Mass Spectrometry of Nucleic Acid Noncovalent Complexes.

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Pure Chiral Polar Vortex Phase in PbTiO3/SrTiO3 Superlattices with Tunable Circular Dichroism.

Nontrivial polarization textures have been demonstrated in ferroelectric/dielectric superlattices, where the electrostatic, elastic, and different gradient energies compete in a delicate balance. When PbTiO3/SrTiO3 superlattices are grown on DyScO3, the coexistence of ferroelectric domains and vortex structure is observed for n = 12-20 unit cells. Here, we report an approach to achieve single-phase vortex structures in superlattices by controlling the epitaxial strain using Sr1.04Al0.12Ga0.35Ta0.50O3 substrates. The domain width follows Kittel's law with the thickness of the ferroelectric PbTiO3 layers. A phase transition from vortex to a disordered phase with temperature is characterized by the correlation length. Resonant soft X-ray diffraction circular dichroism at the titanium L-edge reveals enhanced chirality with the thickness of the ferroelectric layer. These results are supported by second-principles simulations, which demonstrate that the integrated helicity increases with n. The stabilization of chiral single-phase polar vortices in ferroelectric/dielectric superlattices can enable novel optoelectronic devices with enhanced ferroelectric-light interaction.

Risk of seizures in a population of women with BRCA-positive metastatic breast cancer from an electronic health record database in the United States.

BACKGROUND: Incidence and risk factors for seizures among women with advanced breast cancer (BC) and brain metastases are not well characterized across treatment-related or clinical subtypes. This study leveraged a large real-world dataset to describe incidence and risk factors for seizures in BRCA-associated metastatic breast cancer. METHODS: The Optum® de-identified electronic health records database was used. Females with a BC diagnoses between 2008 and 2018, with clinic visits 12 months before BC index date, evidence of BRCA mutation (BRCA+), evidence of metastasis, and no previous cancers were included. Analyses were stratified by the overall BRCA+ cohort and 4 molecular phenotypes: HER2+/HR- (human epidermal growth factor 2/hormone receptor), HER2-/HR+, HER2+/HR+, and triple negative BC (TNBC; HER2-/HR-). Seizures were identified using diagnosis codes and natural language processing. Incidence, occurrence rates, and cumulative incidence of seizures from the diagnosis of metastasis to the end of follow up were calculated. Comparisons were made between phenotypes and stratified on PARP inhibitor use, diagnosed brain metastases, history of seizures, and anticonvulsants use before BC. All comparisons included age at metastasis, number of prior lines of treatment, and metastasis location as covariates. RESULTS: 27.8% of 7941 BRCA+ patients had ≥1 seizure over a mean follow-up time of 2.35 years. Incidence and occurrence rates were 11.83 (95% CI: 11.35-12.33) and 201.3 (95% CI: 198.05-204.50), respectively, per 100 person-years. HER2-/HR+ and TNBC patients had the lowest and highest seizure incidence rates, respectively (10.94 [95% CI: 10.23-11.71] and 16.83 [95% CI: 15.34-18.46]). With HER2-/HR+ as the reference group in a competing risk analysis, TNBC (hazard ratio, HR = 1.35; 95%CI: 1.21, 1.52; p < 0.001) and HER2+/HR- (HR = 1.29; 95%CI: 1.07, 1.56; p < 0.01) patients had a greater risk of seizures. Patients with diagnosed brain metastases or a history of seizures had higher seizure rates. Incidence trended higher with PARP inhibitor use, but patient numbers were low. CONCLUSIONS: This study provides novel real-world evidence on seizure incidence rates in BRCA+ BC patients, even those without diagnosed brain metastases, and underscores the need to understand patients' tumor phenotypes when assessing seizure risk. These findings may have implications for clinical practice and assessment of benefit-risk ratios of new therapeutic agents.

Covalent Organic Framework as a Metal-Free Photocatalyst for Dye Degradation and Radioactive Iodine Adsorption.

