Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification.

BACKGROUND: SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts. METHODS: This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern. RESULTS: Initial valid results were obtained from 95.8% [95% confidence interval (CI): 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI: 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5. CONCLUSIONS: This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.

E-type delayed fluorescence of a phosphine-supported Cu2(mu-NAr2)2 diamond core: harvesting singlet and triplet excitons in OLEDs.

A highly emissive bis(phosphine)diarylamido dinuclear copper(I) complex (quantum yield = 57%) was shown to exhibit E-type delayed fluorescence by variable temperature emission spectroscopy and photoluminescence decay measurement of doped vapor-deposited films. The lowest energy singlet and triplet excited states were assigned as charge transfer states on the basis of theoretical calculations and the small observed S(1)-T(1) energy gap. Vapor-deposited OLEDs doped with the complex in the emissive layer gave a maximum external quantum efficiency of 16.1%, demonstrating that triplet excitons can be harvested very efficiently through the delayed fluorescence channel. The function of the emissive dopant in OLEDs was further probed by several physical methods, including electrically detected EPR, cyclic voltammetry, and photoluminescence in the presence of applied current.

Multifrequency EPR studies of [Cu(1.5)Cu(1.5)](+) for Cu2(mu-NR2)2 and Cu2(mu-PR2)2 diamond cores.

Multifrequency electron paramagnetic resonance (EPR) spectroscopy is used to explore the electronic structures of a series of dicopper complexes of the type {(LXL)Cu}(2)(+). These complexes contain two four-coordinate copper centers of highly distorted tetrahedral geometries linked by two [LXL](-) ligands featuring bridging amido or phosphido ligands and associated thioether or phosphine chelate donors. Specific chelating [LXL](-) ligands examined in this study include bis(2-tert-butylsulfanylphenyl)amide (SNS), bis(2-di-iso-butylphosphinophenyl)amide (PNP), and bis(2-di-iso-propylphosphinophenyl)phosphide (PPP). To better map the electronic coupling to copper, nitrogen, and phosphorus in these complexes, X-, S-, and Q-band EPR spectra have been obtained for each complex. The resulting EPR parameters implied by computer simulation are unusual for typical dicopper complexes and are largely consistent with previously published X-ray absorption spectroscopy and density functional theory data, where a highly covalent {Cu(2)(mu-XR(2))(2)}(+) diamond core has been assigned in which removal of an electron from the neutral {Cu(2)(mu-XR(2))(2)} can be viewed as ligand-centered to a substantial degree. To our knowledge, this is the first family of dicopper diamond core model complexes for which the compendium of X-, S-, and Q-band EPR spectra have been collected for comparison to Cu(A).

Nickel complexes of a pincer NN2 ligand: multiple carbon-chloride activation of CH2Cl2 and CHCl3 leads to selective carbon-carbon bond formation.

A new pincer-type bis(amino)amine (NN2) ligand and its lithium and nickel complexes, including Ni(II) methyl, ethyl, and phenyl complexes, were synthesized. The Ni(II) alkyl complexes react cleanly with alkyl halides including chlorides to form C-C coupled products and Ni(II) halides. More interestingly, the Ni(II) alkyls undergo unprecedented reactions with CH2Cl2 and CHCl3 to cleave all the C-Cl bonds and replace them with C-C bonds. The reactions are highly selective and lead to the first efficient catalytic coupling of CH2Cl2 with alkyl Grignards. A conversion of 82% and a turnover number of 47 are achieved within minutes. Coupling of CD2Cl2 and 1,1-dichloro-3,3-dimethylbutane with nBuMgCl is also realized. Preliminary mechanistic study suggests a radical initiated process for these reactions.

Probing the electronic structures of [Cu2(mu-XR2)]n+ diamond cores as a function of the bridging X atom (X = N or P) and charge (n = 0, 1, 2).

A series of dicopper diamond core complexes that can be isolated in three different oxidation states ([Cu2(mu-XR2)]n+, where n = 0, 1, 2 and X = N or P) is described. Of particular interest is the relative degree of oxidation of the respective copper centers and the bridging XR2 units, upon successive oxidations. These dicopper complexes feature terminal phosphine and either bridging amido or phosphido donors, and as such their metal-ligand bonds are highly covalent. Cu K-edge, Cu L-edge, and P K-edge spectroscopies, in combination with solid-state X-ray structures and DFT calculations, provides a complementary electronic structure picture for the entire set of complexes that tracks the involvement of a majority of ligand-based redox chemistry. The electronic structure picture that emerges for these inorganic dicopper diamond cores shares similarities with the Cu2(mu-SR)2 CuA sites of cytochrome c oxidases and nitrous oxide reductases.

Unexpected photoisomerization of a pincer-type amido ligand leads to facial coordination at Pt(IV).

The divalent complex (BQA)PtMe undergoes oxidative addition with MeI to afford the octahedral complex cis-(mer-BQA)PtMe2I {(BQA)- = bis(8-quinolinyl)amide}. When this molecule is irradiated with visible light, it isomerizes to (fac-BQA)PtMe2I, where the BQA ligand adopts an unexpected facial coordination mode. The amide nitrogen in this molecule is sp3 hybridized and can be easily quarternized with HBF4, resulting in [H(fac-BQA)PtMe2I][BF4], with only minor perturbation to the coordination sphere.

Alpha-synuclein structures probed by 5-fluorotryptophan fluorescence and 19F NMR spectroscopy.

