| 1. |
- Labuhn, Maurice, et al.
(författare)
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Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications
- 2018
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 46:3, s. 1375-1385
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Tidskriftsartikel (refereegranskat)abstract
- Genome editing with the CRISPR-Cas9 system has enabled unprecedented efficacy for reverse genetics and gene correction approaches. While off-target effects have been successfully tackled, the effort to eliminate variability in sgRNA efficacies-which affect experimental sensitivity-is in its infancy. To address this issue, studies have analyzed the molecular features of highly active sgRNAs, but independent cross-validation is lacking. Utilizing fluorescent reporter knock-out assays with verification at selected endogenous loci, we experimentally quantified the target efficacies of 430 sgRNAs. Based on this dataset we tested the predictive value of five recently-established prediction algorithms. Our analysis revealed a moderate correlation (r = 0.04 to r = 0.20) between the predicted and measured activity of the sgRNAs, and modest concordance between the different algorithms. We uncovered a strong PAM-distal GC-content-dependent activity, which enabled the exclusion of inactive sgRNAs. By deriving nine additional predictive features we generated a linear model-based discrete system for the efficient selection (r = 0.4) of effective sgRNAs (CRISPRater). We proved our algorithms' efficacy on small and large external datasets, and provide a versatile combined on-and off-target sgRNA scanning platform. Altogether, our study highlights current issues and efforts in sgRNA efficacy prediction, and provides an easily-applicable discrete system for selecting efficient sgRNAs.
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| 2. |
- Naumova, Maria A., et al.
(författare)
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Exploring the light-induced dynamics in solvated metallogrid complexes with femtosecond pulses across the electromagnetic spectrum
- 2020
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Ingår i: The Journal of chemical physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- Oligonuclear complexes of d4-d7 transition metal ion centers that undergo spin-switching have long been developed for their practical role in molecular electronics. Recently, they also have appeared as promising photochemical reactants demonstrating improved stability. However, the lack of knowledge about their photophysical properties in the solution phase compared to mononuclear complexes is currently hampering their inclusion into advanced light-driven reactions. In the present study, the ultrafast photoinduced dynamics in a solvated [2 × 2] iron(II) metallogrid complex are characterized by combining measurements with transient optical-infrared absorption and x-ray emission spectroscopy on the femtosecond time scale. The analysis is supported by density functional theory calculations. The photocycle can be described in terms of intra-site transitions, where the FeII centers in the low-spin state are independently photoexcited. The Franck-Condon state decays via the formation of a vibrationally hot high-spin (HS) state that displays coherent behavior within a few picoseconds and thermalizes within tens of picoseconds to yield a metastable HS state living for several hundreds of nanoseconds. Systematic comparison with the closely related mononuclear complex [Fe(terpy)2]2+ reveals that nuclearity has a profound impact on the photoinduced dynamics. More generally, this work provides guidelines for expanding the integration of oligonuclear complexes into new photoconversion schemes that may be triggered by ultrafast spin-switching.
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| 3. |
- Naumova, Maria A., et al.
(författare)
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Revealing Hot and Long-Lived Metastable Spin States in the Photoinduced Switching of Solvated Metallogrid Complexes with Femtosecond Optical and X-ray Spectroscopies
- 2020
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 11:6, s. 2133-2141
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Tidskriftsartikel (refereegranskat)abstract
- An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d4-d7 transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. In this work, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. This finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.
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