One-Step Construction of 1,3,4-Oxadiazoles with Anticancer Activity from Tertiary Amines via a Sequential Copper(I)-Catalyzed Oxidative Ugi/aza-Wittig Reaction.

An unparalleled copper(I)-catalyzed synthesis of 1,3,4-oxadiazoles from tertiary amines in one step has been described. The one-pot reactions involving (N-isocyanimine)triphenylphosphorane, tertiary amines, and carboxylic acids resulted in the formation of 1,3,4-oxadiazoles in moderate to good yields through a consecutive oxidative Ugi/aza-Wittig reaction, enabling the direct functionalization of sp3 C-H bonds adjacent to the nitrogen atom. This method offered several notable advantages, including ligands-free, exceptional productivity and a high functional group tolerance. The preliminary biological evaluation demonstrated that compound 4f inhibited hepatoma cells efficiently, suggesting potentially broad applications of the approach for synthesis and medicinal chemistry.

Insight into Interfacial Polarization for Enhancing Piezoelectricity in Ferroelectric Nanocomposites.

The interfacial effect is widely used to optimize the properties of ferroelectric nanocomposites, however, there is still a lack of direct evidence to understand its underlying mechanisms limited by the nano size and complex structures. Here, taking piezoelectricity, for example, the mechanism of interfacial polarization in barium titanate/poly(vinylidene fluoride-ran-trifluoroethylene) (BTO/P(VDF-TrFE)) nanocomposite is revealed at multiple scales by combining Kelvin probe force microscope (KPFM) with theoretical stimulation. The results prove that the mismatch of permittivity between matrix and filler leads to the accumulation of charges, which in turn induces local polarization in the interfacial region, and thus can promote piezoelectricity independently. Furthermore, the strategy of interfacial polarization to enhance piezoelectricity is extended and validated in other two similar nanocomposites. This work uncovers the mechanism of interfacial polarization and paves newfangled insights to boost performances in ferroelectric nanocomposites.

Fault Knowledge Graph Construction and Platform Development for Aircraft PHM.

To tackle the problems of over-reliance on traditional experience, poor troubleshooting robustness, and slow response by maintenance personnel to changes in faults in the current aircraft health management field, this paper proposes the use of a knowledge graph. The knowledge graph represents troubleshooting in a new way. The aim of the knowledge graph is to improve the correlation between fault data by representing experience. The data source for this study consists of the flight control system manual and typical fault cases of a specific aircraft type. A knowledge graph construction approach is proposed to construct a fault knowledge graph for aircraft health management. Firstly, the data are classified using the ERNIE model-based method. Then, a joint entity relationship extraction model based on ERNIE-BiLSTM-CRF-TreeBiLSTM is introduced to improve entity relationship extraction accuracy and reduce the semantic complexity of the text from a linguistic perspective. Additionally, a knowledge graph platform for aircraft health management is developed. The platform includes modules for text classification, knowledge extraction, knowledge auditing, a Q&A system, and graph visualization. These modules improve the management of aircraft health data and provide a foundation for rapid knowledge graph construction and knowledge graph-based fault diagnosis.

Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

Bacterium Thermus thermophilus Argonaute (Ago; TtAgo) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The TtAgo active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically around it. An interesting challenge is to understand how they can collaboratively facilitate enzymatic catalysis. In Kluyveromyces polysporus Ago, a eukaryotic Ago, the evolutionarily symmetrical residues are arginine and histidine, both of which function to stabilize the plugged-in catalytic tetrad conformation. Surprisingly, our simulation results indicated that, in TtAgo, only R545 is involved in the cleavage reaction by serving as a critical structural anchor to stabilize the catalytic tetrad Asp-Glu-Asp-Asp that is completed by the insertion of the glutamate finger, whereas R486 is not involved in target cleavage. The TtAgo-mediated target DNA cleavage occurs in a substrate-assisted mechanism, in which the pro-Rp (Rp, a tetrahedral phosphorus center with "R-type" chirality) oxygen of scissile phosphate acts as a general base to activate the nucleophilic water. Our unexpected theoretical findings on distinct roles played by R545 and R486 in TtAgo catalysis have been validated by single-point site-mutagenesis experiments, wherein the target cleavage is abolished for all mutants of R545. In sharp contrast, the cleavage activity is maintained for all mutants of R486. Our work provides mechanistic insights on the catalytic specificity of Ago proteins and could facilitate the design of new gene-editing tools in the long term.

