Solution scattering at the Life Science X-ray Scattering (LiX) beamline

Yang, Lin; Antonelli, Stephen; Chodankar, Shirish; Byrnes, James R.; Lazo, Edwin; Qian, Kun

doi:10.1107/s1600577520002362

Cited by 51 publications

(59 citation statements)

References 21 publications

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“…The solution x-ray scattering measurements for both ATDNA and MixDNA were conducted at 16-ID [Life Science X-ray Scattering (LiX)] beamline of National Synchrotron Light Source II (NSLS-II) ( 84 ) at Brookhaven National Laboratory. The DNA samples were diluted and measured at 80, 100, and 120 μM.…”

Section: Methodsmentioning

confidence: 99%

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

Chen

Pollack

et al. 2021

Sci. Adv.

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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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Section: Methodsmentioning

confidence: 99%

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

Chen

Pollack

et al. 2021

Sci. Adv.

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“…The SAXS data were collected at the Life Sciences X-Ray Scattering Beamline (LIX) at Brookhaven National Laboratory using their standard solution scattering set-up, experimental procedures, and data-processing packages (24). SEC-SAXS was performed on a Superdex 200 increase 5/150 GL column (GE) equilibrated in the SAXS buffer condition.…”

Section: Saxs Measurementsmentioning

confidence: 99%

Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

Kelly

Olson

Neupane

et al. 2020

Journal of Biological Chemistry

190

359

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About 17 years after the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic, the world is currently facing the COVID-19 pandemic caused by SARS coronavirus 2 (SARS-CoV-2). According to the most optimistic projections, it will take more than a year to develop a vaccine, so the best short-term strategy may lie in identifying virus-specific targets for small molecule–based interventions. All coronaviruses utilize a molecular mechanism called programmed −1 ribosomal frameshift (−1 PRF) to control the relative expression of their proteins. Previous analyses of SARS-CoV have revealed that it employs a structurally unique three-stemmed mRNA pseudoknot that stimulates high −1 PRF rates and that it also harbors a −1 PRF attenuation element. Altering −1 PRF activity impairs virus replication, suggesting that this activity may be therapeutically targeted. Here, we comparatively analyzed the SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar −1 PRF rates and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablate −1 PRF activity. We noted that the upstream attenuator hairpin activity is also functionally retained in both viruses, despite differences in the primary sequence in this region. Small-angle X-ray scattering analyses indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 have the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit −1 PRF was similarly effective against −1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may be promising lead compounds to combat the current COVID-19 pandemic.

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“…Round et al, 2015;Hura et al, 2009;Nielsen et al, 2012). The instrumentation at the LiX beamline, however, is not compatible with this format, due to the design choices that we made to optimize the instrument performance (Yang et al, 2020). We have therefore devised two solutions to reliably track large numbers of samples and reduce the workload of the beamline staff at the same time.…”

Section: Sample Formatmentioning

confidence: 99%

“…Recently, we described the instrumentation and software at the LiX beamline of NSLS-II for automated biomolecular solution scattering data collection and processing (Yang et al, 2020). Mail-in and remote measurements are the logical next steps after a high degree of automation has been achieved, as demonstrated in the macromolecular crystallography community (e.g.…”

Section: Introductionmentioning

confidence: 99%

Tools for supporting solution scattering during the COVID-19 pandemic

et al. 2021

Self Cite

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During the COVID-19 pandemic, synchrotron beamlines were forced to limit user access. Performing routine measurements became a challenge. At the Life Science X-ray Scattering (LiX) beamline, new instrumentation and mail-in protocols have been developed to remove the access barrier to solution scattering measurements. Our efforts took advantage of existing instrumentation and coincided with the larger effort at NSLS-II to support remote measurements. Given the limited staff–user interaction for mail-in measurements, additional software tools have been developed to ensure data quality, to automate the adjustments in data processing, as users would otherwise rely on the experience of the beamline staff, and produce a summary of the initial assessments of the data. This report describes the details of these developments.

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Solution scattering at the Life Science X-ray Scattering (LiX) beamline

Cited by 51 publications

References 21 publications

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

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

Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

Tools for supporting solution scattering during the COVID-19 pandemic

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