RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

Matouskova, Eva; Dršata, Tomáš; Pfeifferová, Lucie; Šponer, Jiřı́; Réblová, Kamila; Lankaš, Filip

doi:10.1016/j.bpj.2022.01.025

Cited by 2 publications

(2 citation statements)

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“…The kink-turn motif [32], one of the most well-studied RNA tertiary motifs [7,[33][34][35], exemplifies the consequences of the aforementioned limitations. Kink-turns are typically characterized by a canonical stem (C-stem) followed by a bulge that forms a sharp kink in the backbone and a non-canonical stem (NC-stem) starting with trans-Sugar-Hoogsteen (tSH) G-A base pairs [7] (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

Baulin,

Bohdan,

Kowalski

et al. 2024

Preprint

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The functions of non-coding RNAs are largely defined by their three-dimensional structures. RNA 3D structure is organized hierarchically and consists of recurrent building blocks called tertiary motifs. The computational problem of RNA tertiary motif search remains largely unsolved, as standard approaches are restrained by sequence, interaction network, or backbone topology. We developed the ARTEM superposition algorithm, which is free from these limitations. Here, we present a version of ARTEM that allows automated searches of RNA structure databases to identify 3D structure motifs. We exemplify it by a search of motifs isosteric to the kink-turn motif. This widespread motif plays a role in many aspects of RNA function, and its mutations are known to cause several human syndromes. With ARTEM, we discovered two new kink-turn topologies, multiple no-kink variants of the motif, and showed that a ribosomal junction in bacteria forms either a kink or a no-kink variant depending on the species. Additionally, we identified kink-turns in the catalytic core of group II introns, whose structures have not previously been characterized as containing kink-turns. ARTEM opens a fundamentally new way to study RNA 3D folds and motifs and analyze their correlations and variations.

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Section: Introductionmentioning

confidence: 99%

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

Baulin,

Bohdan,

Kowalski

et al. 2024

Preprint

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show abstract

“…After a series of energy minimizations and short MD runs to equilibrate the system, a 1 µs trajectory has been produced. The 4 bp portions of the duplexes flanking the crossing points from outside are each assigned an effective rigid body, as described (6). Briefly, each of the 8 bases involved in a body are fitted with a standard reference point and frame (7).…”

mentioning

confidence: 99%

Mechanical Properties of DNA Double-Crossover Motif

Matouskova

Růžička

Réblová

et al. 2023

Preprint

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The double-crossover (DX) motif is a key building block of DNA nanostructures. It connects two double helices by two closely spaced Holliday junctions. Despite its prominent importance, the structure and elasticity of the DX motif is not fully understood. Here we employ extensive all-atom molecular dynamics (MD) simulations of an antiparallel DNA DX motif with two full turns between crossovers to infer its global structure and deformability. We quantitatively reproduce the experimentally known two-fold increase of bending stiffness upon incorporation of a DNA duplex into the DX motif, and find out that its stretching and twisting stiffness are only slightly influenced. To further describe the motif, we define four effective rigid bodies, each involving several base pairs flanking the Holliday junctions from the outside, and consider internal coordinates capturing relative displacement and orientation of the bodies. Time series of the coordinates from MD then yield the global structure of the DX motif and its stiffness in the harmonic approximation.

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RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

Cited by 2 publications

References 44 publications

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

Mechanical Properties of DNA Double-Crossover Motif

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