Abstract
Dynamic light scattering represents an accurate, robust, and reliable technique to analyze molecule size in solution and monitor their interactions in real time. Here, we describe how to analyze by DLS an RNA-protein interaction. In our frame, we studied complexes formed between RNA fragments derived from the genome of HIV-1 in association with the viral precursor Pr55Gag. These interactions are crucial for the specific selection of the viral genomic RNA (gRNA) from the bulk of the viral spliced and cellular RNAs. This chapter displays how DLS allows to characterize the interactions that regulate the early steps of viral assembly.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Strutt JW (1871) On the scattering of the light by small particles. Philos Mag. Series 275:447–454
Einstein A (1905) über einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt. Ann Phys 322:132–148
Mie G (1908) Beitrage zur Optik trüber Medien, speziell kolloidaler Metallosungen. Ann Phys 330:337–445
Wyatt PJ (1993) Light scattering and the absolute characterization of macromolecules. Anal Chim Acta 272:1–40
Sutherland W (1905) A dynamical theory of diffusion for non-electrolytes and the molecular mass of albumin. Philos Mag. Series 9:781–785
Fujime S (1972) Quasi-elastic scattering laser light. A new tool for the dynamic study of biological macromolecules. Adv Biophys 3:1–43
Friksen B (2001) Revisiting the method of cumulants for the analysis of dynamic light scattering data. Appl Opt 40:4087–4091
Patel TR, Chojnowski G, Koul A, McKenna SA, Bujnicki JM (2017) Structural studies of RNA-protein complexes: a hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 118:146–162
Maguire CM, Rösslein M, Wickc P, Prina-Mello A (2018) Characterisation of particles in solution – a perspective on light scattering and comparative technologies. Sci Technol Adv Mater 19:732–745
Paillart J-C, Shehu-Xhilaga M, Marquet R, Mak J (2004) Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol 2:461–472
Mailler E, Bernacchi S, Marquet R, Paillart J-C, Vivet-Boudou V, Smyth RP (2016) The life cycle of the HIV-1 gag-RNA complex. Viruses 8. pii: E248. https://doi.org/10.3390/v8090248
Kuzembayeva M, Dilley K, Sardo L, Hu WS (2014) Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles. Virology 454:362–370
Abd El-Wahab EW, Smyth RP, Mailler E, Bernacchi S, Vivet-Boudou V, Hijnen M, Jossinet F, Mak J, Paillart J-C, Marquet R (2014) Specific recognition of the HIV-1 genomic RNA by the gag precursor. Nat Commun 5:4304. https://doi.org/10.1038/ncomms5304
Sinck L, Richer D, Howard J, Alexander M, Purcell DF, Marquet R, Paillart J-C (2007) In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs. RNA 12:2141–2150
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Bernacchi, S. (2020). Dynamic Light Scattering Analysis on RNA Associated to Proteins. In: Arluison, V., Wien, F. (eds) RNA Spectroscopy. Methods in Molecular Biology, vol 2113. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0278-2_4
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0278-2_4
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0277-5
Online ISBN: 978-1-0716-0278-2
eBook Packages: Springer Protocols