Cyclohexanyl peptide nucleic acids (chPNAs) for preferential RNA binding: effective tuning of dihedral angle beta in PNAs for DNA/RNA discrimination

[structures: see text] A serious drawback of peptide nucleic acids (PNAs) from an application perspective that has not been adequately dealt with is nondiscrimination of identical DNA and RNA sequences. An analysis of the available X-ray and NMR solution structures of PNA complexes with DNA and RNA suggested that it might be possible to rationally impart DNA/RNA duplex binding selectivity by tuning the dihedral angle beta of the flexible ethylenediamine part of the PNA backbone (II) via suitable chemical modifications. Cyclohexanyl PNAs (chPNAs) with beta approximately = 65 degrees were designed on the basis of this rationale. The chPNAs introduced remarkable differences in duplex stabilities among their DNA and RNA complexes, with melting temperatures (deltaTm(RNA-DNA) = +16-50 degrees C) depending on the number of modifications and the stereochemistry. This is a highly significant, exceptional binding selectivity of a mix sequence of PNA to RNA over the same DNA sequence as that seen to date. In contrast, cyclopentanyl PNAs (cpPNAs) with beta approximately = 25 degrees hybridize to DNA/RNA strongly without discrimination because of the ring puckering of the cyclopentane ring. The high affinity of chPNAs to bind to RNA without losing base specificity will have immediate implications in designing improved PNAs for therapeutic and diagnostic applications.     

Synthesis,structure and magnetic properties of mono- and di-nuclear nickel(II) thiocyanate complexes with tridentate N3 donor Schiff bases

The 1:1 condensation of N-methyl-1,3-diaminopropane and N,N-diethyl-1,2-diminoethane with 2-acetylpyridine, respectively at high dilution gives the tridentate mono-condensed Schiff bases N-methyl-N′-(1-pyridin-2-yl-ethylidene)-propane-1,3-diamine (L¹) and N,N-diethyl-N′-(1-pyridin-2-yl-ethylidene)-ethane-1,2-diamine (L²). The tridentate ligands were allowed to react with methanol solutions of nickel(II) thiocyanate to prepare the complexes [Ni(L¹)(SCN)₂(OH₂) (1) and [{Ni(L²)(SCN)}₂] (2). Single crystal X-ray diffraction was used to confirm the structures of the complexes. The nickel(II) in complex 1 is bonded to three nitrogen donor atoms of the ligand L¹ in a mer orientation, together with two thiocyanates bonded through nitrogen and a water molecule, and it is the first Schiff base complex of nickel(II) containing both thiocyanate and coordinated water. The coordinated water initiates a hydrogen bonded 2D network. In complex 2, the nickel ion occupies a slightly distorted octahedral coordination sphere, being bonded to three nitrogen atoms from the ligand L², also in a mer orientation, and two thiocyanate anions through nitrogen. In contrast to 1, the sixth coordination site is occupied by a sulfur atom from a thiocyanate anion in an adjacent molecule, thus creating a centrosymmetric dimer. A variable temperature magnetic study of complex 2 indicates the simultaneous presence of zero-field splitting, weak intramolecular ferromagnetic coupling and intermolecular antiferromagnetic interactions between the nickel(II) centers.     

Syntheses and crystal structures of cadmium(II)X2-hexamethylenetetramine (X = Br/I/SCN) coordination polymers having different dimensionality

Four new coordination polymers of cadmium(II) with hexamethylenetetramine (htm) have been synthesized and characterized by routine physicochemical techniques as well as by X-ray single crystal structure analysis. They are [CdBr(htm)(SCN)(H₂O)₂·CH₃OH]_n (1), [CdI(htm)(SCN)(H₂O)₂·0.5(CH₃OH)]_n (2), [Cd₂(htm)₃(SCN)₄(H₂O)]_n·nH₂O (3) and [Cd₃Br₆(htm)₂(H₂O)₅·(htm)(H₂O)₆]_n (4). Complexes 1, 2 and 3 exhibit 1D polymeric structure and complex 4 shows a 2D undulated layered arrangement, containing Cd₆(htm)₆ hexagonal units as building block, which extended to a 3D supramolecular architecture through hydrogen bonding. Thorough thermal investigation suggest that as far as the thermal stability of Cd(II)-htm bond is concerned it attains the maximum in complex 1 and minimum in complex 4. In case of complex 3 the thermal study inferred that CdS end product was obtained at ∼730 °C, whereas in case of other complexes the thermally stable end product remained unidentified. Solid state fluorescence study shows that all the complexes are luminescent at room temperature except complex 3.     

Synthesis and catalytic epoxidation potential of oxodiperoxo molybdenum(VI) complexes with 2-hydroxybenzohydroxamate and 2-hydroxybenzoate: the crystal structure of PPh<Subscript>4</Subscript>[MoO(O<Subscript>2</Subscript>)<Subscript>2</Subscript>(HBA)]

(PPh₄)₂[MoO(O₂)₂(SHAH)]·H₂O and PPh₄[MoO(O₂)₂(HBA)] (SHAH₃ = 2-hydroxybenzohydroxamic acid and HBAH = 2-hydroxybenzoic acid) have been synthesized and characterized by physico-chemical and spectroscopic methods. In addition, the second complex has been structurally characterized by single-crystal X-ray diffraction analysis. We have compared the catalytic activities of these two new complexes, together with the previously reported PPh₄[MoO(O₂)₂(BZ)] (BZH = benzoic acid), with respect to the epoxidation of alkenes. The hydroxamate complex is the most efficient catalyst among the three complexes, showing excellent catalytic activity for the substrates cyclohexene, cyclooctene, cinnamyl alcohol, pent-4-en-1-ol and hex-1-ene.     

Positive and negative giant Goos–Hänchen shift in a near-symmetric layered medium for illumination from opposite ends

We study giant Goos–Hänchen (GH) shift in reflection from a near-symmetric coupled waveguide structure. We show that broken spatial symmetry can lead to GH shift with different signs for illumination from the opposite ends, a direct consequence of the nonreciprocity relations considered earlier (Opt. Lett. 27,1205 (2002)). We show that the asymmetry due to a tiny 5 nm displacement of the coupled guide to one side can result in giant differential shifts. Due attention is paid to possible beam splittings for tightly focused beams in resonant structures.     

Strangeness enhancement in Cu-Cu and Au-Au collisions at √S(NN)=200 GeV

We report new STAR measurements of midrapidity yields for the Λ, Λ[over ˉ], K(S)(0), Ξ(-), Ξ[over ˉ](+), Ω(-), Ω[over ˉ](+) particles in Cu+Cu collisions at √S(NN)==200 GeV, and midrapidity yields for the Λ, Λ[over ˉ], K(S)(0) particles in Au+Au at √S(NN)==200 GeV. We show that, at a given number of participating nucleons, the production of strange hadrons is higher in Cu+Cu collisions than in Au+Au collisions at the same center-of-mass energy. We find that aspects of the enhancement factors for all particles can be described by a parametrization based on the fraction of participants that undergo multiple collisions.     

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.