The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

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Untwisting of Double-Stranded DNA and RNA Investigated by Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2016.11.413 ◽

2017 ◽

Vol 112 (3) ◽

pp. 69a

Author(s):

Korbinian Liebl

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna And Rna ◽

Double Stranded Dna ◽

Dynamics Simulations

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Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor

Nucleic Acids Research ◽

10.1093/nar/gkaa525 ◽

2020 ◽

Vol 48 (14) ◽

pp. 7640-7652 ◽

Cited By ~ 1

Author(s):

Anna Wypijewska del Nogal ◽

Anders F Füchtbauer ◽

Mattias Bood ◽

Jesper R Nilsson ◽

Moa S Wranne ◽

...

Keyword(s):

Quantum Yield ◽

Nucleic Acids ◽

Photophysical Properties ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Molar Absorptivity ◽

Dna And Rna ◽

Double Stranded Dna ◽

Rna Duplexes

Abstract With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.

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Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins

10.1101/532507 ◽

2019 ◽

Author(s):

Sophie Sacquin-Mora

Keyword(s):

Experimental Data ◽

Mechanical Properties ◽

Small Molecules ◽

Protein Function ◽

Coarse Grain ◽

Conformational Ensemble ◽

Structural Variations ◽

New Approach ◽

Conformational Ensembles ◽

Dynamics Simulations

AbstractDynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein’s internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all atom classic molecular dynamics simulations and coarse grain calculations of the resulting conformational ensemble mechanical properties. Here we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.

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Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins

Journal of The Royal Society Interface ◽

10.1098/rsif.2019.0075 ◽

2019 ◽

Vol 16 (156) ◽

pp. 20190075

Author(s):

Sophie Sacquin-Mora

Keyword(s):

Experimental Data ◽

Mechanical Properties ◽

Small Molecules ◽

Protein Function ◽

Coarse Grain ◽

Conformational Ensemble ◽

Structural Variations ◽

New Approach ◽

Conformational Ensembles ◽

Dynamics Simulations

Dynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein's internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all-atom classic molecular dynamics simulations and coarse-grain calculations of the resulting conformational ensemble mechanical properties. Here, we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.

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Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

Journal of Biomolecular NMR ◽

10.1007/s10858-020-00337-7 ◽

2020 ◽

Vol 74 (8-9) ◽

pp. 457-471 ◽

Cited By ~ 1

Author(s):

Atul Rangadurai ◽

Eric S. Szymanski ◽

Isaac Kimsey ◽

Honglue Shi ◽

Hashim M. Al-Hashimi

Keyword(s):

Dynamic Equilibrium ◽

Isotope Effects ◽

Exchange Process ◽

Relaxation Dispersion ◽

Base Pairs ◽

Carbon And Nitrogen ◽

Dna And Rna ◽

Backbone Conformation ◽

Rna Duplexes ◽

Dynamics Simulations

Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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