Exploring a covalent organic framework (COF) material as an efficient metal-free photocatalyst and as an adsorbent for the removal of pollutants from contaminated water is very challenging in the context of sustainable chemistry. Herein, we report a new porous crystalline COF, C6-TRZ-TPA COF, via segregation of donor-acceptor moieties through the extended Schiff base condensation between tris(4-formylphenyl)amine and 4,4',4″-(1,3,5-triazine-2,4,6-triyl)trianiline. This COF displayed a Brunauer-Emmett-Teller (BET) surface area of 1058 m2 g-1 with a pore volume of 0.73 cc g-1. Again, extended π-conjugation, the presence of heteroatoms throughout the framework, and a narrow band gap of 2.2 eV, all these features collectively work for the environmental remediation in two different perspectives: it could harness solar energy for environmental clean-up, where the COF has been explored as a robust metal-free photocatalyst for wastewater treatment and as an adsorbent for iodine capture. In our endeavor of wastewater treatment, we have conducted the photodegradation of rose bengal (RB) and methylene blue (MB) as model pollutants since these are extremely toxic, are health hazard, and bioaccumulative in nature. The catalyst C6-TRZ-TPA COF showed a very high catalytic efficiency of 99% towards the degradation of 250 parts per million (ppm) of RB solution in 80 min under visible light irradiation with the rate constant of 0.05 min-1. Further, C6-TRZ-TPA COF is found to be an excellent adsorbent as it efficiently adsorbed radioactive iodine from its solution as well as from the vapor phase. The material exhibits a very rapid iodine capturing tendency with an outstanding iodine vapor uptake capacity of 4832 mg g-1.

DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions.

G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).

Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations.

Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts.

Dichotomy in Growth and Invasion from Low- to High-Grade Glioma Cellular Variants.

Glial dysfunction outraging CNS plasticity and integrity results in one of the most dangerous cancers, namely glioma, featuring little median survival period and high recurrence. The hallmark properties of proliferation, invasion and angiogenesis with the infiltrated macrophages in glioma are expected to be tightly coupled or cross-linked, but not properly related so far. The present study is aimed to find a relationship between this featured quadrangle from lower to higher grades (HG) of post-operative glioma tissues and their invading subsets. Elevated Ki67-associated proliferation in lower grades (LG) was supported with VEGF dependent angiogenic maintenance which found a decrease unlikely in HG. In contrast, MMP 2 and 9-associated invasions augmented high in HG with the dominant presence of CD204+ M2 polarized macrophages and a general increase in global DNMT1-associated methylation. Marked differences found in ECM invading cellular subsets of HG showing high proliferative capacity indicating rationally for recurrence, contrasting the nature of gross tumor tissue of the same grade. Thus in LG, the neoplastic lesion is more inclined to its growth while in higher grade more disposed towards tissue wreckage in support with cellular environmental milieu whereas the cellular variants and subsets of invaded cells showed different trends. Therefore, some operational dichotomy or coupling among cellular variants in glioma is active in determining its low- to high-grade transition and aggressive progression.

Persistence of an active asymmetric rigid Brownian particle in two dimensions.

We have studied the persistence probability p(t) of an active Brownian particle with shape asymmetry in two dimensions. The persistence probability is defined as the probability of a stochastic variable that has not changed its sign in a given fixed time interval. We have investigated two cases: (1) diffusion of a free active particle and (2) that of a harmonically trapped particle. In our earlier work, by Ghosh et al. [J. Chem. Phys. 152, 174901 (2020)], we had shown that p(t) can be used to determine the translational and rotational diffusion constant of an asymmetrically shaped particle. The method has the advantage that the measurement of the rotational motion of the anisotropic particle is not required. In this paper, we extend the study to an active anisotropic particle and show how the persistence probability of an anisotropic particle is modified in the presence of a propulsion velocity. Furthermore, we validate our analytical expression against the measured persistence probability from the numerical simulations of single particle Langevin dynamics and test whether the method proposed in our earlier work can help distinguish between active and passive anisotropic particles.

Phen-DC3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation.

Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high resolution. Here we report that Phen-DC3 , one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG)3 to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex.

Akt Phosphorylation Orchestrates T11TS Mediated Cell Cycle Arrest in Glioma Cells.

