Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations

Chen, Yen-Lin; He, Weiwei; Kırmızıaltın, Serdal; Pollack, Lois

doi:10.1016/j.xcrp.2022.100971

Cited by 8 publications

(31 citation statements)

References 70 publications

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“…Within it, signs of structure emerge for rA30, in the form of two loosely separated, broad peaks near q = 1.1 and 1.5 Å −1 , but not for rU30, consistent with base stacking-induced ordering present in the former and absent in the latter (24). Both curves decay at larger q. Duplexes Figure 1B shows the scattering profile of a 62-nt RNA hairpin, consisting of a 29-bp duplex, terminated by a 4-nt loop from (19). Prior studies examined the scattering out to q = 1.25 Å −1 and used molecular dynamics simulations (19) in conjunction with machine learning (21) to confirm that the small, but notable peak at q = 0.8 Å −1 is connected with the helical major groove, a repeated spatial dimension in the duplex structure.…”

Section: Single Strandsmentioning

confidence: 87%

“…Both curves decay at larger q. Duplexes Figure 1B shows the scattering profile of a 62-nt RNA hairpin, consisting of a 29-bp duplex, terminated by a 4-nt loop from (19). Prior studies examined the scattering out to q = 1.25 Å −1 and used molecular dynamics simulations (19) in conjunction with machine learning (21) to confirm that the small, but notable peak at q = 0.8 Å −1 is connected with the helical major groove, a repeated spatial dimension in the duplex structure. A red bar in the figure connects these reciprocal and real-space features.…”

Section: Single Strandsmentioning

confidence: 99%

“…Centering and calibration of the beam on both detectors were performed using a silver behenate standard in BioXTAS RAW, as well as masking, radial averaging, and buffer subtraction (43). Previously published data (19), reproduced here in Fig. 1 (B and C), were also acquired at NSLS-II on the LiX beamline.…”

Section: Data Collection and Analysis At National Synchrotron Lightmentioning

confidence: 99%

“…Scattering to large angles [wide-angle x-ray scattering (WAXS)] enhances measurement resolution to the single angstrom (17,18). Recent WAXS studies (19)(20)(21)(22)(23) have begun to connect distinctive peaks in scattering profiles with real-space features of DNA and RNA, including backbone geometries, structural building blocks (duplexes), and base stacking.…”

Section: Introductionmentioning

confidence: 99%

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RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

Zielinski,

Sui,

Pabit

et al. 2023

Sci. Adv.

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RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

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Section: Single Strandsmentioning

confidence: 87%

Section: Single Strandsmentioning

confidence: 99%

Section: Data Collection and Analysis At National Synchrotron Lightmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

Zielinski,

Sui,

Pabit

et al. 2023

Sci. Adv.

Self Cite

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“…A similar approach was used in Ref. [40] to analyze RNA triplexes. Here, WAXS-driven MD was used to tackle cases where hightemperature sampling was not sufficient.…”

Section: Integrating Experimental Data and Simulations To Improve Ens...mentioning

confidence: 99%

Combining simulations and experiments to investigate RNA dynamics

Bernetti,

Bussi

2022

Preprint

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Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small-and wide-angle X-ray scattering, chemical probing, or even thermal denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.

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Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr

Krause,

Bains,

Blechar

et al. 2024

ChemBioChem

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Long non‐coding RNAs (lncRNAs) are important regulators of gene expression and can associate with DNA as RNA:DNA heteroduplexes or RNA•DNA:DNA triple helix structures. Here, we review in vitro biochemical and biophysical experiments including electromobility shift assays (EMSA), circular dichroism (CD) spectroscopy, thermal melting analysis, microscale thermophoresis (MST), single‐molecule Förster resonance energy transfer (smFRET) and nuclear magnetic resonance (NMR) spectroscopy to investigate RNA•DNA:DNA triple helix and RNA:DNA heteroduplex formation. We present the investigations of the antiparallel triplex‐forming lncRNA MEG3 targeting the gene TGFB2 and the parallel triplex‐forming lncRNA Fendrr with its target gene Emp2. The thermodynamic properties of these oligonucleotides lead to concentration‐dependent heterogeneous mixtures, where a DNA duplex, an RNA:DNA heteroduplex and an RNA•DNA:DNA triplex coexist and their relative populations are modulated in a temperature‐dependent manner. The in vitro data provide a reliable readout of triplex structures, as RNA•DNA:DNA triplexes show distinct features compared to DNA duplexes and RNA:DNA heteroduplexes. Our experimental results can be used to validate computationally predicted triple helix formation between novel disease‐relevant lncRNAs and their DNA target genes.

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Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations

Cited by 8 publications

References 70 publications

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

Combining simulations and experiments to investigate RNA dynamics

Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr

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