Conjugated linoleic acid supplements preserve muscle in high-body-fat adults: A double-blind, randomized, placebo trial.

BACKGROUND AND AIMS: Conjugated linoleic acid (CLA) has been used to improve body composition in weight management. However, clinical trial results are inconsistent and limited among Asians. We aimed to investigate the effect of CLA on body composition of Chinese adults with elevated body fat percentage. METHODS AND RESULTS: In this double-blind, randomized, placebo-controlled trial, 66 Chinese adults (aged 18-45 years old, 37.9% male) with elevated body fat percentage were provided with 3.2 g/day CLA (n = 33) or 3.2 g/day placebo (sunflower oil; n = 33) for 12 weeks. Both groups received lifestyle counseling, featured with low fat and low sugar diet, and moderate physical activity. Body composition was measured using dual-energy X-ray absorptiometry at the baseline and end of the trial. Sixty-four participants finished this study. Compared with the placebo group, the CLA group showed increased trunk muscle mass (MM) (0.6 ± 1.7 vs. -0.3 ± 1.2 kg, P = 0.019). Among those with an adherence score higher than 0.80 (n = 56, 87.5%), a greater increase in both total and trunk MM was observed in the CLA group (both P < 0.05). Moreover, the effect on MM appeared to be more evident in men, those with a body mass index <25 kg/m2, or those with higher self-rated physical activity. CONCLUSIONS: In Chinese adults with elevated body fat percentage, 3.2 g/day CLA supplementation may be effective in preserving MM, especially in the trunk region. REGISTRATION: This study was registered at ClinicalTrials.gov as NCT03915808 on April 9, 2019.

High pressure micromechanical force measurements of the effects of surface corrosion and salinity on CH4/C2H6 hydrate particle-surface interactions.

In order to investigate the mechanism of gas hydrate deposition and agglomeration in gas dominated flowlines, a high-pressure micromechanical force (MMF) apparatus was applied to directly measure CH4/C2H6 hydrate adhesion/cohesion forces under low temperature and high pressure conditions. A CH4/C2H6 gas mixture was used as the hydrate former. Adhesion forces between hydrate particles and carbon steel (CS) surfaces were measured, and the effects of corrosion on adhesion forces were analyzed. The influences of NaCl concentration on the cohesion force between CH4/C2H6 hydrate particles were also studied for gas-dominated systems. It was observed that there was no measurable adhesion force for pristine (no corrosion) and corroded surfaces, when there was no condensed water or water droplet on these surfaces. With water on the surface (the estimated water amount was around 1.7 µg mm-2), a hydrate film growth process was observed during the measurement. CS samples were soaked in NaCl solution to obtain different extents of corrosion on surfaces, and adhesion measurements were performed on both pristine and corroded samples. The adhesion force was found to increase with increasing soak times in 5 wt% NaCl (resulting in more visual corrosion) by up to 500%. For the effect of salinity on cohesion forces, it was found that the presence of NaCl decreased the cohesion force between hydrate particles, and a possible explanation of this phenomenon was given based on the capillary liquid bridge model.

Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder.

DNA mutational events are increasingly being identified in autism spectrum disorder (ASD), but the potential additional role of dysregulation of the epigenome in the pathogenesis of the condition remains unclear. The epigenome is of interest as a possible mediator of environmental effects during development, encoding a cellular memory reflected by altered function of progeny cells. Advanced maternal age (AMA) is associated with an increased risk of having a child with ASD for reasons that are not understood. To explore whether AMA involves covert aneuploidy or epigenetic dysregulation leading to ASD in the offspring, we tested a homogeneous ectodermal cell type from 47 individuals with ASD compared with 48 typically developing (TD) controls born to mothers of ≥35 years, using a quantitative genome-wide DNA methylation assay. We show that DNA methylation patterns are dysregulated in ectodermal cells in these individuals, having accounted for confounding effects due to subject age, sex and ancestral haplotype. We did not find mosaic aneuploidy or copy number variability to occur at differentially-methylated regions in these subjects. Of note, the loci with distinctive DNA methylation were found at genes expressed in the brain and encoding protein products significantly enriched for interactions with those produced by known ASD-causing genes, representing a perturbation by epigenomic dysregulation of the same networks compromised by DNA mutational mechanisms. The results indicate the presence of a mosaic subpopulation of epigenetically-dysregulated, ectodermally-derived cells in subjects with ASD. The epigenetic dysregulation observed in these ASD subjects born to older mothers may be associated with aging parental gametes, environmental influences during embryogenesis or could be the consequence of mutations of the chromatin regulatory genes increasingly implicated in ASD. The results indicate that epigenetic dysregulatory mechanisms may complement and interact with DNA mutations in the pathogenesis of the disorder.

