Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

Genomic DNA in bacteria exists in a condensed state, which exhibits different biochemical and biophysical properties from a dilute solution. DNA was concentrated on streptavidin‐covered single‐walled carbon nanotubes (Strep ? SWNTs) through biotin–streptavidin interactions. We reasoned that confining DNA within a defined space through mechanical constraints, rather than by manipulating buffer conditions, would more closely resemble physiological conditions. By ensuring a high streptavidin loading on SWNTs of about 1 streptavidin tetramer per 4 nm of SWNT, we were able to achieve dense DNA binding. DNA is bound to Strep ? SWNTs at a tunable density and up to as high as 0.5 mg mL^?1 in solution and 29 mg mL^?1 on a 2D surface. This platform allows us to observe the aggregation behavior of DNA at high concentrations and the counteracting effects of HU protein (a histone‐like protein from Escherichia coli strain U93) on the DNA aggregates. This provides an in vitro model for studying DNA–DNA and DNA–protein interactions at a high DNA concentration.     

Allylic Functionalization of 2,5- and 2,4-Cyclo-Hexadiene-1,3-Dicarboxylates

A series of 2,4- and 2,5-cyclohexadiene-1,3-dicarboxylates were functionalized at the allylic position via oxidation (SeO₂, PDC/t-BuOOH) and halogenation (NBS). The regiochemical outcome for different substrates and reactions was studied and the importance of factors such as reaction mechanism, steric hindrance and reaction intermediates stability was discussed.

     

An original approach to determining traces of tetracycline antibiotics in milk and eggs by solid-phase extraction and liquid chromatography/mass spectrometry

An original and highly specific method able to identify and quantify traces of five tetracycline antibiotics (TCAs) in milk and eggs is presented. This method uses a single solid-phase extraction (SPE) cartridge for simultaneous extraction and purification of TCAs in the above matrices. After diluting 5 mL of intact whole milk or 2 g egg samples with Na(2)EDTA-containing water, samples are passed through a 0.5-g Carbograph 4 extraction cartridge. After analyte elution from the SPE cartridge, an aliquot of the final extract is injected into a liquid chromatography/mass spectrometry (LC/MS) instrument equipped with an electrospray ion source and a single quadrupole. MS data acquisition is performed in the positive-ion mode and by a time-scheduled multiple-ion selected ion-monitoring program. With methanol as organic modifier, the in-source collision-induced dissociation (CID) process generated fragment ions able to pick up one methanol molecule. In several cases, these methanol-adduct fragment ions have m/z values higher than those of the protonated molecules. This event is rarely encountered in MS, thus making the analysis of TCAs by this method extremely specific. Compared with a conventional published method, the present protocol extracted larger amounts of TCAs from both milk and egg and decreased the analysis time by a factor of 3. Recovery of TCAs in milk at the 25-ppb level ranged between 81 and 96% with relative standard deviation (RSD) no larger than 9%. Recovery of TCAs in egg at the 50-ppb level ranged between 72 and 92% with RSD no larger than 7%. Estimated limits of quantification(S/N = 10) of the method were 2-9 ppb TCAs in whole milk and 2-19 ppb TCAs in eggs.     

A NMR and computational study of Smac mimics targeting both the BIR2 and BIR3 domains in XIAP protein

In this paper we report an extensive NMR analysis of small ligands (Smac mimics) complexed with different constructs of XIAP. The mimics-binding site of XIAP is known as the BIR3 domain - primary, and the linker BIR2 region - secondary site. Interactions between the BIR3 domain and Smac mimics have been extensively studied by X-ray but, as of today, there are scarce data about the interaction between BIR2, or the whole linker-BIR2-BIR3 construct, and Smac mimics. In order to characterize our Smac mimics, we performed a STD NMR study between our 4-substituted, 1-aza-2-oxobicyclo[5.3.0]decane scaffold-based molecules and three different XIAP fragments: single BIR2 and BIR3 domains, and bifunctional linker-BIR2-BIR3. The results were integrated with docking calculations and molecular dynamics simulations. NMR data, which are consistent with biological tests, indicated that the two BIR subunits interact differently with our Smac mimics and suggest that the ligands enter into more intimate contact with the linker-BIR2-BIR3. In conclusion, we observe that the SMAC mimics showed with the construct linker-BIR2-BIR3 a series of NOE contacts that were not observed in the mono-domain ligand:BIR2 or :BIR3 complexes. So, in agreement with the computational models we believe that the linker moieties of the binding site play a key role in the stability of the protein complex.     

