RNA quaternary structure and global symmetry

Jones, Christopher P.; Ferré-D′Amaré, A.R.

doi:10.1016/j.tibs.2015.02.004

Cited by 44 publications

(32 citation statements)

References 88 publications

(149 reference statements)

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“…This is because these six nucleotides adopt distinctly different conformations in the two protomers of identical sequence. Thus, the RNA in the Corn-DFHO complex exhibits quasisymmetry 16 , 25 , 26 .…”

Section: Resultsmentioning

confidence: 99%

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

et al. 2017

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Corn, a 28-nucleotide RNA, induces yellow fluorescence of its cognate ligand (3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime, DFHO) by >1000-fold. It was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, where six unpaired adenosines break overall 2-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its inter-protomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could form the basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful in analyzing RNA co-expression or association, or in designing self-assembling RNA nanostructures.

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Section: Resultsmentioning

confidence: 99%

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

et al. 2017

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“…First, the overall structure exhibits an internal pseudo‐two‐fold symmetry of the RNA, and second, the RNA requires two c‐di‐AMP molecules for a stable assembly (Fig. ) (Gao and Serganov, ; Jones and Ferré‐D'Amaré, 2014; 2015; Ren and Patel, ). The structure is composed of well‐defined structural elements, namely, two similar three‐way junction elements containing three to four helices each, depending on the organism.…”

Section: C‐di‐amp‐responsive Riboswitchesmentioning

confidence: 99%

A jack of all trades: the multiple roles of the unique essential second messenger cyclic di‐AMP

Commichau

Dickmanns

Gundlach

et al. 2015

Molecular Microbiology

128

114

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SummarySecond messengers are key components of many signal transduction pathways. In addition to cyclic AMP, ppGpp and cyclic di-GMP, many bacteria use also cyclic di-AMP as a second messenger. This molecule is synthesized by distinct classes of diadenylate cyclases and degraded by phosphodiesterases. The control of the intracellular c-di-AMP pool is very important since both a lack of this molecule and its accumulation can inhibit growth of the bacteria. In many firmicutes, c-di-AMP is essential, making it the only known essential second messenger. Cyclic di-AMP is implicated in a variety of functions in the cell, including cell wall metabolism, potassium homeostasis, DNA repair and the control of gene expression. To understand the molecular mechanisms behind these functions, targets of c-di-AMP have been identified and characterized. Interestingly, c-di-AMP can bind both proteins and RNA molecules. Several proteins that interact with c-di-AMP are required to control the intracellular potassium concentration. In Bacillus subtilis, c-di-AMP also binds a riboswitch that controls the expression of a potassium transporter. Thus, c-di-AMP is the only known second messenger that controls a biological process by interacting with both a protein and the riboswitch that regulates its expression. Moreover, in Listeria monocytogenes c-di-AMP controls the activity of pyruvate carboxylase, an enzyme that is required to replenish the citric acid cycle. Here, we review the components of the c-di-AMP signaling system.

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“…The sides of the square are~6 nm and the inner cavity was~1.8 nm. The results demonstrate the feasibility of sequence-dependent programmed selfassembly of structured RNA nanoparticles.In nature, the pRNA from bacteriophage phi29 DNA packing motor forms a hexameric ring to gear the motor via hand-in-hand or loop-loop interactions 21,[67][68][69]. The 4-nt loop sequences of the individual monomers can be engineered to form dimer, trimer, and hexamer nanoparticles by bottom-up self-assembly of reengineered RNA fragments.…”

mentioning

confidence: 99%

RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications

Haque¹,

Pi²,

Zhao³

et al. 2017

WIREs RNA

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In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry. Many structural motifs have been discovered and characterized over the years and the crystal structures of many of these motifs are available for nanoparticle construction. For example, using the flexibility and versatility of RNA structure, RNA triangles, squares, pentagons, and hexagons can be constructed from phi29 pRNA three-way-junction (3WJ) building block. This review will focus on 2D RNA triangles, squares, and hexamers; 3D and 4D structures built from basic RNA building blocks; and their prospective applications in vivo as imaging or therapeutic agents via specific delivery and targeting. Methods for intracellular cloning and expression of RNA molecules and the in vivo assembly of RNA nanoparticles will also be reviewed.

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RNA quaternary structure and global symmetry

Cited by 44 publications

References 88 publications

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

A jack of all trades: the multiple roles of the unique essential second messenger cyclic di‐AMP

RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications

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