Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot

Mg 2+ -dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules

“…One such case is that more cations bind the folded form to stabilize the RNA structure with closer proximity of negative phosphates (22). Assuming that the folded junction can take additional nЈ Mg 2ϩ ions, the reaction scheme should allow a transition between F (n) and F (nϩnЈ) and k o,obs becomes…”

Translational Repression of the Escherichia coli α Operon mRNA

“…Active and Inactive Forms of the mRNA-In previous work, we have shown that the ␣ mRNA pseudoknot folds into two electrophoretically distinct conformations (or sets of conformations), termed slow and fast (11). They are detected in vitro over a wide range of salt and temperature conditions, and they are detected at very short times after transcription with T7 RNA polymerase; 2 we therefore conclude that the conformers are not artifacts of the RNA preparation or renaturation procedures and are potentially relevant to the translational repression mechanism.…”

“…Plasmids for RNA Transcription-Plasmids for transcription of an RNA fragment corresponding to nucleotides 16 -127 of the transcript from the ␣ operon promoter, called 127 RNA, and for transcription of L11-Cys76 mRNA have been described (11,12). A PvuII-HindIII DNA restriction fragment containing a T7 RNA polymerase promoter sequence followed by ␣ operon sequence Ϫ16 to ϩ139 was prepared from a previously described pT7-1 derivative (4) and inserted into pUC19 cut with HindIII and SmaI.…”

“…␣ mRNA fragments and their derivatives were renatured for 8 min at 65°C in buffer containing 350 mM KCl, 10 mM MOPS 1 (pH 7.0) followed by 22 min at 42°C in the same buffer with or without 40 mM MgCl 2 (11). RNA encoding L11-C76 was renatured in buffer A at room temperature, as the RNA precipitated when renaturation conditions for ␣ mRNA were used.…”

Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA

“…36,37 Only the U to I transition was assumed to be cooperative with respect to Mg 2þ . Because the ions are responding to changes in the electrostatic field of the RNA rather than mass action, 38 the Hill constant reflects the relative stabilization of U, I and N by Mg 2þ , rather than the precise number of excess magnesium ions associated with the folded RNA.…”