Synthetic RNA circuits

Davidson, Eric A.; Ellington, Andrew D.

doi:10.1038/nchembio846

Cited by 52 publications

(39 citation statements)

References 80 publications

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“…RNAs that change their shape in response to external stimuli, such as the riboswitch-metabolite interaction, are ideal tools for molecular design, for instance, in the development of nanomechanical devices and synthetic RNA circuits (e.g., Davidson and Ellington 2007), due to its great predictive power in constructing secondaryand tertiary-structure elements in combination with functional diversity. To be able to build such devices, prior knowledge of the three-dimensional structures and concomitant RNA folding processes remains a necessity.…”

Section: Mechanism Of Riboswitchingmentioning

confidence: 99%

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ottink

Rampersad²,

Tessari³

et al. 2007

RNA

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All known guanine-sensing riboswitches regulate gene expression by specifically binding to guanine (G) or related analogs with high affinity to switch off transcription. The aptamers of this class of riboswitches are characterized by three helices (P1-P3), surrounding a central core of phylogenetically conserved nucleotides and a long-range loop-loop interaction. To gain more insight into the switching mechanism, we present here a comparison between the solution-state structures of the G-free and G-bound forms of the guanine aptamer from the xpt-pbuX operon of Bacillus subtilis, as derived from NMR chemical shifts and magnetic-field-induced residual dipolar couplings. The high-resolution NMR analysis shows the G-free aptamer is highly structured with parallel P2 and P3 helices and the long-range loop-loop interaction already present, implying that the structure is largely preformed to bind the ligand. Structural changes upon guanine binding are found to be localized to the central core. In the free state, the G-quadruple interaction and two base pairs of the P1 stem flanking the central core appear to be largely disordered. The ligand thus binds via a combined predetermined-induced fit mechanism, involving a previously unstructured five-residue loop of the J2-3 junction that folds over the ligand. These limited additional interactions within a preorganized setting possibly explain how the aptamer rapidly responds to ligand binding, which is necessary to switch the structural state of the expression platform within a narrow time frame before the RNA polymerase escapes the 59-UTR.

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Section: Mechanism Of Riboswitchingmentioning

confidence: 99%

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ottink

Rampersad²,

Tessari³

et al. 2007

RNA

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“…3,4 The principles of protein modularity have been particularly useful for synthetic biology, with a goal of engineering biological systems with either improved properties or new functions. 1,[5][6][7][8][9][10][11] Repeat proteins represent an interesting subset of proteins characterized by small, structural motifs of 20-50 amino acids 12,13 The repeated motifs stack on each other to form elongated structures, which provide a large surface area that is particularly advantageous in forming macromolecular interactions when compared with typical globular proteins. Often the entire array is required to form the binding surface; however, in a subset of repeat proteins that bind nucleic acids, the repeats act in a modular fashion, with each repeat interacting with a single nucleotide base.…”

Section: Introduction: Modularity In Molecular Recognitionmentioning

confidence: 99%

Pentatricopeptide repeats

Filipovska

Rackham

2013

RNA Biology

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“…Nucleic acid catalysts may prove to be extremely useful as genetic regulatory elements in vivo (Breaker 2004), including in genetic circuits (Davidson and Ellington 2007). For example, hammerhead ribozymes (HHRz) have been engineered to silence gene expression in vivo.…”

Section: Introductionmentioning

confidence: 99%

Direct selection for ribozyme cleavage activity in cells

Chen

Denison

Levy

et al. 2009

RNA

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Selection may prove to be a powerful tool for the generation of functional RNAs for in vivo genetic regulation. However, traditional in vitro selection schemes do not mimic physiological conditions, and in vivo selection schemes frequently use small pool sizes. Here we describe a hybrid in vitro/in vivo selection scheme that overcomes both of these disadvantages. In this new method, PCR-amplified expression templates are transfected into mammalian cells, transcribed hammerhead RNAs self-cleave, and the extracted, functional hammerhead ribozyme species are specifically amplified for the next round of selection. Using this method we have selected a number of cis-cleaving hammerhead ribozyme variants that are functional in vivo and lead to the inhibition of gene expression. More importantly, these results have led us to develop a quantitative, kinetic model that can be used to assess the stringency of the hybrid selection scheme and to direct future experiments.

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Synthetic RNA circuits

Cited by 52 publications

References 80 publications

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Pentatricopeptide repeats

Direct selection for ribozyme cleavage activity in cells

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