Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs

Badmalia, Maulik D.; Siddiqui, Mohd Quadir; Mrozowich, Tyler; Gemmill, Darren L.; Patel, Trushar R.

doi:10.1007/s00249-020-01470-9

Cited by 4 publications

(2 citation statements)

References 127 publications

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“…An emerging technique that is particularly useful for studying long non-coding RNAs (lncRNAs) is analytical ultracentrifugation (AUC). Using the sedimentation velocity (SV) and sedimentation equilibrium (SE) modes can give information about molecule size, purity, aggregation, hydrodynamic shape, and ensemble composition whilst requiring very small sample sizes compared to other biophysical techniques [70]. AUC is beginning to be used as a reliable quality control step for assessing RNA integrity before proceeding with more laborious techniques such as SAXS, as demonstrated by Mrozowich et al when interrogating flavivirus non-coding regions.…”

Section: Other Techniquesmentioning

confidence: 99%

Evaluating RNA Structural Flexibility: Viruses Lead the Way

Fairman

Lever

Kenyon

2021

Viruses

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Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked.

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Section: Other Techniquesmentioning

confidence: 99%

Evaluating RNA Structural Flexibility: Viruses Lead the Way

Fairman

Lever

Kenyon

2021

Viruses

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“…However, as RNA molecules are flexible and require careful optimisation of buffer components for structural studies, their purity must be assessed by a reliable method. Therefore, the Patel laboratory contribute an article that demonstrates the application and benefits of SV-AUC to evaluate solution properties and homogeneity of non-coding RNAs (Badmalia et al 2020). At the heart of gene regulation are the interactions between nucleic acids and the proteins that act to repress or promote transcription.…”

Section: Nucleic Acids and Their Interactionsmentioning

confidence: 99%

Analytical ultracentrifugation: still the gold standard that offers multiple solutions

Dobson

Patel

2020

Eur Biophys J

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Understanding the nature of macromolecules and their interactions in solution underpins many fields, including biology, chemistry and materials science. The 24th International Analytical Ultracentrifugation Workshop and Symposium (AUC2019, held in Christchurch, New Zealand, August 2019), brought together 77 international delegates to highlight recent developments in the field. There was a focus on analytical ultracentrifugation, although we recognise that this is but one of the key methods in the biophysicist's toolkit. Many of the presentations showcased the versatility of analytical ultracentrifugation and how such experiments are integrated with other solution techniques, such as small-angle X-ray scattering, cryo-electron microscopy, isothermal titration calorimetry and more. This special issue emphasises a wide range of themes covered in the meeting, including carbohydrate chemistry, protein chemistry, polymer science, and macromolecular interactions.

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