Atomic force microscopy of RNA: State of the art and recent advancements

Schön, Peter

doi:10.1016/j.semcdb.2017.08.040

Cited by 23 publications

(23 citation statements)

References 60 publications

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“…[10][11][12][13] However, there are only limited, more recent applications of AFM for the analysis of RNA and RNA-protein complexes. 14 The structural heterogeneity associated with functional biological RNA molecules, in conjunction with the difficulties associated with synthesis and purification of intact RNA in the absence of deleterious ribonucleases that degrade RNA have limited the opportunities for the biophysical and structural analysis. Previously AFM was applied to image viral dsRNA to calculate its length.…”

Section: Introductionmentioning

confidence: 99%

Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC

Nwokeoji

Kumar

Kilby

et al. 2019

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Section: Introductionmentioning

confidence: 99%

Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC

Nwokeoji

Kumar

Kilby

et al. 2019

Analyst

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“…To investigate the native 3D structure at single-molecule resolution of representative viroid RNAs of the families Pospiviroidae (PSTVd) and Avsunviroidae (PLMVd and ELVd), a systematic and comparative AFM analysis was performed. RNA adsorption on mica surfaces was performed using 3-aminopropyltriethoxysilane (APTES), one of the currently available reagents that promotes a tight adhesion of RNA molecules via electrostatic interactions without damaging or disrupting their native structure [45,49,50]. Other reported routes for the surface binding of RNA, such as those comprising the addition of salts containing divalent cations (e.g.…”

Section: Afm Analysis Of Viroid Structurementioning

confidence: 99%

“…Other reported routes for the surface binding of RNA, such as those comprising the addition of salts containing divalent cations (e.g. Mg 2+ , Zn 2+ or Ni 2+ ) [45,51,52], are not appropriate for this study given our interest in examining the effect exerted by a divalent cation (Mg 2+ ) on viroid 2D and, particularly, 3D RNA structure.…”

Section: Afm Analysis Of Viroid Structurementioning

confidence: 99%

“…AFM permits visualization and manipulation across length scales that range from biomolecules to cells. Therefore, this technology is increasingly used in different fields, including virology [43][44][45]. In particular, AFM has matured to provide nanometer spatial resolution of RNA molecules of different lengths and structures, as well as of RNA-RNA or RNA-protein complexes [46][47][48][49].…”

Section: Introductionmentioning

confidence: 99%

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Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy

et al. 2019

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Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.

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“…The secondary and tertiary structure of RNA can be studied by a variety of techniques including nucleic acid melting curves, 16 chemical probing and mapping using techniques such as selective 2-hydroxyl acylation analyzed by primer extension (SHAPE), 17 cryo-electron microscopy, 18 atomic force microscopy, 19 Forster resonance energy transfer, 20 optical tweezers. 21 Nanopores are an interesting platform for the study of RNA structure as they offer an inexpensive, fast, label-free, single-molecule alternative.…”

Section: Figure 11 -Nanopore Experimental Illustrationmentioning

confidence: 99%

Studying RNA sequence and structure using solid-state and hybrid biomimetic nanopores

Henley¹

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I would like to dedicate this thesis to three individuals. Firstly, my mother, Hermin Youssefian. You are my true academic inspiration in this world, mentally and emotionally the strongest individual I have ever known. When I felt as though I could not go any further I only needed to think of you to remember that we are capable of overcoming damn near everything set in front of us. I never believed I would get here, but you never stopped believing in me, I don't think I can ever express how much that means to me, thank you. I didn't become a lawyer or a medical doctor but I hope this is good enough. Secondly, my father, Gary Henley. I count myself blessed to have the hardest working individual walking the face of the earth as a father. I know that your hard work has never been for you, you're the most selfless individual I've ever met and every day you go to work to give your family a better life. You are the true American dream and I thank you for the fact that I never had to struggle because you bore that burden. Lastly, Coltin Sims. I will never know a better friend. I miss you every day. I wish many things were different, but I'm lucky to have felt your pure friendship and support. Your kind words have kept me going, this is for you buddy.

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Atomic force microscopy of RNA: State of the art and recent advancements

Cited by 23 publications

References 60 publications

Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC

Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC

Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy

Studying RNA sequence and structure using solid-state and hybrid biomimetic nanopores

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