Alpha-synuclein, the main protein component of fibrillar deposits found in Parkinson's disease, is intrinsically disordered in vitro. Site-specific information on the protein conformation has been obtained by biosynthetic incorporation of an unnatural amino acid, 5-fluorotryptophan (5FW), into the recombinant protein. Using fluorescence and 19F NMR spectroscopy, we have characterized three proteins with 5FW at positions 4, 39, and 94. Steady-state emission spectra (maxima at 353 nm; quantum yields approximately 0.2) indicate that all three indole side chains are exposed to the aqueous medium. Virtually identical single-exponential excited-state decays (tau approximately 3.4 ns) were observed in all three cases. Single 19F NMR resonances were measured for W4, W39, and W94 at -49.0 +/- 0.1 ppm. Our analysis of the spectroscopic data suggests that the protein conformations are very similar in the regions near the three sites.

Structural snapshots of a flexible Cu2P2 core that accommodates the oxidation states Cu(I)Cu(I), Cu1.5Cu1.5, and Cu(II)Cu(II).

The phosphido-bridged dicopper(I) complex {(PPP)Cu}2 has been synthesized and structurally characterized ([PPP]- = bis(2-di-iso-propylphosphinophenyl)phosphide). Cyclic voltammetry of {(PPP)Cu}2 in THF shows fully reversible oxidations at -1.02 V (Cu1.5Cu1.5/CuICuI) and -0.423 V (CuIICuII/Cu1.5Cu1.5). Chemical oxidation of {(PPP)Cu}2 by one electron yields the class III mixed-valence species [{(PPP)Cu}2]+ (EPR, UV-vis). Structural data establish an unexpectedly large change (0.538 A) in the Cu...Cu distance upon oxidation state. Oxidation of {(PPP)Cu}2 by two electrons yields the dication [{(PPP)Cu}2]2+, an antiferromagnetically coupled dicopper(II) complex. Maintenance of a pseudotetrahedral geometry that is midway between a square plane and an ideal tetrahedron at the copper centers, along with a high degree of flexibility at the phosphide hinges, allows for efficient access to CuICuI, Cu1.5Cu1.5, and CuIICuII redox states without the need for ligand exchange, substitution, or redistribution processes.

A highly emissive Cu2N2 diamond core complex supported by a [PNP]- ligand.

A Cu2N2 diamond core structure, {(PNP)CuI}2 (2), supported by a [PNP]- ligand (1) ([PNP]- = bis(2-(diisobutylphosphino)phenyl)amide) has been prepared. 2 is highly emissive at ambient temperature in both the solid and solution states and is characterized by a relatively long-lived excited state (tau > 10 mus) and an unusually high quantum yield (phi > 0.65). These observations are consistent with a low degree of structural reorganization between the ground state of 2 and its excited state *2, and also with a high degree of steric protection of the two copper centers of 2 afforded by the bulky [PNP]- ligand. An estimate for the excited-state reduction potential of *2 (ca. -3.2 V vs Fc+/Fc), and the availability of two well-separated and reversible ground-state redox processes, suggests that bimetallic copper systems of these types may be interesting candidates to consider for photochemically driving multielectron redox transformations.

Amido-bridged Cu2N2 diamond cores that minimize structural reorganization and facilitate reversible redox behavior between a Cu1Cu1 and a class III delocalized Cu1.5Cu1.5 species.

A novel Cu(2)N(2) diamond core structure supported by an [SNS](-) ligand (1) ([SNS](-) = bis(2-tert-butylsulfanylphenyl)amido) has been prepared. This dicopper system exhibits a fully reversible one-electron redox process between a reduced Cu(1)Cu(1) complex, [[SNS][Cu]](2) (2), and a class III delocalized Cu(1.5)Cu(1.5) state, [[[SNS][Cu]](2)][B(3,5-(CF(3))(2)C(6)H(3))(4)] (3). Structural snapshots of both redox forms have been obtained to reveal remarkably little overall structural reorganization. The Cu...Cu bond distance nonetheless undergoes an appreciable compression (approximately 0.13 A) upon oxidation, providing a Cu...Cu distance of 2.4724(4) A in the mixed-valence state that is virtually identical to the Cu...Cu distance observed in the reduced form of the Cu(A) site of thiolate-bridged cytochrome c oxidase. Despite the low structural reorganization evident between 2 and 3, the [SNS](-) ligand is quite flexible. For example, square-planar geometries can prevail for divalent copper ions supported by [SNS](-) as evident from the crystal structure of [SNS]CuCl (4). Physical characterization for the mixed valence complex 3 includes electrochemical, magnetic (SQUID), EPR, and optical data. The complex has also been examined by density functional methods. An attempt was made to measure the rate of electron self-exchange k(s) between the Cu(1)Cu(1) and the Cu(1.5)Cu(1.5) complexes 2 and 3 by NMR line-broadening analysis in dichloromethane solution. While the system is certainly in the fast-exchange regime, the exchange process is too fast to be accurately measured by this technique. The value for k(s) can be bracketed with a conservative lower boundary of > or =10(7) M(-1) s(-1), a value that appears to be larger than other low molecular weight copper model complexes for which similar data is available. The unusually large magnitude of k(s) likely reflects the minimal structural reorganization that accompanies Cu(1)Cu(1) <--> Cu(1.5)Cu(1.5) interchange.