Chemical mutagens with an aromatic ring system may be enzymatically transformed to afford aryl radical species that preferentially react at the C8-site of 2′-deoxyguanosine (dG). The resulting carbon-linked C8-aryl-dG adduct possesses altered biophysical and genetic coding properties compared to the precursor nucleoside. Described herein are structural and in vitro mutagenicity studies of a series of fluorescent C8-aryl-dG analogues that differ in aryl ring size and are representative of authentic DNA adducts. These structural mimics have been inserted into a hotspot sequence for frameshift mutations, namely, the reiterated G3-position of the NarI sequence within 12mer (NarI(12)) and 22mer (NarI(22)) oligonucleotides. In the NarI(12) duplexes, the C8-aryl-dG adducts display a preference for adopting an anti-conformation opposite C, despite the strong syn preference of the free nucleoside. Using the NarI(22) sequence as a template for DNA synthesis in vitro, mutagenicity of the C8-aryl-dG adducts was assayed with representative high-fidelity replicative versus lesion bypass Y-family DNA polymerases, namely, Escherichia coli pol I Klenow fragment exo− (Kf−) and Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Our experiments provide a basis for a model involving a two-base slippage and subsequent realignment process to relate the miscoding properties of C-linked C8-aryl-dG adducts with their chemical structures.

Bis(1,1,1-trifluoro-5,5-dimethyl-5-methoxy-acetylacetonato)copper(II) was prepared in two polymorphic modifications. The orthorhombic R-form is stable and densely packed, with four trans and four cis square bischelate building blocks per unit cell. These are connected through additional coordination bonds to form a dense polymer network. For the trigonal β-form, the square bischelate complex units are present exclusively as the trans isomers. The distinctive assembly of these units results in a lattice with an open pore volume of about 17% that is accessible to a wide range of guests. The compound has a remarkably strong affinity for the porous β-form as evident from the efficient R-to-β conversion on contact not only with liquid guests but also with organic vapors at pressures well below the saturation pressure. Although the open β-form is metastable, it has a remarkable kinetic stability, most likely because of the trans-to-cis isomerization that must accompany the β-to-R transformation. Many sorbents play a dual role as stabilizing guest and as catalyst promoting the R-to-β or β-to-R conversion. Because of its versatile sorption properties and relative robustness, the β-form of the complex can be classified as a novel organic zeolite mimic.

Robust porous frameworks are formed by the dipeptides L‐Ala‐L‐Val (see structure) and L‐Val‐L‐Ala that have a high capacity and selectivity for gas sorption. The dipeptides assemble through hydrogen bonds as a 61 helix to form channels with average diameters of 5.13 and 4.90 Å, respectively.

Background:The human innate immune system can discriminate between Candida albicans yeast and hyphal forms. Results: C. albicans hyphae possess glucan structures that are unique to the hyphae and are not found in yeast. Conclusion: Hyphal glucan elicits robust immune responses.Significance: These data provide a structural basis for differential immune recognition of C. albicans yeast versus hyphae.

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Eight crystalline dipeptides were studied: AV (Ala-Val), VA (Val-Ala), AI (Ala-Ile), VV (Val-Val), IA (Ile-Ala), IV (Ile-Val), VI (Val-Ile), and LS (Leu-Ser) (all LL isomers). The first seven form an isostructural series (space group P6(1)), whereas LS has a different structure (P6(5)). All structures display H-bonded tubular assemblies of the dipeptide molecules resulting in open ultramicropores in the form of isolated one-dimensional (1D) channels. The total porosity of the materials ranges from 4 to 12% (micropore volume from 0.04 to 0.12 cm(3)/g). Calculations based on the crystal structures, He pycnometry, and solid-state (129)Xe NMR methods were used to obtain a comprehensive description of the geometry and properties of the micropores. The following order was established for the channel diameter: AV > VA > AI > VV > IA > IV > VI, with >5 A for AV and <4 A for VI; LS is close to AI. The observed sorption behavior cannot be described adequately based on the crystal structure and can only be understood if one takes into account the dynamics of the host matrix. The pores are chiral, with the center of the channel describing a right-handed helix (left-handed for LS). The following order was established for the channel helicity: VA > IA > IV > AV approximately AI approximately VV > VI > LS, with a helix diameter of approximately 2 A for VA, IA, and IV and approximately 1 A or less for the remaining dipeptides. A comparison of the dipeptides studied with other supramolecular materials is given and the potential for applications is discussed.