Biosynthetic Mechanism of Lanosterol: Cyclization.

The remarkable cyclization mechanism of the formation of the 6-6-6-5 tetracyclic lanosterol (a key triterpenoid intermediate in the biosynthesis of cholesterol) from the acyclic 2,3-oxidosqualene catalyzed by oxidosqualene cyclase (OSC) has stimulated the interest of chemists and biologists for over a half century. Herein, the elaborate, state-of-the-art two-dimensional (2D) QM/MM MD simulations have clearly shown that the cyclization of the A-C rings involves a nearly concerted, but highly asynchronous cyclization, to yield a stable intermediate with "6-6-5" rings followed by the ring expansion of the C-ring concomitant with the formation of the D-ring to yield the "6-6-6-5" protosterol cation. The calculated reaction barrier of the rate-limiting step (≈22 kcal mol(-1)) is comparable to the experimental kinetic results. Furthermore all previous experimental mutagenic evidence is highly consistent with the identified reaction mechanism.

Droplet Digital™ PCR quantitation of HER2 expression in FFPE breast cancer samples.

UNLABELLED: The human epidermal growth factor receptor 2 (HER2, also known as erbB2) gene is involved in signal transduction for cell growth and differentiation. It is a cell surface receptor tyrosine kinase and a proto-oncogene. Overexpression of HER2 is of clinical relevance in breast cancer due to its prognostic value correlating elevated expression with worsening clinical outcome. At the same time, HER2 assessment is also of importance because successful anti-tumor treatment with Herceptin® is strongly correlated with HER2 overexpression in the tumor (approximately 30% of all breast tumors overexpress HER2). In a comprehensive national study, Wolff et al. [1] state that "Approximately 20% of current HER2 testing may be inaccurate" which underscores the importance of developing more accurate methods to determine HER2 status. Droplet Digital™ PCR (ddPCR™) has the potential to improve upon HER2 measurements due to its ability to quantitate DNA and RNA targets with high precision and accuracy. Here we present a study which investigates whether ddPCR can be used to assess HER2 transcript levels in formalin-fixed paraffin embedded (FFPE) human breast tumors and whether these ddPCR measurements agree with prior assessments of these same samples by pathologists using immunohistochemistry (IHC) and in some cases fluorescence in situ hybridization (FISH). We also determined the copy number of HER2 in these samples as compared to the CEP17 reference gene. RESULTS: Clinical FFPE samples were successfully studied using ddPCR and compared to results from standard FISH and IHC methodology. The results demonstrate that ddPCR can rank order the samples in complete agreement with the current standard methods and that ddPCR has the added benefit of providing quantitative results, rather than relying on the expert skill of a seasoned pathologist for determination.

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion.

Human DNA Pol κ is a polymerase enzyme, specialized for near error-free bypass of certain bulky chemical lesions to DNA that are derived from environmental carcinogens present in tobacco smoke, automobile exhaust and cooked food. By employing ab initio QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamics) simulations with umbrella sampling, we have determined the entire free energy profile of the nucleotidyl transfer reaction catalyzed by Pol κ and provided detailed mechanistic insights. Our results show that a variant of the Water Mediated and Substrate Assisted (WMSA) mechanism that we previously deduced for Dpo4 and T7 DNA polymerases is preferred for Pol κ as well, suggesting its broad applicability. The hydrogen on the 3'-OH primer terminus is transferred through crystal and solvent waters to the γ-phosphate of the dNTP, followed by the associative nucleotidyl transfer reaction; this is facilitated by a proton transfer from the γ-phosphate to the α,ß-bridging oxygen as pyrophosphate leaves, to neutralize the evolving negative charge. MD simulations show that the near error-free incorporation of dCTP opposite the major benzo[a]pyrene-derived dG lesion is compatible with the WMSA mechanism, allowing for an essentially undisturbed pentacovalent phosphorane transition state, and explaining the bypass of this lesion with little mutation by Pol κ.

Synthesis, Characterization, and Applications of Rare-Earth-Based Complexes with Antibacterial and Antialgal Properties.

