Synthesis and analysis of oligonucleotides containing abasic site analogues

DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.     

Chemoenzymatic synthesis of 7-deaza cyclic adenosine 5'-diphosphate ribose analogues, membrane-permeant modulators of intracellular calcium release

An optimized synthetic route to 7-deaza-8-bromo-cyclic adenosine 5'-diphosphate ribose (7-deaza-8-bromo-cADPR 3), an established cell-permeant, hydrolysis-resistant cyclic adenosine 5'-diphosphate ribose (cADPR) antagonist, is presented. Using NMR analysis, we found that 3 adopted a C-2' endo conformation in the N9-linked ribose and a syn conformation about the N9-glycosyl linkage, which are similar to that of cADPR. The synthetic route was also employed to produce 7-deaza-2'-deoxy-cADPR 4, a potential cell-permeant cADPR analogue. 3 and 4 were more stable to chemical hydrolysis, consistent with the observation that 7-deaza-cADPR analogues are more stable than their parent adenosine derivatives. 3 was also found to be stable to enzyme-mediated hydrolysis using CD38 ectoenzyme.     

Experimental Confirmation of a Predicted Porous Hydrogen-Bonded Organic Framework

Hydrogen-bonded organic frameworks (HOFs) with low densities and high porosities are rare and challenging to design because most molecules have a strong energetic preference for close packing. Crystal structure prediction (CSP) can rank the crystal packings available to an organic molecule based on their relative lattice energies. This has become a powerful tool for the a priori design of porous molecular crystals. Previously, we combined CSP with structure-property predictions to generate energy-structure-function (ESF) maps for a series of triptycene-based molecules with quinoxaline groups. From these ESF maps, triptycene trisquinoxalinedione (TH5) was predicted to form a previously unknown low-energy HOF (TH5-A) with a remarkably low density of 0.374 g cm⁻³ and three-dimensional (3D) pores. Here, we demonstrate the reliability of those ESF maps by discovering this TH5-A polymorph experimentally. This material has a high accessible surface area of 3,284 m² g⁻¹, as measured by nitrogen adsorption, making it one of the most porous HOFs reported to date.     

Quantum mechanical calculations for the H2O + hnu --> O(1D) + H2 photodissociation process

Quantum mechanical wavepacket calculations for the photodissociation of water in the second absorption band are presented. Using O + H2 Jacobi coordinates, partial cross sections for the O(1D) + H2 channel are calculated for different initial rotational states. Conical intersection and Renner-Teller effects are included. The branching ratios for the four accessible dissociation channels at 121.6 nm are in good agreement with experiment (J. Chem. Phys. 1982, 77, 2432). The calculations predict significant rotational and vibrational excitation of the H2 fragments. Photodissociation of ortho and para water produces predominantly, but not exclusively, ortho and para H2 fragments, respectively.     

On realistic terrains

We study worst-case complexities of visibility and distance structures on terrains under realistic assumptions on edge length ratios and the angles of the triangles, and a more general low-density assumption. We show that the visibility map of a point for a realistic terrain with n triangles has complexity . We also prove that the shortest path between two points p and q on a realistic terrain passes through triangles, and that the bisector of p and q has complexity . We use these results to show that the shortest path map for any point on a realistic terrain has complexity , and that the Voronoi diagram for any set of m points on a realistic terrain has complexity and . Our results immediately imply more efficient algorithms for computing the various structures on realistic terrains.     

Compactness of sequences of two-dimensional energies with a zero-order term. Application to three-dimensional nonlocal effects

In this paper we study the limit, in the sense of the Γ-convergence, of sequences of two-dimensional energies of the type , where A _n is a symmetric positive definite matrix-valued function and μ _n is a nonnegative Borel measure (which can take infinite values on compact sets). Under the sole equicoerciveness of A _n we prove that the limit energy belongs to the same class, i.e. its reads as , where is a diffusion independent of μ _n and μ is a nonnegative Borel measure which does depend on . This compactness result extends in dimension two the ones of [11,23] in which A _n is assumed to be uniformly bounded. It is also based on the compactness result of [7] obtained for sequences of two-dimensional diffusions (without zero-order term). Our result does not hold in dimension three or greater, since nonlocal effects may appear. However, restricting ourselves to three-dimensional diffusions with matrix-valued functions only depending on two coordinates, the previous two-dimensional result provides a new approach of the nonlocal effects. So, in the periodic case we obtain an explicit formula for the limit energy specifying the kernel of the nonlocal term.     

