Biochemical Characterization of Nucleic Acid Molecules

All chemicals and antibiotics were purchased from Sigma. The primers used for primer extension analysis have been previously described (23 (link)). Enzymes were purchased from New England Biolabs or Takara, except for RNase T1 used for enzymatic probing (Life Technologies). DMS reagent used for chemical modification experiments was from Sigma. Plasmid DNA was prepared using the NucleoSpin Plasmid Mini Kit and PCR products were purified by NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). [γ-³²P] ATP (6000 Ci/mmol) and [α-³²P] UTP (800Ci/mmol) were from Izotop (Hungary). Radiolabeled RNA elution and desalting was performed using mini Quick Spin RNA Columns (Roche). Purification of RNA molecules was performed using a gel filtration chromatography column Superdex 200 10/300 GL from GE Healthcare Life Sciences attached to an ÄKTA FPLC system (Amersham Biosciences).