The pursuit of environmentally friendly and highly effective antifouling materials for marine applications is of paramount importance. In this study, we successfully synthesized novel rare earth-based complexes by coordinating cerium (Ce III), samarium (Sm III), and europium (Eu III) with pyrithione (1-hydroxy-2-pyridinethione; PT). Extensive characterizations were performed, including single-crystal X-ray analysis, which revealed the intriguing binuclear structure of these complexes. This structural motif comprises two rare-earth ions intricately double-bridged by two oxygen atoms from the PT ligand, resulting in a distinctive and intriguing geometry. Furthermore, the central rare earth ion is surrounded by three sulfur atoms and two additional oxygen atoms, forming a unique distorted bicapped trigonal prismatic configuration. Compared with conventional antifouling biocides such as sodium pyrithione (NaPT), copper pyrithione (CuPT), and zinc pyrithione (ZnPT), these newly synthesized rare-earth complexes exhibited a remarkable boost in their in vitro antibacterial efficacy against both Gram-positive and Gram-negative bacteria. Additionally, these complexes demonstrated significant potential as antialgal agents, displaying impressive activity against marine planktonic organisms. These findings underscore the promising application prospects of these rare-earth complexes in the field of marine antifouling.

Synthesis, antimicrobial activity and application of polymers of praseodymium complexes based on pyridine nitrogen oxide.

The traditional pyridine nitrogen oxide-based antimicrobial agents are often associated with health risks due to heavy metal enrichment. To mitigate this concern, we synthesized two novel complexes, Pr2(mpo)6(H2O)2 and Pr(hpo)(mpo)2(H2O)2, and integrated rare-earth salts, Hhpo (2-hydroxypyridine-N-oxide) and Nampo (2-mercapto-pyridine-N-oxide sodium salt). These complexes were characterized through infrared analysis, elemental analysis, thermogravimetric analysis, and X-ray crystallographic analysis. Our comparative analyses demonstrate that the synthesized rare-earth complexes exhibit stronger antimicrobial activity against Staphylococcus aureus (S. aureus ATCC6538) and Escherichia coli (E. coli ATCC25922) compared to the ligands and rare-earth salts alone. Quantitative results revealed the lowest inhibitory concentrations of the two complexes against S. aureus ATCC6538 and E. coli ATCC25922 at 3.125 µg mL-1, 6.25 µg mL-1, 3.125 µg mL-1 and 6.25 µg mL-1, respectively. Preliminary investigations indicated that the antibacterial mechanism of these complexes involved promoting intracellular substance exudation to achieve antibacterial effects. Incorporation of these complexes into polymeric antimicrobial films resulted in a potent antimicrobial effect, achieving a 100% inhibition rate against S. aureus ATCC6538 and E. coli ATCC25922 at a low addition level of 0.6 wt%. Our results suggest that nitrogen oxide-based praseodymium complexes have potential for various antimicrobial applications.

Reciprocal regulation of SIRT1 and AMPK by Ginsenoside compound K impedes the conversion from plasma cells to mitigate for podocyte injury in MRL/lpr mice in a B cell-specific manner.

Background: Deposition of immune complexes drives podocyte injury acting in the initial phase of lupus nephritis (LN), a process mediated by B cell involvement. Accordingly, targeting B cell subsets represents a potential therapeutic approach for LN. Ginsenoside compound K (CK), a bioavailable component of ginseng, possesses nephritis benefits in lupus-prone mice; however, the underlying mechanisms involving B cell subpopulations remain elusive. Methods: Female MRL/lpr mice were administered CK (40 mg/kg) intragastrically for 10 weeks, followed by measurements of anti-dsDNA antibodies, inflammatory chemokines, and metabolite profiles on renal samples. Podocyte function and ultrastructure were detected. Publicly available single-cell RNA sequencing data and flow cytometry analysis were employed to investigate B cell subpopulations. Metabolomics analysis was adopted. SIRT1 and AMPK expression were analyzed by immunoblotting and immunofluorescence assays. Results: CK reduced proteinuria and protected podocyte ultrastructure in MRL/lpr mice by suppressing circulating anti-dsDNA antibodies and mitigating systemic inflammation. It activated B cell-specific SIRT1 and AMPK with Rhamnose accumulation, hindering the conversion of renal B cells into plasma cells. This cascade facilitated the resolution of local renal inflammation. CK facilitated the clearance of deposited immune complexes, thus reinstating podocyte morphology and mobility by normalizing the expression of nephrin and SYNPO. Conclusions: Our study reveals the synergistic interplay between SIRT1 and AMPK, orchestrating the restoration of renal B cell subsets. This process effectively mitigates immune complex deposition and preserves podocyte function. Accordingly, CK emerges as a promising therapeutic agent, potentially alleviating the hyperactivity of renal B cell subsets during LN.