The novel anti-neoplastic glycopeptide T11TS retards glioma both in in-vitro clinical samples and in-vivo models. This study investigates the correlation between altering the glioma microenvironment with glioma arrest and death. Flow cytometry, immunoblotting, ELISA, and co-immunoprecipitation were employed to investigate glioma cell arrest and death. Results include a decline in phosphorylation of Akt and attenuation of p21 phosphorylation (Thr145,Ser146) and disassociation of p-Akt-Mdm2 and p-Akt-BAD facilitating death by Akt>BAD. T11TS influence phosphorylation patterns in two focal axes Akt>p21 and Akt>Mdm2>p53. The current article provides crucial insight in deciphering the mechanism of T11TS induced glioma cell arrest and death.

Watt-level, ultrafast, tunable yellow source based on single-pass, fourth-harmonic generation of Cr2+:ZnS laser at 2360 nm.

We report a compact source of high power, tunable, ultrafast yellow radiation using fourth-harmonic generation of a mid-IR laser in two-stage frequency-doubling processes. Using Cr2+:ZnS laser at 2360 nm frequency-doubled in a multi-grating MgO:PPLN crystal, we have generated near-IR radiation tunable across 1137-1200 nm with average output power as high as 2.4 W and pulse width of ∼60fs. Subsequently, the near-IR radiation is frequency-doubled using a bismuth triborate (BIBO) crystal to produce coherent yellow radiation tunable across 570-596 nm with a maximum average power of ∼1W. The source has a maximum mid-IR to yellow (near-IR to yellow) single-pass conversion efficiency as high as ∼29.4% (∼47%). Without any pulse compression, the yellow source has output pulses at a repetition rate of 80 MHz with a pulse width of ∼130fs in Gaussian-shaped and a spectral width of ∼4nm corresponding to a time-bandwidth product of 0.45. The generated output beam has a Gaussian transverse beam profile with measured M2 values of Mx2∼1.07 andMy2∼1.01.

Persistence in Brownian motion of an ellipsoidal particle in two dimensions.

We investigate the persistence probability p(t) of the position of a Brownian particle with shape asymmetry in two dimensions. The persistence probability is defined as the probability that a stochastic variable has not changed its sign in the given time interval. We explicitly consider two cases-diffusion of a free particle and that of a harmonically trapped particle. The latter is particularly relevant in experiments that use trapping and tracking techniques to measure the displacements. We provide analytical expressions of p(t) for both the scenarios and show that in the absence of the shape asymmetry, the results reduce to the case of an isotropic particle. The analytical expressions of p(t) are further validated against numerical simulation of the underlying overdamped dynamics. We also illustrate that p(t) can be a measure to determine the shape asymmetry of a colloid and the translational and rotational diffusivities can be estimated from the measured persistence probability. The advantage of this method is that it does not require the tracking of the orientation of the particle.

Affinity Captured Urinary Extracellular Vesicles Provide mRNA and miRNA Biomarkers for Improved Accuracy of Prostate Cancer Detection: A Pilot Study.

Serum prostate-specific antigen (sPSA) testing has helped to increase early detection of and decrease mortality from prostate cancer. However, since sPSA lacks specificity, an invasive prostate tissue biopsy is required to confirm cancer diagnosis. Using urinary extracellular vesicles (EVs) as a minimally invasive biomarker source, our goal was to develop a biomarker panel able to distinguish prostate cancer from benign conditions with high accuracy. We enrolled 56 patients in our study, 28 negative and 28 positive for cancer based on tissue biopsy results. Using our Vn96 peptide affinity method, we isolated EVs from post-digital rectal exam urines and used quantitative polymerase chain reaction to measure several mRNA and miRNA targets. We identified a panel of seven mRNA biomarkers whose expression ratio discriminated non-cancer from cancer with an area under the curve (AUC) of 0.825, sensitivity of 75% and specificity of 84%. We also identified two miRNAs whose combined score yielded an AUC of 0.744. A model pairing the seven mRNA and two miRNA panels yielded an AUC of 0.843, sensitivity of 79% and specificity of 89%. Addition of EV-derived PCA3 levels and clinical characteristics to the biomarker model further improved test accuracy. An AUC of 0.955, sensitivity of 86% and specificity of 93% were obtained. Hence, Vn96-isolated urinary EVs are a clinically applicable and minimally invasive source of mRNA and miRNA biomarkers with potential to improve on the accuracy of prostate cancer screening and diagnosis.

