Base-base interactions in the minor groove of double-stranded DNA

A method has been developed for the synthesis of bisheaded nucleosides with thymine and adenine base moieties. We have demonstrated that, when incorporated in oligonucleotides, extrahelical A-T base interactions are possible when the bisheaded nucleosides are positioned in opposite strands of the duplex and are separated from each other by one regular base pair.     

Hydrodynamic chromatography separations in micro- and nanopillar arrays produced using deep-UV lithography (J. Sep. Science 35'15)

DOI: 10.1002/jssc.201200076 Micro-pillar array columns with an inter-pillar spacing down to 500 nm have been designed and fabricated enabling hydrodynamic chromatography separations of fluorescently labeled polystyrene nano-particles. Injecting sub-nanoliter sized sample volumes and detecting the fluorescent signal on-chip, fluorescein, 20 and 40 nm diameter particles could be separated in less than 1.5 minutes.     

Photo-orientation of axial molecules

We examine the photo-orientation of molecules in a linearly polarized field and the ensuing optical anisotropy of a sample. We propose a theoretical model that considers both photoinduced reorientation and rotational diffusion, for the case of linear or axial molecules not interacting among them, as in dilute solutions in viscous media. We perform numerical simulations to highlight the dependence on the parameters of the molecular reorientation processes, on the intensity of the exciting light, and on the use of cross polarized pulses. As a realistic example we simulate the photo-orientation of azobenzene in ethylene glycol.     

Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA

We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 ?) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.     

Symmetry breaking in the relaxed S(1) excited state of bianthryl derivatives in weakly polar solvents.

The flash-photolysis time-resolved microwave conductivity technique (FP-TRMC) has been used to investigate the nature of the relaxed S(1) state of 9,9'-bianthryl (AA), 10-cyano-9,9'-bianthryl (CAA), and 10,10'-dicyano-9,9'-bianthryl (CAAC). Changes in both the real, Deltaepsilon' (dielectric constant), and imaginary, Deltaepsilon' ' (dielectric loss), components of the complex permittivity have been measured. The dielectric loss transients conclusively demonstrate the dipolar nature of S(1) for all three compounds in the pseudopolar solvents benzene and 1,4-dioxane, and even in the nonpolar solvents n-hexane and cyclohexane. The required symmetry breaking is considered to result from density and structural fluctuations in the solvent environment. The dipole relaxation times for AA (CAAC) are ca. 2 ps for the alkanes and 7.9 (5.3) and 14 (14) ps for benzene and dioxane, respectively. The time scale of dipole relaxation for the symmetrical compounds is much shorter than that for rotational diffusion and is attributed to intramolecular, flip-flop dipole reversal via a neutral excitonic state. The dipole moment of the transient dipolar state is estimated to be ca. 8 D, that is much lower than the value of ca. 20 D determined from the solvatochromic shifts in the fluorescence in intermediate to highly polar solvents which corresponds to close to complete charge separation. For the asymmetric compound, CAA, a dipole moment close to 20 D is found in all solvents, including n-hexane. Dipole relaxation in this case occurs on a time scale of several hundred picoseconds and is controlled mainly by diffusional rotation of the molecules. The mechanism and kinetics of formation of the dipolar excited states are discussed in the light of these results.     

A Generic Design of a Flow-Through Potentiometric Sensor Array

 In this paper, a flow-through potentiometric microsensor is described which is based on semi-permeable tubing. The ion selective electrodes proposed are of the liquid membrane type in which a dialysis tube captures the ion selective cocktail. Ion selective sensors and a reference electrode based on the same design were constructed by guiding a 0.3 mm diameter dialysis tube through a cavity precision machined in Perspex?. Commercia lly available ionophore or ion-exchanger cocktails were applied to provide ion selectivity whilst a saturated KCl solution was used in the reference electrode. A number of flow-through microsensors selective to different ions (Na, K, Li, pH) were constructed and tested. Each showed good performance in a broad range of concentrations. Advantages of the proposed approach are the generic technology to make sensors with incorporate d reference electrodes, capable of measuring a wide variety of analytes for which cocktails are readily available and the fact that sub-microliter amounts of sample can be measured. Secondly, in comparison to other sensors applied in microchannels, the impedance of the flow-through sensor is much smaller because of the relatively large sensing surface formed by the tube wall. Moreover, the use of dialysis tubing enables easy integration with a so-called microdialysis probe for in-vivo sampling of the blood stream or subcutaneous tissue. Received December 6, 1999. Revision March 24, 2000.     

Precise Block‐Copolymers by Efficient Coupling of End‐Functionalized Polymers Using Phosgene

Summary: We report the synthesis of well‐defined block copolymers by covalent coupling of hydroxy end‐functionalized polymers. Using the high volatility of the coupling agent phosgene as compared to the solvent, very high conversion (up to 96%) is obtained in a one‐pot reaction with as little as 10⁻⁵ moles of each of the reacting polymers, even without prior purification of the as‐received reagents. This has potential as an alternative to the currently practiced method of sequential living polymerization of constituent monomers, with the added advantage of direct knowledge and control over the length distribution of each block.

Coupling of end‐functionalized polymers using phosgene to form block copolymers of controlled composition.