NMR and UV studies of 3'-S-phosphorothiolate modified DNA in a DNA : RNA hybrid dodecamer duplex; implications for antisense drug design

High-resolution NMR spectroscopy has been used to establish the conformational consequences of the introduction of a single 3[prime or minute]-S-phosphorothiolate link in the DNA strand of a DNA : RNA hybrid. These systems are of interest as potential antisense therapeutic agents. Previous studies on similarly modified dinucleotides have shown that the conformation of the sugar to which the sulfur is attached shifts to the north (C(3[prime or minute])-endo/C(2[prime or minute])-exo). Comparisons made between NOESY cross-peak intensities, and coupling constants from PE-COSY spectra, for both non-modified and modified duplexes confirm that this conformational shift is also present in the double helical oligonucleotide system. In addition it is noted that in both the dinucleotides and the modified duplex, the conformation of the sugar ring 3[prime or minute] to the site of modification is also shifted to the north. That this pattern is observed in the small monomeric system as well as the larger double helix is suggestive of some pre-ordering of the sequences. The conclusion is supported by consideration of the (1)H chemical shifts of the heterocyclic bases near the site of the modification. The enhanced stability that these conformational changes should bring was confirmed by UV thermal melting studies. Subsequently a series of singly and doubly 3[prime or minute]-S-phosphorothiolate-modified duplexes were investigated by UV. The results are indicative of an additive effect of the modification with thermodynamic benefit being derived from alternate spacing of two modified linkers.     

An effective method for the discrimination of motional anisotropy and chemical exchange

Analysis of the ratio of transverse and longitudinal relaxation rates (R2/R1) is an approach commonly used for estimation of overall correlation time and identification of chemical exchange in biological macromolecules. However, this analysis fails to distinguish between chemical exchange and motional anisotropy. We describe a simple method for identifying chemical exchange and motional anisotropy using the product, R1R2. In the slow tumbling regime, the R1R2 product results in a constant value that is independent of overall correlation time and motional anisotropy. This analysis provides a simple method for rapidly estimating and dissociating the effects of motional anisotropy and chemical exchange in NMR heteronuclear spin relaxation data. We demonstrate the utility of the method with 15N relaxation data collected on the proteins E. coli ribonuclease H and the trimeric E. coli membrane associated lipoprotein lpp.     

Matrix-assisted laser desorption/ionisation mass spectrometry for the direct analysis of enzymatically digested kappa- iota- and hybrid iota/nu-carrageenans

Enzymatically digested oligosaccharides of kappa-, iota- and hybrid iota/nu-carrageenans were analysed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry in the negative-ion mode. nor-Harmane was used as matrix. Depending on the stock concentration and the laser intensity applied, the oligosaccharides exhibited losses of sulphate units (neutralised by the Na+ ion, and thus non-stable), leaving the primary backbone structure in most cases with only the deprotonated sulphate groups (carrying the negative charge, stable). This meant that kappa- and iota-oligosaccharides could not be easily distinguished from one another since they share the same primary backbone structure. However, for the hybrid iota/nu-oligosaccharides the primary backbone structure could be identified since the nu-carrageenan repeating unit differs from that of the kappa/iota-carrageenan unit. For all types of oligosaccharides, the results indicated cleavage of an anhydrogalactose unit from the non-reducing end. Specifically, for the hybrid oligosaccharides of iota/nu-carrageenans, this type of fragmentation means that the nu-carrageenan unit is not positioned on the non-reducing end of the hybrid oligosaccharides. Dehydration reactions, and exchange reactions of Na+ with K+ and Ca2+, were also observed.     

Structure and dynamics of ND3BF3 in the solid and gas phases: a combined NMR,neutron diffraction,and Ab initio study

The decrease in D-->A bond lengths, previously reported for some Lewis acid/base complexes, in going from the gas to the solid phases is investigated by obtaining an accurate crystal structure of solid ND(3)BF(3) by powder neutron diffraction. The B-N internuclear distance is 1.554(3) A, 0.118 A shorter than the most recent gas-phase microwave value and 0.121 A shorter than the single molecule geometry optimized (1.672 A, CISD/6-311++G(d,p)) bond length. The crystal structure also shows N-D.F-B hydrogen bonds. The effects of this change in structure and of intermolecular hydrogen-bonding on nuclear magnetic shielding (i.e., chemical shifts) and the nuclear quadrupolar coupling constants (QCC) are investigated by ab initio molecular orbital and density functional theory calculations. These calculations show that the nitrogen ((15)N and (14)N) and boron ((11)B and (10)B) chemical shifts should be rather insensitive to changes in r(BN) and that the concomitant changes in molecular structure. Calculations on hydrogen-bonded clusters, based on the crystal structure, indicate that H-bonding should also have very little effect on the chemical shifts. On the other hand, the (11)B and (14)N QCCs show large changes because of both effects. An analysis of the (10)B[(19)F] line shape in solid ND(3)(10)BF(3) yields a (11)B QCC of +/-0.130 MHz. This is reasonably close an earlier value of +/-0.080 MHz and the value of +/-0.050 MHz calculated for a [NH(3)BF(3)](4) cluster. The gas-phase value is 1.20 MHz. Temperature-dependent deuterium T(1) measurements yield an activation energy for rotation of the ND(3) group in solid ND(3)BF(3) of 9.5 +/- 0.1 kJ/mol. Simulations of the temperature-dependent T(1) anisotropy gave an E(a) of 9.5 +/- 0.2 kJ/mol and a preexponential factor, A, of 3.0 +/- 0.1 x 10(12) s(-)(1). Our calculated value for a [NH(3)BF(3)](4) cluster is 16.4 kJ/mol. Both are much higher than the previous value of 3.9 kJ/mol, from solid-state proton T(1) measurements.     