To further an understanding of the nature of information available from Xe chemical shifts in cavities in biological systems, it would be advantageous to start with Xe in regular nanochannels that have well known ordered structures built from amino acid units. In this paper, we report the experimental observation of Xe NMR lineshapes in peptide channels, specifically the self-assembled nanochannels of the dipeptide L-Val-L-Ala and its retroanalog L-Ala-L-Val in the crystalline state. We carry out grand canonical Monte Carlo simulations of Xe in these channels to provide a physical understanding of the observed Xe lineshapes in these two systems.S elf-assembling structures with nanochannels have been of increasing interest (1, 2). A subset of these (peptide-based nanochannels) have demonstrated applicability as transmembrane pores and ion channels, as well as size-selective ion sensors (1). Görbitz and coworkers (3, 4) have described peptide nanochannels formed by the aggregation of dipeptides in a head-to-tail hydrogen-bonded network, forming a channel with a hydrophobic interior. Two such systems, the dipeptide L-Val-L-Ala (3) (VA) and its retroanalog, L-Ala-L-Val (4) (AV), form two distinct channels, which have been demonstrated to act as supramolecular hosts for organic molecules. These dipeptide systems are the subject of the present study.Binding of Xe within cavities in proteins is common because of several favorable factors. The Xe atom has a large electric dipole polarizability; cavities within proteins are about the correct size to hold one or more Xe atoms, and the unfavorable entropic term related to the need to orient the ligand in the binding site is absent for Xe atom. The affinity of Xe for hydrophobic cavities in the interiors of macromolecules (5-10) coupled with the development of techniques for hyperpolarization of Xe nuclear spins have inspired an array of NMR studies of Xe in proteins (11), cells, (12, 13), and tissues (14-16). For example, hyperpolarized (HP) 129 Xe has been developed as a tool for the characterization of protein cavities which bind Xe, by using its nuclear spin polarization to enhance the signals of the protons in the cavity (10, 17), by using the Xe chemical shift itself as a reporter of cavity structure in both solution and the solid state (11), and in applications to biomolecular assays (18,19).Xe adsorbed into nanochannels and cavities gives rise to an anisotropic lineshape in the NMR spectrum. Such lineshapes have been observed experimentally in 1D channels in various crystalline materials (20)(21)(22)(23), with the observed lineshape varying with changing Xe occupancy within the channel. A theoretical understanding, using the dimer tensor model in grand canonical Monte Carlo (GCMC) simulations (24), permits the prediction of the average Xe chemical shift tensor and the lineshapes that are observed in the Xe NMR spectrum of a polycrystalline sample (24, 25) or of a single crystal (26), with no adjustable parameters. The lineshapes calculated for a uniform distribution...

In this contribution we show that host materials based on metal dibenzoylmethanates (DBM) can be extended in a versatile way by decreasing the packing efficiency of the simpler metal DBM's reported earlier. Specifically, this can be accomplished by coordinating two 4-vinylpyridines (4-ViPy) to the metal (Ni or Co) DBM units to give [M(4-ViPy)2(DBM)2] host complexes. These display a remarkable polymorphism and an ability to form inclusion compounds with a large variety of organic species. Five non-clathrate phases representing three polymorphic types and twenty-eight inclusion compounds with nineteen guests, representing five structural types were isolated and studied in varying degrees of detail. The inclusion compounds can be prepared by recrystallization or by interaction of the solid host with guest vapor. In the latter case, the process realization, kinetics and final product strongly depend on the host polymorph chosen as starting material. Kinetic studies executed with powder XRD suggest that transient formation of inclusion compounds may occur even during solvent vapor induced transformation of one guest-free polymorph to another. The beta polymorph of the Ni-host reveals the strongest clathratogenic ability as well as a high selectivity towards certain homologues and isomers. Its properties give insight into the concept of "flexible zeolite mimics", or "apohosts", as this empty host form is energetically and structurally predisposed towards inclusion processes. In all eleven (three host and eight clathrate) structures studied by single crystal X-ray diffraction the [M(4-Vi-Py)2(DBM)2] complex molecule is transconfigured. In most, the host molecules show effective packing in one dimension by forming parallel chains. Guest species are located between the chains in cages or channels formed by combining voids in the host molecules belonging to adjacent chains. The corresponding Ni and Co versions of the compounds studied were similar.