Peptide-Affinity Precipitation of Extracellular Vesicles and Cell-Free DNA Improves Sequencing Performance for the Detection of Pathogenic Mutations in Lung Cancer Patient Plasma.

Liquid biopsy is a minimally-invasive diagnostic method that may improve access to molecular profiling for non-small cell lung cancer (NSCLC) patients. Although cell-free DNA (cf-DNA) isolation from plasma is the standard liquid biopsy method for detecting DNA mutations in cancer patients, the sensitivity can be highly variable. Vn96 is a peptide with an affinity for both extracellular vesicles (EVs) and circulating cf-DNA. In this study, we evaluated whether peptide-affinity (PA) precipitation of EVs and cf-DNA from NSCLC patient plasma improves the sensitivity of single nucleotide variants (SNVs) detection and compared observed SNVs with those reported in the matched tissue biopsy. NSCLC patient plasma was subjected to either PA precipitation or cell-free methods and total nucleic acid (TNA) was extracted; SNVs were then detected by next-generation sequencing (NGS). PA led to increased recovery of DNA as well as an improvement in NGS sequencing parameters when compared to cf-TNA. Reduced concordance with tissue was observed in PA-TNA (62%) compared to cf-TNA (81%), mainly due to identification of SNVs in PA-TNA that were not observed in tissue. EGFR mutations were detected in PA-TNA with 83% sensitivity and 100% specificity. In conclusion, PA-TNA may improve the detection limits of low-abundance alleles using NGS.

Single-pass, second-harmonic generation of high-power, ultrafast mid-IR Cr2+:ZnS laser at 2360 nm.

We report on a compact and simple ultrafast source producing tunable radiation in the near-IR wavelength range. Based on single-pass frequency doubling of an ultrafast Cr2+:ZnS laser at 2360 nm with pulse width of 43 fs at a repetition rate of 80 MHz in MgO:PPLN crystal, the source produces maximum average output power of ∼2.43 W tunable across 1137-1200 nm with a maximum single-pass conversion efficiency as high as 65%. Without use of any pulse compression technique, the source produces output pulses in Gaussian shape with measured pulse width of ∼60 fs and spectral width of 39 nm centered at 1180 nm corresponding to a time-bandwidth product of 0.5. The output beam has a Gaussian spatial profile with measured M2<1.32 and a peak-to-peak power fluctuation of 3% over 2 h. Using MgO:PPLN crystal of two different lengths, 1 mm and 2 mm, we have observed that the optimum second-harmonic generation efficiency of an ultrafast pulse laser, even in the presence of temporal walk-off, appears in the low pump focusing condition.

Defect-Induced (Dis)Order in Relaxor Ferroelectric Thin Films.

The effect of intrinsic point defects on relaxor properties of 0.68 PbMg_{1/3}Nb_{2/3}O_{3}-0.32 PbTiO_{3} thin films is studied across nearly 2 orders of magnitude of defect concentration via ex post facto ion bombardment. A weakening of the relaxor character is observed with increasing concentration of bombardment-induced point defects, which is hypothesized to be related to strong interactions between defect dipoles and the polarization. Although more defects and structural disorder are introduced in the system as a result of ion bombardment, the special type of defects that are likely to form in these polar materials (i.e., defect dipoles) can stabilize the direction of polarization against thermal fluctuations, and in turn, weaken relaxor behavior.

High pressure activation of the Mrr restriction endonuclease in Escherichia coli involves tetramer dissociation.

