Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis

A convenient method of oligonucleotide labeling using click chemistry has been developed. A 2′-mesyloxyethyl ribothymidine phosphoramidite monomer was incorporated into DNA at several loci during solid phase oligonucleotide synthesis and converted to 2′-azidoethyl ribothymidine in high yield on the synthesis resin. The resultant azide oligonucleotides were doubly and triply labeled with alkyne-modified cyanine dyes and their biophysical properties were studied. The influence of the dye structures and method of labeling on the fluorescence properties of the DNA probes is discussed and compared with a standard labeling method using active esters of Cy-Dyes.     

Expanding the Toolbox of Metal–Phenolic Networks via Enzyme‐Mediated Assembly

Functional coatings are of considerable interest because of their fundamental implications for interfacial assembly and promise for numerous applications. Universally adherent materials have recently emerged as versatile functional coatings; however, such coatings are generally limited to catechol, (ortho‐diphenol)‐containing molecules, as building blocks. Here, we report a facile, biofriendly enzyme‐mediated strategy for assembling a wide range of molecules (e.g., 14 representative molecules in this study) that do not natively have catechol moieties, including small molecules, peptides, and proteins, on various surfaces, while preserving the molecule's inherent function, such as catalysis (≈80 % retention of enzymatic activity for trypsin). Assembly is achieved by in situ conversion of monophenols into catechols via tyrosinase, where films form on surfaces via covalent and coordination cross‐linking. The resulting coatings are robust, functional (e.g., in protective coatings, biological imaging, and enzymatic catalysis), and versatile for diverse secondary surface‐confined reactions (e.g., biomineralization, metal ion chelation, and N‐hydroxysuccinimide conjugation).     

Polyphenol‐Mediated Assembly of Proteins for Engineering Functional Materials

Functional materials composed of proteins have attracted much interest owing to the inherent and diverse functionality of proteins. However, establishing general techniques for assembling proteins into nanomaterials is challenging owing to the complex physicochemical nature and potential denaturation of proteins. Here, a simple, versatile strategy is introduced to fabricate functional protein assemblies through the interfacial assembly of proteins and polyphenols (e.g., tannic acid) on various substrates (organic, inorganic, and biological). The dominant interactions (hydrogen‐bonding, hydrophobic, and ionic) between the proteins and tannic acid were elucidated; most proteins undergo multiple noncovalent stabilizing interactions with polyphenols, which can be used to engineer responsiveness into the assemblies. The proteins retain their structure and function within the assemblies, thereby enabling their use in various applications (e.g., catalysis, fluorescence imaging, and cell targeting).     

Characterization of singlet ground and low-lying electronic excited states of phosphaethyne and isophosphaethyne

