Nucleic Acid (NA) nanotechnology is a rapidly emerging field demonstrating application of polynucleotides as a versatile biopolymer to fabricate nanostructures of various dimensions and shapes in a programmable and highly predictable way. The folding of DNA or RNA strands into a stable double helix configuration mainly relies on the Watson-Crick (Canonical) base pair composition (G=C and A-T or A-U in the case of RNA), base stacking, and metal ion concentrations. The thermodynamic parameters of DNA B-form helix formation and A-form helix of RNA can be computed using empirically defined sets of nearest neighboring parameters encompassed within the 2D structure predicting programs for example mfold, NUPAC. However, these programs are lacking parameters for a hybrid DNA/RNA base pairing and non-canonical base interactions. In this report, we focused our study to evaluate thermodynamic parameters of several in silico designed three-way junction (3WJ) DNA and hybrid DNA-RNA structural elements. The designed 3WJ motifs contain three helical stems linked with 4,3,2,1, and 0 single stranded Thymidine (T) or Uridine (U) nucleotides. We will report assembly efficiency of the 3WJs investigated by gel shift assay and thermodynamic parameters measured by UV-melting technique. Our experiments reveal that the amount of Ts and Us linkages in the three-way junction dictate the stability of the overall 3WJ conformations. This study is important as we expect it will contribute to the existing set of parameters used for NA structure prediction algorithms as well as provide a guidance for rational design of NA nanostructures.
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RNA multimerization as an organizing force for liquid–liquid phase separation
RNA interactions are exceptionally strong and highly redundant. As such, nearly any two RNAs have the potential to interact with one another over relatively short stretches, especially at high RNA concentrations. This is especially true for pairs of RNAs that do not form strong self-structure. Such phenomena can drive liquid–liquid phase separation, either solely from RNA–RNA interactions in the presence of divalent or organic cations, or in concert with proteins. RNA interactions can drive multimerization of RNA strands via both base-pairing and tertiary interactions. In this article, we explore the tendency of RNA to form stable monomers, dimers, and higher order structures as a function of RNA length and sequence through a focus on the intrinsic thermodynamic, kinetic, and structural properties of RNA. The principles we discuss are independent of any specific type of biomolecular condensate, and thus widely applicable. We also speculate how external conditions experienced by living organisms can influence the formation of nonmembranous compartments, again focusing on the physical and structural properties of RNA. Plants, in particular, are subject to diverse abiotic stresses including extreme temperatures, drought, and salinity. These stresses and the cellular responses to them, including changes in the concentrations of small molecules such as polyamines, salts, and compatible solutes, have the potential to regulate condensate formation by melting or strengthening base-pairing. Reversible condensate formation, perhaps including regulation by circadian rhythms, could impact biological processes in plants, and other organisms.
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- NSF-PAR ID:
- 10358421
- Date Published:
- Journal Name:
- RNA
- Volume:
- 28
- Issue:
- 1
- ISSN:
- 1355-8382
- Page Range / eLocation ID:
- 16 to 26
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, two of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies, in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1261/rna.078999.121
