer 102 (complementary to 18S H21) was used for primer extension analyses of the H18 region. (B) The graphs present the intensity of bands in each lane: newly synthesized RNA: (red line) 2 min; (green line) 4 min; (blue line) 6 min of 4TU labeling and total RNA (black line on the lower graph). (C) Secondary structure model of H18. Nucleotides involved in the pseudoknot are boxed. DMS modified positions, C554, A567, A570, and A579, which are discussed in the text, are marked on the structure. (D) The same positions are indicated on the tertiary structure of H18 (Ben-Shem et al. 2010). (E) Structure of the pseudoknot with C554 highlighted in blue, which takes part in the stacking interaction. The PyMol program was used to present tertiary structure of H18 (data from NDB ID: NA0650) (Ben-Shem et al. 2010, 2011).
