Dynamics of large elongated RNA by NMR carbon relaxation

We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbons with a domain elongation strategy for decoupling internal from overall motions and residual dipolar coupling (RDC) measurements for determining the average RNA global conformation and orientation of the principal axis of the axially symmetric rotational diffusion. TROSY-detected pulse sequences are presented for the accurate measurement of nucleobase carbon R1 and R1rho rates in large RNAs. The relaxation data is analyzed using a model free formalism which takes into account the very high anisotropy of overall rotational diffusion (Dratio approximately 4.7), asymmetry of the nucleobase CSAs and noncollinearity of C-C, C-H dipolar and CSA interactions under the assumption that all interaction tensors for a given carbon experience identical isotropic internal motions. The approach is demonstrated and validated on an elongated HIV-1 TAR RNA (taum approximately 18 ns) both in free form and bound to the ligand argininamide (ARG). Results show that, while ARG binding reduces the amplitude of collective helix motions and local mobility at the binding pocket, it leads to a drastic increase in the local mobility of "spacer" bulge residues linking the two helices which undergo virtually unrestricted internal motions (S2 approximately 0.2) in the ARG bound state. Our results establish the ability to quantitatively study the dynamics of RNAs which are significantly larger and more anisotropic than customarily studied by NMR carbon relaxation.     

Tin-Naphthalene Sulfonic Acid Complexes as Photostabilizers for Poly(vinyl chloride)

Poly(vinyl chloride) degrades when exposed to ultraviolet light for long durations; therefore, the photostability of polymeric materials should be enhanced through the application of additives. New organotin complexes containing 4-aminonaphthalene-1-sulfonic acid were synthesized and their role as poly(vinyl chloride) photostabilizers were evaluated. The reaction of 4-amino-3-hydroxynaphthalene-1-sulfonic acid and appropriate di- or trisubstituted tin chloride (triphenyltin chloride, tributyltin chloride, dibutyltin dichloride, and dimethyltin dichloride) in methanol under reflux gave the corresponding tin-naphthalene complexes with yields of 75%–95%. Elemental analyses and spectroscopic techniques including infrared and nuclear magnetic resonance (proton and tin) were used to confirm their structures. The tin complexes were added to poly(vinyl chloride) to produce thin films that irradiated with ultraviolet light. Various parameters were assessed, such as the weight loss, formation of specific functional groups, changes in the surface due to photoirradiation, and rate constant of photodegradation, to test the role played by the organotin complexes to reduce photodegradation in polymeric films. The results proved that organotin complexes acted as photostabilizers in these circumstances. The weight loss, formation of fragments containing specific functional groups, and undesirable changes in the surface of polymeric films were limited in the presence of organotin complexes. Organotin complexes containing three phenyl groups showed the most desirable stabilization effect. These act as efficient primary and secondary photostabilizers, and as decomposers for peroxides. In addition, such an additive inhibits the dehydrochlorination process, which is the main cause of poly(vinyl chloride) photodegradation.     

Theoretical studies on mechanical and electronic properties of s-triazine sheet

Abstract

Mechanical and electronic properties of s-triazine sheet are studied using first-principles calculations based on density functional theory. The in-plane stiffness and bulk modulus for s-triazine sheet are found to be less than that of heptazine. The reduction can be related to the nature of the covalent bonds connecting the adjacent sheets and the number of atoms per unit cell. The Poisson’s ratio of s-triazine sheet is half the value to that of graphene. Additionally, the calculated values of the two critical strains (elastic and yielding points) of s-triazine sheet are in the same order of magnitude to that for heptazine which was calculated using MD simulations in the literature. It is also demonstrated that s-triazine sheet can withstand larger tension in the plastic region. These results established a stable mechanical property for s-triazine sheet. We found a linear relationship of bandgap as a function of bi-axial tensile strain within the harmonic elastic region. The reduced steric repulsion of the lone pairs (p_x-, p_y-) causes the p_z-like orbital to shift to high energy, and consequently an increase in the bandgap. We find no electronic properties modulation of the s-triazine sheet under electric field up to a peak value of 10 V/nm. Such noble properties may be useful in future nanomaterial applications.     

Synthesis of 4-alkyl-, 4-aryl- and 4-arylamino-5-aminoisoquinolin-1-ones and identification of a new PARP-2 selective inhibitor

The considerable interest in substituted isoquinolin-1-ones related to 5-aminoisoquinolin-1-one (5-AIQ) as drugs points to a need for an efficient and straightforward synthesis of the 4,5-disubstituted bicycles. Bromination of 5-nitroisoquinolin-1-one gave 4-bromo-5-nitroisoquinolin-1-one but neither this nor 5-amino-4-bromoisoquinolin-1-one would participate in Pd-catalysed couplings. Protection of the lactam as 1-methoxy- and 1-benzyloxy-4-bromo-5-nitroisoquinolines, however, permitted Stille, Suzuki and Buchwald-Hartwig couplings to take place in high yields, insensitive to electronic demands and severe steric bulk in the arylboronic acids. Lithiation of 4-bromo-1-methoxy-5-nitroisoquinoline and quench with iodomethane gave 1-methoxy-4-methyl-5-nitroisoquinoline in low yield. Demethylation of the 1-methoxy-4-substituted-5-nitroisoquinolines with hydrogen bromide gave 4-substituted-5-nitroisoquinolin-1-ones, whereas hydrogenolytic debenzylation was achieved with simultaneous reduction of the 5-nitro group. 5-Amino-4-(4-trifluoromethylphenyl)isoquinolin-1-one was identified as a new potent and selective inhibitor of poly(ADP-ribose)polymerase-2 (PARP-2).     