UV-barrier poly(lactic acid) film with light-stabilized Eu complexes as filler.

The poor UV shielding property of PLA limit it further applications on food packaging. The rare-earth complex Eu(DBM)3phen converts absorbed ultraviolet (UV) light to red light, which inspires the development of new UV shielding materials. However, this complex has low photostability and decomposes easily under UV irradiation. Thus, we prepared a long-lasting rare-earth complex transluminant Eu(DBM)2(BP-2)phen by introducing BP-2 into Eu(DBM)3phen, and blended it with PLA to obtain PLA/Eu(DBM)2(BP-2)phen composite films. The test results showed that the complex could reduce the UV transmittance of PLA films by emitting luminescence and heat. The UV transmittance of the composite film with 0.5 % mass fraction decreased from 87.4 % to 7.7 %, compared to pure PLA films, and remained at 11.6 % after 12 days of UV aging. The film had long-lasting UV shielding performance, good transparency and mechanical properties. Finally, In the storage experiments of flaxseed oil, the P/E25 film effectively retarded the oxidation process of the oil.

Synthesis of cerium-based flame retardant containing phosphorus and its impact on the flammability of polylactic acid.

The synthesis and characterization of [Ce2(PPPA)4(OH)2]·4H2O, wherein PPPA denotes 3-(hydroxy(phenyl)phosphoryl)propanoate, were conducted. Its potential as a flame-retardant additive for poly(L-lactic acid) (PLA) in conjunction with ammonium polyphosphate (APP) was investigated. Remarkably, with just incorporation of the 1 % Ce-complex and 4 % APP, the resulting PLA composite (PLA-8) meets the V-0 standard, exhibiting an impressive limiting oxygen index (LOI) of 29.4 %. Moreover, the introduction of the Ce-complex leads to a significant extension of ignition time (TTI), a significant 24.1 % decrease in total heat release (THR) compared to pure PLA, and a notable increase in residual carbon rate from 0.3 % to 3.51 %. Although PLA-8 exhibits a minor decline of 8.7 % in tensile strength and 3.4 % in elongation at break, respectively, compared to pure PLA, there is a substantial improvement of 32.2 % in Young's modulus and 29.9 % in impact resistance. These results emphasise the potential of cerium-based phosphorus-containing flame retardants, with cerium playing a key role in enhancing the flammability characteristics of PLA. This study contributes to the development of sustainable and fire-resistant materials in polymer chemistry.

Hierarchical Piezoelectric Composites for Noninvasive Continuous Cardiovascular Monitoring.

Continuous monitoring of blood pressure (BP) and multiparametric analysis of cardiac functions are crucial for the early diagnosis and therapy of cardiovascular diseases. However, existing monitoring approaches often suffer from bulky and intrusive apparatus, cumbersome testing procedures, and challenging data processing, hampering their applications in continuous monitoring. Here, a heterogeneously hierarchical piezoelectric composite is introduced for wearable continuous BP and cardiac function monitoring, overcoming the rigidity of ceramic and the insensitivity of polymer. By optimizing the hierarchical structure and components of the composite, the developed piezoelectric sensor delivers impressive performances, ensuring continuous and accurate monitoring of BP at Grade A level. Furthermore, the hemodynamic parameters are extracted from the detected signals, such as local pulse wave velocity, cardiac output, and stroke volume, all of which are in alignment with clinical results. Finally, the all-day tracking of cardiac function parameters validates the reliability and stability of the developed sensor, highlighting its potential for personalized healthcare systems, particularly in early diagnosis and timely intervention of cardiovascular disease.

Mass-Produced Skin-Inspired Piezoresistive Sensing Array with Interlocking Interface for Object Recognition.

