2 research outputs found
NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations
Gene
repression induced by the formation of transcriptional terminators
represents a prime example for the coupling of RNA synthesis, folding,
and regulation. In this context, mapping the changes in available
conformational space of transcription intermediates during RNA synthesis
is important to understand riboswitch function. A majority of riboswitches,
an important class of small metabolite-sensing regulatory RNAs, act
as transcriptional regulators, but the dependence of ligand binding
and the subsequent allosteric conformational switch on mRNA transcript
length has not yet been investigated. We show a strict fine-tuning
of binding and sequence-dependent alterations of conformational space
by structural analysis of all relevant transcription intermediates
at single-nucleotide resolution for the I-A type 2′dG-sensing
riboswitch from <i>Mesoplasma florum</i> by NMR spectroscopy.
Our results provide a general framework to dissect the coupling of
synthesis and folding essential for riboswitch function, revealing
the importance of metastable states for RNA-based gene regulation
Noncovalent Spin Labeling of Riboswitch RNAs To Obtain Long-Range Structural NMR Restraints
Paramagnetic relaxation enhancement
(PRE) NMR is a powerful method
to study structure, dynamics and function of proteins. Up to now,
the application of PRE NMR on RNAs is a significant challenge due
to the limited size of chemically synthesized RNA. Here, we present
a noncovalent spin labeling strategy to spin label RNAs in high yields
required for NMR studies. The approach requires the presence of a
helix segment composed of about 10 nucleotides (nt) but is not restricted
by the size of the RNA. We show successful application of this strategy
on the 2′dG sensing aptamer domain of <i>Mesoplasma florum</i> (78 nt). The aptamer domain was prepared in two fragments. A larger
fragment was obtained by biochemical means, while a short spin labeled
fragment was prepared by chemical solid-phase synthesis. The two fragments
were annealed noncovalently by hybridization. We performed NMR, cw-EPR
experiments and gel shift assays to investigate the stability of the
two-fragment complex. NMR analysis in <sup>15</sup>N-TROSY and <sup>1</sup>H,<sup>1</sup>H-NOESY spectra of both unmodified and spin
labeled aptamer domain show that the fragmented system forms a stable
hybridization product, is in structural agreement with the full length
aptamer domain and maintains its function. Together with structure
modeling, experimentally determined <sup>1</sup>H-Γ<sub>2</sub> rates are in agreement with reported crystal structure data and
show that distance restraints up to 25 Ã… can be obtained from
NMR PRE data of RNA