Lignans and other constituents from aerial parts of Haplophyllum villosum

During our phytochemical investigation of Haplophyllum villosum (Rutaceae), a perennial herb from Iran, a new 4,8-diaryl-3,7-dioxobicyclo-(3,3,0)-octane type lignan, eudesmin A (1), together with four known compounds--eudesmin (2), haplamine (3), umbelliferone (4) and scopoletin (5)--were isolated from aerial parts of the plant. The structures of the compounds were elucidated using NMR spectral analysis (1H-NMR, 13C-NMR, HSQC, COSY and HMBC) as well as UV, IR and MS spectra and comparison with previously reported data.     

Identification of potential complementary serum biomarkers to differentiate prostate cancer from benign prostatic hyperplasia using gel- and lectin-based proteomics analyses

Diagnosis of prostate cancer (PCa) is currently much reliant on the invasive and time-consuming transrectal ultrasound-guided biopsy of the prostate gland, particularly in light of the inefficient use of prostate-specific antigen as its biomarker. In the present study, we have profiled the sera of patients with PCa and benign prostatic hyperplasia (BPH) using the gel- and lectin-based proteomics methods and demonstrated the significant differential expression of apolipoprotein AII, complement C3 beta chain fragment, inter-alpha-trypsin inhibitor heavy chain 4 fragment, transthyretin, alpha-1-antitrypsin, and high molecular weight kininogen (light chain) between the two groups of patients' samples. Our data are suggestive of the potential use of the serum proteins as complementary biomarkers to effectively discriminate PCa from BPH, although this requires further extensive validation on clinically representative populations.     

Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution

Nucleic acids transiently morph into alternative conformations that can be difficult to characterize at the atomic level by conventional methods because they exist for too little time and in too little abundance. We recently reported evidence for transient Hoogsteen (HG) base pairs in canonical B-DNA based on NMR carbon relaxation dispersion. While the carbon chemical shifts measured for the transient state were consistent with a syn orientation for the purine base, as expected for A(syn)?T(anti) and G(syn)?C(+)(anti) HG base pairing, HG type hydrogen bonding could only be inferred indirectly. Here, we develop two independent approaches for directly probing transient changes in N-H···N hydrogen bonds and apply them to the characterization of transient Hoogsteen type hydrogen bonds in canonical duplex DNA. The first approach takes advantage of the strong dependence of the imino nitrogen chemical shift on hydrogen bonding and involves measurement of R(1ρ) relaxation dispersion for the hydrogen-bond donor imino nitrogens in G and T residues. In the second approach, we assess the consequence of substituting the hydrogen-bond acceptor nitrogen (N7) with a carbon (C7H7) on both carbon and nitrogen relaxation dispersion data. Together, these data allow us to obtain direct evidence for transient Hoogsteen base pairs that are stabilized by N-H···N type hydrogen bonds in canonical duplex DNA. The methods introduced here greatly expand the utility of NMR in the structural characterization of transient states in nucleic acids.     

The role of pulse time Toff on porous silicon as template for Au nanoparticles by using the integrated electrochemical technique

Gold nanoparticles (AuNPs) having variety of sizes and shape were prepared using the template synthesis approach. Porous silicon (PSi) was fabricated using the pulsed electrochemical anodization method at different pause times, T_off as template for gold deposition. Choosing suitable pulse parameter produces PSi with higher porosity and smaller crystallite size. SEM showed that the variation of T_off affects the pores formation and the growth of gold nanoparticles while EDX suggested the presence of Au inside the pores structure. Photoluminescence spectra showed emission enhancement and a blue shifted relative to porous silicon before deposited with AuNPs. XRD shows a high degree crystallinity of the samples and the presence of cubic gold with crystalline sizes was around 42 nm.     

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints

Using residual chemical shift anisotropies (RCSAs) measured in a weakly aligned stem-loop RNA, we examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measured RCSAs and the values back-calculated using three nucleobase carbon CSA sets [D. Stueber, D.M. Grant, 13C and 15N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551; D. Sitkoff, D.A. Case, Theories of chemical shift anisotropies in proteins and nucleic acids, Prog. NMR Spectrosc. 32 (1998) 165-190; R. Fiala, J. Czernek, V. Sklenar, Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids, J. Biomol. NMR 16 (2000) 291-302] reported previously for mononucleotides (1.4 Hz) is significantly smaller than the predicted RCSA range (-10-10 Hz) but remains larger than the RCSA measurement uncertainty (0.8 Hz). Fitting of the traceless principal CSA values to the measured RCSAs using a grid search procedure yields a cytosine C5 CSA magnitude (CSAa=(3/2.(delta11(2)+delta22(2)+delta33(2)))1/2=173+/-21 ppm), which is significantly higher than the reported mononucleotide values (131-138 ppm) and a guanine C8 CSAa (148+/-13 ppm) that is in very good agreement with the mononucleotide value reported by solid-state NMR [134 ppm, D. Stueber, D.M. Grant, 13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551]. Owing to a unique sensitivity to directions normal to the base plane, the RCSAs can be translated into useful long-range orientational constraints for RNA structure determination even after allowing for substantial uncertainty in the nucleobase carbon CSA tensors.