Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence

Sjekloća, Ljiljana; Ferré-D′Amaré, A.R.

doi:10.1016/j.chembiol.2019.04.012

Cited by 27 publications

(28 citation statements)

References 37 publications

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“…Recently, the Corn RNA was selected to bind DFHO (3,5-difluoro-4-hydroxybenzylidene- imidazolinone-2-oxime), a compound that mimics the fluorescent properties of the red fluorescent protein (RFP). The Corn aptamer was shown to dimerize in solution through direct stacking between the two G-quadruplex base planes from each protomer in the absence of DFHO [ 177 , 178 ] ( Figure 6 ). Although stacking of G-quadruplexes in solution is well-known [ 179 ], this structure represents the first example of a homodimeric RNA relying solely on stacking by G-quadruplexes and unpaired purines with no inter-protomer base pairing in the dimerization interface.…”

Section: Dimeric Fluorogenic Rna Aptamersmentioning

confidence: 99%

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Bou‐Nader

Zhang

2020

Molecules

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In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing (“kissing”) interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.

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Section: Dimeric Fluorogenic Rna Aptamersmentioning

confidence: 99%

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Bou‐Nader

Zhang

2020

Molecules

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“…Thus, shape complementarity between the ligand and the RNA pocket may be sufficient for binding and fluorescence turn-on, but may not provide specificity. For instance, the Corn aptamer was found to promote bright fluorescence of two general nucleic acid dyes (ThT and TO), but crystal structures of these complexes revealed disorder in the binding pockets (Sjekloca and Ferré-D'Amaré, 2019). DFHO, the cognate fluorophore of Corn, was designed by adding a hydrogen bonding ‘handle’ (an oxime function) onto DFHBI, which the aptamer could use to increase specificity.…”

Section: Discussionmentioning

confidence: 99%

“…To gain further insight into how the quasisymmetric Corn interface arises, its crystal structures in the absence of fluorophore, and also in the presence of the non-specific but Gquadruplex-preferent fluorophores thioflavin-T (ThT) and thiazole orange (TO) were determined (Sjekloca & Ferré-D'Amaré, 2019). The ligand-free Corn crystallized as an exactly symmetric homodimer, but at least in the crystalline form of the RNA, the ligand binding pocket had collapsed, such that the G-quadruplexes of the two protomers stacked directly on each other.…”

Section: Quasisymmetry In the Corn Aptamermentioning

confidence: 99%

Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers

Trachman

Ferré-D′Amaré

2019

Quart. Rev. Biophys.

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Fluorescence turn-on aptamers,in vitroevolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA–fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.

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“…50 Interestingly, the quadruplex dimer is also formed in the apo state (i.e., in the absence of the ligand), with a collapsed, symmetric conformation. 51 Moreover, structures of Corn in complex with the quadruplexbinders thioflavin T (ThT) and thiazol orange (TO) helped to rationalize their strong fluorescence activation by binding to the Corn quadruplex dimer. 51 Spinach, Broccoli and Corn bind fluorinated HBI analogues with low pK a values that are easily deprotonated and exist predominantly as phenolates under physiological conditions.…”

Section: Hbi-binding Aptamers -Spinach Broccoli Corn Chilimentioning

confidence: 99%

“…51 Moreover, structures of Corn in complex with the quadruplexbinders thioflavin T (ThT) and thiazol orange (TO) helped to rationalize their strong fluorescence activation by binding to the Corn quadruplex dimer. 51 Spinach, Broccoli and Corn bind fluorinated HBI analogues with low pK a values that are easily deprotonated and exist predominantly as phenolates under physiological conditions. In contrast, the Chili aptamer, 52 which is derived from the earlier reported 13-2 aptamer, 40 binds and activates the dimethoxy-substituted analogue DMHBI exclusively in the protonated state.…”

Section: Hbi-binding Aptamers -Spinach Broccoli Corn Chilimentioning

confidence: 99%