A sub-lethal hydrostatic pressure (HP) shock of ∼100 MPa elicits a RecA-dependent DNA damage (SOS) response in Escherichia coli K-12, despite the fact that pressure cannot compromise the covalent integrity of DNA. Prior screens for HP resistance identified Mrr (Methylated adenine Recognition and Restriction), a Type IV restriction endonuclease (REase), as instigator for this enigmatic HP-induced SOS response. Type IV REases tend to target modified DNA sites, and E. coli Mrr activity was previously shown to be elicited by expression of the foreign M.HhaII Type II methytransferase (MTase), as well. Here we measured the concentration and stoichiometry of a functional GFP-Mrr fusion protein using in vivo fluorescence fluctuation microscopy. Our results demonstrate that Mrr is a tetramer in unstressed cells, but shifts to a dimer after HP shock or co-expression with M.HhaII. Based on the differences in reversibility of tetramer dissociation observed for wild-type GFP-Mrr and a catalytic mutant upon HP shock compared to M.HhaII expression, we propose a model by which (i) HP triggers Mrr activity by directly pushing inactive Mrr tetramers to dissociate into active Mrr dimers, while (ii) M.HhaII triggers Mrr activity by creating high affinity target sites on the chromosome, which pull the equilibrium from inactive tetrameric Mrr toward active dimer.

Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study.

In recent years, several studies based on the interaction of self-assembling short peptides derived from viroporins with model membranes, have improved our understanding of the molecular mechanism of corona virus (CoV) infection under physiological conditions. In this study, we have characterized the mechanism of membrane interaction of a short, 9-residue peptide TK9 (T55VYVYSRVK63) that had been derived from the carboxyl terminal of the Severe Acute Respiratory Syndrome (SARS) corona virus (SARS CoV) envelope (E) protein. The peptide has been studied for its physical changes in the presence of both zwitterionic DPC and negatively charged SDS model membrane micelles, respectively, with the help of a battery of biophysical techniques including two-dimensional solution state NMR spectroscopy. Interestingly, in both micellar environments, TK9 adopted an alpha helical conformation; however, the helical propensities were much higher in the case of DPC compared to those of SDS micelle, suggesting that TK9 has more specificity towards eukaryotic cell membrane than the bacterial cell membrane. The orientation of the peptide TK9 also varies in the different micellar environments. The peptide's affinity was further manifested by its pronounced membrane disruption ability towards the mammalian compared to the bacterial membrane mimic. Collectively, the in-depth structural information on the interaction of TK9 with different membrane environments explains the host specificity and membrane orientation owing to subsequent membrane disruption implicated in the viral pathogenesis.

Simultaneous generation of high-power, ultrafast 1D and 2D Airy beams and their frequency-doubling characteristics.

We report on a simple experimental scheme based on a pair of cylindrical lenses (convex and concave) of the same focal length and common optical elements, producing high power optical beams in 1D and/or 2D Airy intensity profiles with laser polarization as the control parameter. Using an ultrafast Yb-fiber laser at 1064 nm of average power of 5 W in a Gaussian spatial profile and pulse width of ∼180 fs, we have generated 1D and 2D Airy beams at an efficiency of 80% and 70%, respectively, and a pulse width of ∼188 and ∼190 fs, respectively. We have measured the transverse deflection rate of 1D and 2D beams to be ∼5.0×10-5 1/mm and ∼2.0×10-5 1/mm, respectively. Simply rotating the polarization state of the 1D cubic phase modulated beam in the experiment, we can produce 1D and 2D Airy beams on demand. Using a 5 mm long bismuth borate (BiB3O6), we have also studied frequency-doubling characteristics of both 1D and 2D Airy beams. Like the 2D Airy beam, the 1D Airy beam also produces a frequency-doubled 1D Airy and an additional 1D spatial cubic structure. Like the Gaussian beams, we have observed the focusing dependence of conversion efficiency for both 1D and 2D Airy beams, producing green 1D and 2D Airy beams of output powers in excess of 110 and 150 mW for 3.4 and 2.8 W of fundamental power, respectively.

Nonproductive Binding Modes as a Prominent Feature of Aß40 Fiber Elongation: Insights from Molecular Dynamics Simulation.

The formation of amyloid fibers has been implicated in a number of neurodegenerative diseases. The growth of amyloid fibers is strongly thermodynamically favorable, but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and to date has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations, in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 310 helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and the monomer. A Markov state model shows that the unfolded monomer is trapped at the end of the fiber in a set of interconverting antiparallel ß-hairpin conformations. The simulation here may serve as a model for the binding of other non-ß-sheet conformations to amyloid fibers.