E-skins, capable of responding to mechanical stimuli, hold significant potential in the field of robot haptics. However, it is a challenge to obtain e-skins with both high sensitivity and mechanical stability. Here, we present a bioinspired piezoresistive sensor with hierarchical structures based on polyaniline/polystyrene core-shell nanoparticles polymerized on air-laid paper. The combination of laser-etched reusable templates and sensitive materials that can be rapidly synthesized enables large-scale production. Benefiting from the substantially enlarged deformation of the hierarchical structure, the developed piezoresistive electronics exhibit a decent sensitivity of 21.67 kPa-1 and a subtle detection limit of 3.4 Pa. Moreover, an isolation layer is introduced to enhance the interface stability of the e-skin, with a fracture limit of 66.34 N/m. Furthermore, the e-skin can be seamlessly integrated onto gloves without any detachment issues. With the assistance of deep learning, it achieves a 98% accuracy rate in object recognition. We anticipate that this strategy will render e-skin with more robust interfaces and heightened sensing capabilities, offering a favorable pathway for large-scale production.

DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism.

DNA cytosine methyltransferases regulate the expression of the genome through the precise epigenetic marking of certain cytosines with a methyl group, and aberrant methylation is a hallmark of human diseases including cancer. Targeting these enzymes for drug design is currently a high priority. We have utilized ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to investigate extensively the reaction mechanism of the representative DNA methyltransferase HhaI (M.HhaI) from prokaryotes, whose overall mechanism is shared with the mammalian enzymes. We obtain for the first time full free energy profiles for the complete reaction, together with reaction dynamics in atomistic detail. Our results show an energetically preferred mechanism in which nucleophilic attack of cytosine C5 on the S-adenosyl-L-methionine (AdoMet) methyl group is concerted with formation of the Michael adduct between a conserved Cys in the active site with cytosine C6. Spontaneous and reversible proton transfer between a conserved Glu in the active site and cytosine N3 at the transition state was observed in our simulations, revealing the chemical participation of this Glu residue in the catalytic mechanism. Subsequently, the ß-elimination of the C5 proton utilizes as base an OH(-) derived from a conserved crystal water that is part of a proton wire water channel, and this syn ß-elimination reaction is the rate-limiting step. Design of novel cytosine methylation inhibitors would be advanced by our structural and thermodynamic characterization of the reaction mechanism.

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility.

The crystal structure of Rad4/Rad23, the yeast homolog of the human nucleotide excision repair (NER) lesion recognition factor XPC-RAD23B ( Min , J. H. and Pavletich , N. P. ( 2007 ) Nature 449 , 570 - 575 ) reveals that the lesion-partner base is flipped out of the helix and binds to amino acids of the protein. This suggests the hypothesis that the flipping of this partner base must overcome a free energy barrier, which constitutes one element contributing to changes in the thermodynamic properties induced by the DNA damage and sensed by the recognition protein. We explored this hypothesis by computing complete flipping free energy profiles for two lesions derived from the procarcinogenic polycyclic aromatic hydrocarbons (PAHs), dibenzo[a,l]pyrene (DB[a,l]P) and benzo[a]pyrene (B[a]P), R-trans-anti-DB[a,l]P-N(6)-dA (R-DB[a,l]P-dA) and R-trans-anti-B[a]P-N(6)-dA (R-B[a]P-dA), and the corresponding unmodified duplex. The DB[a,l]P and B[a]P adducts differ in number and organization of their aromatic rings. We integrate these results with prior profiles for the R-trans-anti-DB[a,l]P-dG adduct ( Zheng , H. et al. ( 2010 ) Chem. Res. Toxicol. 23 , 1868 - 1870 ). All adopt conformational themes involving intercalation of the PAH aromatic ring system into the DNA duplex; however, R-DB[a,l]P-dA and R-B[a]P-dA intercalate from the major groove, while R-DB[a,l]P-dG intercalates from the minor groove. These structural differences produce different computed van der Waals stacking interaction energies between the flipping partner base with the lesion aromatic ring system and adjacent bases; we find that the better the stacking, the higher the relative flipping free energy barrier and hence lower flipping probability. The better relative NER susceptibilities correlate with greater ease of flipping in these three differently intercalated lesions. In addition to partner base flipping, the Rad4/Rad23 crystal structure shows that a protein-ß-hairpin, BHD3, intrudes from the major groove side between the DNA strands at the lesion site. We present a molecular modeling study for the R-DB[a,l]P-dG lesion in Rad4/Rad23 showing BHD3 ß-hairpin intrusion with lesion eviction, and we hypothesize that lesion steric effects play a role in the recognition of intercalated adducts.