Does 5S RNA from E. coli have a pseudoknotted structure?
Chemical modification and limited enzymatic hydrolysis on isolated E. coli 5S RNA have provided informations on the secondary- and tertiary structure compatible with pseudoknotted structures for the A- and B-conformers of the molecule. Changes in the accessibility and reactivity of nucleotides in loop C and at the stem of helix IV in two different 5S RNA conformers are highly suggestive for interactions between bases C35 to C37 with G105 to G107 for the A-form and C38 to U40 and A94 to G96 with additional interactions of C35, C37 with G98 and G100 for the B-form. In both cases the molecules are folded forming pseudoknots and two quasi--continuous double stranded helices with coaxial stacking. The two structures are in perfect agreement with the biochemical data concerning the stability of the molecule and the chemical reactivities of individual nucleotides of the 5S RNA A- and B-conformers.
D001483:Base Sequence; D004720:Endonucleases; D004926:Escherichia coli / Q000032:analysis*; D007202:Indicators and Reagents; D008958:Models, Molecular; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000302:isolation & purification; D012335:RNA, Ribosomal / Q000302:isolation & purification; D006163:Ribonuclease T1; D015719:Single-Strand Specific DNA and RNA Endonucleases
D007202:Indicators and Reagents; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D004720:Endonucleases; D006163:Ribonuclease T1; D015719:Single-Strand Specific DNA and RNA Endonucleases