Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits.
Intra-RNA cross-links were introduced into E. coli 30S ribosomal subunits by mild ultraviolet irradiation. The subunits were partially digested with cobra venom nuclease, followed in some cases by a second partial digestion with ribonuclease H in the presence of the hexanucleotide d-(CTTCCC). The cross-linked RNA complexes were separated by two-dimensional gel electrophoresis and the sites of cross-linking analysed by our published procedures. Tertiary structural cross-links in the 16S RNA were identified between positions 31 and 48, between oligonucleotides 1090-1094 and 1161-1164, and between oligonucleotides 1125-1127 and 1280-1281. The first of these imposes a rigid constraint on the relative orientations of helices 3 and 4 of the 16S secondary structure. A further tertiary cross-link (which could not be precisely localised) was found between regions 1-72 and 1020-1095, and secondary structural cross-links were identified between positions 497 and 545-548, and positions 1238-1240 and 1298.
D004546:Elapid Venoms; D004720:Endonucleases; D004722:Endoribonucleases; D004926:Escherichia coli / Q000648:ultrastructure; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides; D012335:RNA, Ribosomal / Q000528:radiation effects; D012270:Ribosomes / Q000648:ultrastructure*; D014466:Ultraviolet Rays
D004546:Elapid Venoms; D009843:Oligoribonucleotides; D012335:RNA, Ribosomal; D004720:Endonucleases; D004722:Endoribonucleases; C043004:cobra venom endonuclease