The singlet ground ((approximate)X(1)Sigma1+) and excited (1Sigma-,1Delta) states of HCP and HPC have been systematically investigated using ab initio molecular electronic structure theory. For the ground state, geometries of the two linear stationary points have been optimized and physical properties have been predicted utilizing restricted self-consistent field theory, coupled cluster theory with single and double excitations (CCSD), CCSD with perturbative triple corrections [CCSD(T)], and CCSD with partial iterative triple excitations (CCSDT-3 and CC3). Physical properties computed for the global minimum ((approximate)X(1)Sigma+HCP) include harmonic vibrational frequencies with the cc-pV5Z CCSD(T) method of omega1=3344 cm(-1), omega2=689 cm(-1), and omega3=1298 cm(-1). Linear HPC, a stationary point of Hessian index 2, is predicted to lie 75.2 kcal mol(-1) above the global minimum HCP. The dissociation energy D0[HCP((approximate)X(1)Sigma+)-->H(2S)+CP(X2Sigma+)] of HCP is predicted to be 119.0 kcal mol(-1), which is very close to the experimental lower limit of 119.1 kcal mol(-1). Eight singlet excited states were examined and their physical properties were determined employing three equation-of-motion coupled cluster methods (EOM-CCSD, EOM-CCSDT-3, and EOM-CC3). Four stationary points were located on the lowest-lying excited state potential energy surface, 1Sigma- -->1A", with excitation energies Te of 101.4 kcal mol(-1) (1A"HCP), 104.6 kcal mol(-1)(1Sigma-HCP), 122.3 kcal mol(-1)(1A" HPC), and 171.6 kcal mol(-1)(1Sigma-HPC) at the cc-pVQZ EOM-CCSDT-3 level of theory. The physical properties of the 1A" state with a predicted bond angle of 129.5 degrees compare well with the experimentally reported first singlet state ((approximate)A1A"). The excitation energy predicted for this excitation is T0=99.4 kcal mol(-1) (34 800 cm(-1),4.31 eV), in essentially perfect agreement with the experimental value of T0=99.3 kcal mol(-1)(34 746 cm(-1),4.308 eV). For the second lowest-lying excited singlet surface, 1Delta-->1A', four stationary points were found with Te values of 111.2 kcal mol(-1) (2(1)A' HCP), 112.4 kcal mol(-1) (1Delta HPC), 125.6 kcal mol(-1)(2(1)A' HCP), and 177.8 kcal mol(-1)(1Delta HPC). The predicted CP bond length and frequencies of the 2(1)A' state with a bond angle of 89.8 degrees (1.707 A, 666 and 979 cm(-1)) compare reasonably well with those for the experimentally reported (approximate)C(1)A' state (1.69 A, 615 and 969 cm(-1)). However, the excitation energy and bond angle do not agree well: theoretical values of 108.7 kcal mol(-1) and 89.8 degrees versus experimental values of 115.1 kcal mol(-1) and 113 degrees. of 115.1 kcal mol(-1) and 113 degrees.     

Investigation of free base, Mg, Sn, and Zn substituted porphyrin LB films as gas sensors for organic analytes

The visible absorption spectra of various substituted porphyrin compounds both in chloroform solution and as Langmuir-Blodgett (LB) solid-state films have been investigated. The porphyrin compounds examined were the Zn, Sn, Mg, and free base derivatives of 5,10,15,20-tetrakis[3,4-bis(2-ethylhexyloxy)phenyl]-21H,23H-porphine (EHO). Changes in the absorption spectra of these materials induced by their exposure to various organic compounds are reported with a view toward determining whether this is a useful approach toward an optical gas sensor.     

Effect of surfactant and solvent properties on the stacking behavior of non-aqueous suspensions of organically modified clays

Montmorillonite clay was treated with quaternary ammonium surfactants with 1-3 long chains of 10-18 carbons to form organoclays which can be suspended in non-aqueous solvents. The effects of surfactant chain length, number of long chains, and the properties of the solvent on the colloidal behavior of the surfactant coated clay plates were studied using small-angle X-ray scattering. The scattering data were modeled using a one-dimensional aggregation theory to describe the stacking of the clay plates. The plates self-organize into stacks with a reproducible basal spacing in the range of 30-50 A, and for each surfactant, the basal spacing falls into one of two preferred distances. We interpret this by considering that the surfactant layer on the clay has two strata, one being the polar near-clay headgroup region and the other the nonpolar alkane chain region. Polar solvents will swell the polar stratum preferentially while nonpolar solvents will swell the nonpolar stratum of the surfactant. As the nonpolar stratum is larger than the polar one, the nonpolar solvents increase the basal spacing between the clay plates more than the polar solvents. The number of long chains on the surfactant does not have an effect on the basal spacing, as the density of surfactant molecules on the surface is low enough to allow the unimpeded swelling of the chains. The one-dimensional aggregation theory can be used to determine the number of plates in a stack, but the effect of changing clay particle size or concentration is not as great as would be expected from this theory. This may be due to the formation of large-scale structures in the suspensions which prevent a true equilibrium stack size being attained.     

Substituent effects on 15N and 13C NMR chemical shifts of 3-phenylisoxazoles: a theoretical and spectroscopic study

The synthesis and assignment of 15N and 13C NMR signals of the isoxazole ring in a series of para-substituted 3-phenyl derivatives are reported. DFT calculations of 15N and 13C chemical shifts are presented and compared to observed values. Substituent effects are interpreted in terms of the Hammett correlation and calculated bond orders.