| 1. |
- Conn, Vanessa M., et al.
(författare)
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A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation
- 2017
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Ingår i: Nature Plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 3:5
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Tidskriftsartikel (refereegranskat)abstract
- Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA: DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
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| 2. |
- Sakir, Menekse, et al.
(författare)
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Fabrication of Plasmonically Active Substrates Using Engineered Silver Nanostructures for SERS Applications
- 2017
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Ingår i: ACS Applied Materials & Interfaces. - : American Chemical Society (ACS). - 1944-8252 .- 1944-8244. ; 9:45, s. 39795-39803
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Tidskriftsartikel (refereegranskat)abstract
- Demanding applications in sensing, metasurfaces, catalysis, and biotechnology require fabrication of plasmonically active substrates. Herein, we demonstrate a bottom-up, versatile, and scalable approach that relies on direct growth of silver nanostructures from seed particles that were immobilized on polymer brush-grafted substrates. Our approach is based on (i) the uniform and tunable assembly of citrate-stabilized gold nanoparticles on poly(ethylene glycol) brushes to serve as seeds and (ii) the use of hydroquinone as a reducing agent, which is extremely selective to the presence of seed particles, confining the growth of silver nanostructures on the surface of the substrate. The diameter of the seed particles, concentration, as well as ratio of reactants and duration of the growth process are investigated for large-area growth of silver nanostructures with high surface coverage and plasmonic activity. The resulting silver nanostructures exhibit high levels of surface-enhanced Raman scattering activity at two different laser lines and allow detection of molecules at concentrations as low as 10 pM. The plasmonic properties of the silver nanostructures are further studied using ultrafast pump-probe spectroscopy. Spatially defined silver nanostructures are fabricated through the seed particles that are patterned via soft lithography, showing the capabilities of the presented approach in device applications.
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