Hydrogen Atoms Location in Os<Subscript>3</Subscript>(μ-H)(CO)<Subscript>9</Subscript>(μ<Subscript>3</Subscript>, η<Superscript>2</Superscript>-C<Subscript>2</Subscript>H) from Accurate X-Ray Data at 100 K

Abstract  

The structure of the complex Os₃(μ-H)(CO)₉(μ₃, η²-C₂H) has been determined using X-ray data collected at low temperature (100 K); all hydrogen atoms have been located. The asymmetric unit is formed by two molecules joined through hydrogen bonds involving the hydrogen atoms of C₂H moiety and the oxygen atoms of carbonyl groups. The complex crystallizes in the monoclinic space group P2₁/c with a = 12.94040(2), b = 15.4705(2), c = 16.0164(2) ?, β = 106.0860(10)°, and V = 3,080.85(7) ?³, Z = 8. A molecule is formed by a triangular Os₃ cluster, with metal atoms bearing terminal CO groups. The acetylenic residual is formally π-bonded to two Os atoms in a perpendicular mode and σ-linked to the third Os atom. A bridging hydride atom completes the coordination.     

Antioxidant and antiproliferative activity of Laurus nobilis L. (Lauraceae) leaves and seeds essential oils against K562 human chronic myelogenous leukaemia cells

The antioxidant and antiproliferative activities of the essential oils from Laurus nobilis leaves and seeds in relation to their composition were analysed. The most abundant components of the leaf essential oil were 1,8-cineole, 1-p-menthen-8-ethyl acetate, linalool and sabinene, while the seed oil was characterised by β-ocimene, 1,8-cineole, α-pinene and β-pinene as main constituents. Both seed and leaf essential oils exhibited a scavenging effect on the DPPH radical, with IC?? values of 66.1 and 53.5?μg?mL?1, respectively. The leaf essential oil showed the strongest antioxidant activity in the β-carotene/linoleic acid system, with an IC?? value of 35.6?μg?mL?1 after 30?min of incubation. Both leaf and seed oils inhibited proliferation of the K562 tumour cell line with IC?? values of 95 and 75?μg?mL?1, respectively. The L. nobilis leaf oil showed a percentage of erythroide differentiation of 15% at a concentration of 10?μg?mL?1. A value of 12% was found for the seed essential oil at a concentration of 50?μg?mL?1. When the oils were added to a suboptimal concentration of the commercial drug, cytosine arabinoside, a clear synergic effect was observed.     

Comparative chemical composition and antioxidant activity of Calamintha nepeta (L.) Savi subsp. glandulosa (Req.) Nyman and Calamintha grandiflora (L.) Moench (Labiatae)

The two studied Calamintha species showed different polyphenolic content and sterol composition. Calamintha grandiflora possessed twice the polyphenolic content of Calamintha nepeta subsp. glandulosa, while the latter contained a higher number of sterols. Among them, stigmast-5-en-3β-ol was found to be the major constituent. The methanolic extract of C. grandiflora was more potent than the C. nepeta subsp. glandulosa methanolic extract in a DPPH assay, while the activity of the C. grandiflora EtOAc fraction was weaker than its C. nepeta subsp. glandulosa counterpart. Fractions of C. nepeta subsp. glandulosa showed higher activity using a β-carotene bleaching test. The petrol ether fraction of C. grandiflora showed significant inhibition of NO production.