Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions

Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotides with noncontiguous guanines G and grouped as contiguous GG and GGG sequences were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd:YAG laser pulses, the DNA-bound BPT molecules were photoionized to BPT*+ radicals by a consecutive two-photon ionization mechanism. The BPT*+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron-transfer reactions, and the rate constants of these reactions follow the trend 5'-..GGG.. > 5'-..GG.. > 5'-..G... In the case of CO3*- radicals, the oxidation of guanine occurs by intermolecular collision pathways, and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO3*- radicals, as well as by BPT*+, are base sequence context-dependent and are greater than those in isolated guanines at the 5'-G in 5'-...GG... sequences, and the first two 5'- guanines in the 5'-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkali-labile guanine products. In the case of the intermolecular one-electron oxidant CO3*-, the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA-bound oxidant BPT*+, the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.     

Density functional studies of AnF6 (An=U,Np, and Pu) and UF6−nCln (n=1–6) using hybrid functionals: geometries and vibrational frequencies

We have compared the performance of widely used hybrid functionals for calculating the bond lengths and harmonic vibrational frequencies of AnF₆ (An=U, Np, and Pu) and UF_6?nCl_n (n=1–6) molecules using “small‐core” relativistic effective core potentials and extended basis sets. The calculated spectroscopic constants compare favorably with experimental data for the bond lengths (average error ≤ 0.01 Å) and vibrational frequencies (average error ≤ 7 cm^?1) of the AnF₆ molecules. The experimental vibrational frequencies of the stretching modes were available for most of the UF_6?nCl_n (n=1–6) molecules. The calculated vibrational frequencies are in good agreement with the experimental data to within 4.6 cm^?1 and 7.6 cm^?1 for selected Becke1 and Lee, Yang, Parr (B1LYP), and Becke3 and Perdew, Wang (B3PW91) functionals, respectively. We conclude that one can predict reliable geometries and vibrational frequencies for the unknown related systems using hybrid density functional calculations with the RECPs. The geometries and vibrational frequencies of the UF_6?nCl_n (n=1–6) molecules that have not been determined experimentally are also presented and discussed. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 2010–2017, 2001     

One-Pot Synthesis of 1-Alkynylphosphonates

1-Alkynylphosphonates 3 are prepared in a one-pot procedure from diethyl phosphorochloridates 2 and alkynyllithiums 1, which are readily generated by the reaction of 1-alkynes with n-BuLi.     

Soluble and easily crystallized anthracene derivatives: precursors of solution-processable semiconducting molecules

New soluble anthracene derivatives containing thiophene and phenylenevinylene derivatives were synthesized via well-known synthetic routes. TIPS derivatives were added at the 9,10-positions of anthracene for the solubility and crystallinity. Both of the molecules were found to be promising for high charge mobility and stable organic semiconductors. The soluble anthracene core (TIPSAnt) is a potential precursor for the synthesis of novel semiconducting materials.     

High-density targeting of a viral multifunctional nanoplatform to a pathogenic, biofilm-forming bacterium

Nanomedicine directed at diagnosis and treatment of infections can benefit from innovations that have substantially increased the variety of available multifunctional nanoplatforms. Here, we targeted a spherical, icosahedral viral nanoplatform to a pathogenic, biofilm-forming bacterium, Staphylococcus aureus. Density of binding mediated through specific protein-ligand interactions exceeded the density expected for a planar, hexagonally close-packed array. A multifunctionalized viral protein cage was used to load imaging agents (fluorophore and MRI contrast agent) onto cells. The fluorescence-imaging capability allowed for direct observation of penetration of the nanoplatform into an S. aureus biofilm. These results demonstrate that multifunctional nanoplatforms based on protein cage architectures have significant potential as tools for both diagnosis and targeted treatment of recalcitrant bacterial infections.     

Protein recognition by a self-assembled deep cavitand monolayer on a gold substrate

This paper details the first use of a self-folding deep cavitand on a gold surface. A sulfide-footed deep, self-folding cavitand has been synthesized, and its attachment to a cleaned gold surface studied by electrochemical and SPR methods. Complete monolayer formation is possible if the cavitand folding is templated by noncovalent binding of choline or by addition of space-filling thiols to cover any gaps in the cavitand adsorption layer. The cavitand is capable of binding trimethylammonium-tagged guests from an aqueous medium and can be deposited in 2 × 2 microarrays on the surface for characterization by SPR imaging techniques. When biotin-labeled guests are used, the cavitand:guest construct can recognize and immobilize streptavidin proteins from aqueous solution, acting as an effective supramolecular biosensor for monitoring protein recognition.     

Poly(diphenylacetylene)s with Electron‐Donating Alkoxy and Electron‐Withdrawing Fluoroalkyl Groups: Effect of the Substituent on Fluorescence

New poly(diphenylacetylene)s with alkoxy and fluoroalkyl groups as electron‐donating and electron‐withdrawing groups, respectively, were synthesized by using a WCl₆‐n‐Ph₄Sn catalyst. The polymer solutions emitted strong, bluish‐green lights when photo‐excited. The polymers that contained the electron‐donating alkoxy groups showed longer fluorescence‐maximum peaks when compared to the polymers that contained the electron‐withdrawing fluoroalkyl groups. However, such an effect of the substituent on the absorption property was not clearly seen. The emission bands of the solid films did not show any significant red shift, relative to that of the dilute solution.

     

Synthesis of multifunctional metal- and metal oxide core@mesoporous silica shell structures by using a wet chemical approach

We demonstrate a facile wet chemical approach for fabricating spherical metal/metal-oxide core@mesoporous silica shell hybrid nanoparticles with different core and shell thicknesses. Vertically aligned mesoporous silica (mSiO(2) ) shells were fabricated over the pre-synthesized spherical SiO(2) nanoparticles through a three-step strategy: 1)?synthesis of core materials, 2)?covering the core with an organic-inorganic composite layer, and 3)?removing the organic template through calcinations in air. The mechanisms of hybrid structure formation are proposed. The multifunctional nature of the hybrid structures could be induced by incorporating guest ions/molecules, such as Ag, Mn, and TiO(2) , into the pores of an mSiO(2) shell. Mn and TiO(2) cluster- incorporated composite structures have been tested to be antioxidizing agents and effective photocatalysts through electron spin resonance, radical scavenging tests, and the photocatalytic degradation of rhodamine B. The possibility of incorporating several hetero-element guest clusters in these mesoporous composite particles makes them highly attractive for multifunctional applications.     

Reactivity of acid fluoride-terminated self-assembled monolayers on gold

This report describes the reactivity of acid fluoride (AF)-terminated self-assembled monolayers (SAMs) on gold toward amine and alcohol compounds and the potentiality of AF as a reactive intermediate for surface functionalizations. The AF group was generated in situ on a gold surface by reacting the terminal carboxylic acid group in the SAM of 16-mercaptohexadecanoic acid with cyanuric fluoride and pyridine under the optimized conditions. AF was found to be highly reactive toward various amine groups, such as primary and secondary amines, but it did not react effectively with alcohol. In addition, the amide coupling reaction by microcontact printing (microCP) was compared with the solution-based reaction: when amine-derivatized ferrocene compound was used for 1-min microCP on the AF-activated surface, the surface coverage of the reaction product was about 83% of 3.45 x 1014 cm-2, the coverage obtained in the solution-based reaction. On the basis of the high reaction efficiency of microCP, the AF-activated surface was also used as a platform for patterning a biological ligand, biotin.