Steering the Selectivity of Electrocatalytic Glucose Oxidation by the Pt Oxidation State

Electrocatalytic glucose oxidation can produce high value chemicals, but selectivity needs to be improved. Here we elucidate the role of the Pt oxidation state on the activity and selectivity of electrocatalytic oxidation of glucose with a new analytical approach, using high-pressure liquid chromatography and high-pressure anion exchange chromatography. It was found that the type of oxidation, i.e. dehydrogenation of primary and secondary alcohol groups or oxygen transfer to aldehyde groups, strongly depends on the Pt oxidation state. Pt⁰ has a 7-fold higher activity for dehydrogenation reactions than for oxidation reactions, while PtO_x is equally active for both reactions. Thus, Pt⁰ promotes glucose dialdehyde formation, while PtO_x favors gluconate formation. The successive dehydrogenation of gluconate is achieved selectively at the primary alcohol group by Pt⁰, while PtO_x also promotes the dehydrogenation of secondary alcohol groups, resulting in more complex reaction mixtures.     

Combinatorial Screening of Water/Proton Permeation of Self-Assembled Pillar[5]arene Artificial Water Channel Libraries

Artificial water channels (AWCs) that selectively transport water and reject ions through bilayer membranes have potential to act as synthetic Aquaporins (AQPs). AWCs can have a similar osmotic permeability, better stability, with simpler manufacture on a larger-scale and have higher functional density and surface permeability when inserted into the membrane. Here, we report the screening of combinatorial libraries of symmetrical and unsymmetrical rim-functionalized PAs A – D that are able to transport ca. 10⁷–10⁸ water molecules/s/channel, which is within 1 order of magnitude of AQPs’ and show total ion and proton rejection. Among the four channels, C and D are 3–4 times more water permeable than A and B when inserted in bilayer membranes. The binary combinations of A – D with different molar ratios could be expressed as an independent (linear ABA ), a recessive (inhibition AB , AC , DB , ACA ), or a dominant (amplification, DBD ) behavior of the water net permeation events.     

Ultrafast vibrational dynamics of interfacial water

We report investigations of the vibrational dynamics of water molecules at the water–air and at the water–lipid interface. Following vibrational excitation with an intense femtosecond infrared pulse resonant with the O–H stretch vibration of water, we follow the subsequent relaxation processes using the surface-specific spectroscopic technique of sum frequency generation. This allows us to selectively follow the vibrational relaxation of the approximately one monolayer of water molecules at the interface. Although the surface vibrational spectra of water at the interface with air and lipids are very similar, we find dramatic variations in both the rates and mechanisms of vibrational relaxation. For water at the water–air interface, very rapid exchange of vibrational energy occurs with water molecules in the bulk, and this intermolecular energy transfer process dominates the response. For membrane-bound water at the lipid interface, intermolecular energy transfer is suppressed, and intramolecular relaxation dominates. The difference in relaxation mechanism can be understood from differences in the local environments experienced by the interfacial water molecules in the two different systems.     

Synthesis,spectroscopic analysis and structure deduction of gold(III), palladium(II) and platinum(II) complexes with the tripeptide glycyl-<Emphasis Type="SmallCaps">l</Emphasis>-phenylalanyl-glycine

The coordination behaviour of the tripeptide glycyl-l-phenylalanyl-glycine (H-Gly-Phe-Gly-OH) with Au(III), Pd(II), and Pt(II) in both solution and in the solid state has been investigated experimentally. In addition, quantum chemical calculations have been carried out with a view to obtain the structures and spectroscopic properties of the ligand and its complexes. Both in solution and in the solid state the tripeptide interacts in a tetradentate manner with the Au(III) and Pd(II) ions through the NH₂, two deprotonated amide N atoms and the COO⁻group, forming [Au(H-Gly-Phe-Gly-OH)H₋₂)] × H₂O and [Pd(H-Gly-l-Phe-Gly-OH)H₋₂)]Na × H₂O complexes. The MN₃O chromophores are calculated to be near planar. Interaction with cisplatin leads to the formation of a mononuclear complex with tridentate coordination of the ligand by NH₂ and two N- atoms from the deprotonated amide groups ([Pt(H-Gly-l-Phe-Gly-OH)H₋₂)NH₃] × 2H₂O). The fourth coordination position of the Pt(II) is occupied by an NH₃ ligand. The PtN₄ chromophore is flat with a deviation from planarity of 0.3°. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.