Chemical probing analysis of glyQS T-box from S. pneumoniae. (A) Α 6% PAGE/8 M urea denaturing gel showing primer extension analysis of modified with DMS or KE (+) and unmodified (−) S. pneumoniae glyQS T-box transcript (20 pmol). The triangles on the left correspond to DMS modifications, whereas the hexagons on the right identify KE modifications, according to the sequencing tracks (lanes T, G, A, and C). (B) Predicted secondary structure of S. pneumoniae glyQS T-box. Spneum_PE_3 primer (in green) was used for Stem I primer extension analysis and Spneum_PE_5 (in blue) for the analysis of the whole T-box region. Highly conserved (100%) and moderately conserved (66%) nucleotides are indicated with orange and yellow circles, respectively. The specifier codon is indicated with red letters. The trinucleotide at the T-box bulge that interacts with the 3′ CCA of the tRNA is indicated with red circles.