Molecular ordering and 2D conductivity in ultrathin poly(3-hexylthiophene)/gold nanoparticle composite films

This paper reports the first comparison of the structure and electrical conductivity properties of spin cast (SC) and Langmuir-Schaeffer (LS) films of regioregular poly(3-hexylthiophene) (P3HT). In addition, the effect of incorporating highly monodisperse Au nanoparticles (NPs), with a core diameter of approximately 5 nm, into SC and LS P3HT films is described. A detailed picture of molecular organization in the films has been obtained using ultraviolet-visible absorption spectroscopy, atomic force microscopy, field-emission scanning electron microscopy, X-ray diffraction, and X-ray reflectivity. Film morphology was correlated with pseudo-two-dimensional conductivity measured using scanning electrochemical microscopy, with P3HT in the semiconducting regime. It was found that SC films, which were slightly thicker than those formed with the LS technique, exhibited greater organization. This resulted in an order of magnitude higher lateral conductivity for the SC films. Inclusion of Au NPs (50 wt %) into both SC and LS films resulted in the formation of uniform and relatively flat (rms roughness approximately 1 nm) composite films. Surprisingly, the addition of NPs did not disrupt the characteristic crystal structure found for the native P3HT films. The effect of Au NPs on film lateral conductivity was found to be determined by the distribution of Au NPs within the polymer, which varied significantly between SC and LS films. Whereas Au NPs aggregated into hexagonally packed clusters in SC films, NPs in LS films were predominantly uniformly distributed between the lamella bilayer. It was found that, while the inclusion of Au NPs caused the lateral conductivity to decrease in SC films, in LS films, the lateral conductivity increased by a factor of 2.     

Rapid serial analysis of multiple oligonucleotide samples on a microchip using optically-gated injection

Optically-gated injection of fluorescently-labeled DNA has been accomplished for the first time. Rapid, serial analysis of oligonucleotide ladders has been shown on a microchip using this injection technique. Separations of five- and six-component samples have been completed in 60 s or less with a capability to carry out serial injections of these samples every 15 s. The technique has been shown to have better than five base resolution for small oligonucleotides and excellent reproducibility in migration times (< or = 0.75% RSD). Currently, the limit of detection for the system is 0.23 microM. Additionally, multiple unique samples of DNA have been consecutively analyzed in a single separation lane using optical gating. Six consecutive injections of three different samples have been achieved with no sample carryover and a total analysis time of approximately 10 min. These results show the potential of optical gating as an alternative injection technique for high-throughput DNA applications, such as genotyping and monitoring dynamic processes.     

Palladium-catalyzed carbon-carbon bond-forming 1,2-ligand migration of organoalanes

A one-pot, two-step process that transforms terminal alkynes into ethyl methyl-substituted benzylic quaternary carbon centers is described. (E)-2,2-Disubstituted-1-alkenyldimethylalanes have been shown to participate in 1,2-alkyl migration from aluminum to carbon with concomitant arylation at the 2-position to furnish ethyl methyl-substituted benzylic quaternary carbon centers, when reacted intramolecularly with aryl halides and triflates in the presence of a Pd(0) catalyst. The protocol is initiated with Cp2ZrCl2-catalyzed methylalumination of terminal alkynes followed by palladium-catalyzed intramolecular arylation of the resulting (E)-2,2-disubstituted-1-alkenyldimethylalanes, leading to 1,2-methyl shift from aluminum to carbon. In that sequence, a total of three new C-C single bonds are made, and two of the three alkyl groups on Me3Al transferred to the substrate on vicinal carbons. This method was applied to a variety of substrates, and the mechanism was investigated by deuterium-labeling experiments, which revealed that protodealumination of the final dialkylaluminum triflate or halide intermediates by CH3CN results in the formation of the fourth bond in the course of the transformation.