Changing DNA grooves--a 1,4,5,8-naphthalene tetracarboxylic diimide bis-intercalator with the linker (beta-Ala)(3)-Lys in the minor groove

We have been investigating a modular, threading DNA polyintercalator design based upon the 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit. Previously, we have reported the NMR analysis of a bis-intercalator-DNA complex in which the peptide linker between NDI units was found to occupy the DNA major groove (Guelev, Lee, Sorey, Hoffman, Iverson, Chem. Biol. 2001, 8, 415-425). Here we describe the NMR analysis of a complex between a related bis-intercalator known to display altered DNA sequence specificity. In this case, the linker resides in the DNA minor groove. We have thus shown that within this set of sequence specific bis-intercalators, both DNA grooves can be accessed, setting the stage for longer threading polyintercalators designed to have linkers occupying both grooves in an alternating fashion.     

A needle-and-thread approach to bilayer transport: permeation of a molecular umbrella-oligonucleotide conjugate across a phospholipid membrane

A di-walled molecular umbrella, composed of two choloyl groups, one spermidine moiety, and a 5-thiol(2-nitrobenzoyl) "handle", was covalently attached to a 16-mer oligonucleotide (S-dT16) through a disulfide bond. Incubation of this conjugate (1) with vesicles made from 1-palmitoyl-2-oleyol-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (95/5, mol/mol) (200 nm diameter, extrusion) that contained entrapped glutathione (GSH) at 37 degrees C resulted in the liberation of the oligonucleotide and the umbrella-bound 5-mercapto(2-nitrobenzoyl) moiety (USH) via thiolate-disulfide interchange. The appearance of USH, together with the absence of leakage of entrapped GSH and a vesicular capture of the oligonucleotide that matches the extent of USH formation, provides compelling evidence for delivery of S-dT16 into the aqueous compartment of these vesicles. In a sense, the molecular umbrella functions like a "needle" in providing a pathway for the oligonucleotide (the "thread") to cross the membrane.     

Controlled shrinkage polymers: Characterization of epoxy resins cured with spirobislactones

The diglycidyl ether of bisphenol A (DGEBA) was cured with either an aliphatic or an aromatic spirobislactone using a tertiary amine catalyst. The products were characterized by FTIR, TGA, DSC, dilatometry, and single-fiber adhesion measurements, and their performance was compared to that of DGEBA cured with acid anhydrides. Both aliphatic and aromatic bislactones are effective curing agents for DGEBA. FTIR and dilatometry confirm that both lactone rings open early in the curing reaction and initially offset shrinkage caused by polymerization. After the bislactone has been consumed, oxirane reactions proceed in a normal fashion. The final shrinkage of cured DGEBA polymers, with or without addition of bislactones, is 3.0–3.5%. Bislactone-modified materials possess superior thermal properties, when compared to those of anhydride-cured materials.     

Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives

The tautomerism of 2'-deoxy-7-deaza-isoguanosine (2) was studied and compared to that of 2'-deoxyisoguanosine (1). The fixed (1)N-methyl (8) and O-methyl (4) derivatives were synthesized to represent the pure extremes of each tautomer. The replacement of the imidazole ring in 1 with a pyrrole ring in 2 makes the keto form in the latter more favored by 2 orders of magnitude (K(TAUT) for 2 approximately 10(3), as opposed to K(TAUT) for 1 approximately 10).     

Tandem (quadrupole-time-of-flight) electrospray mass spectrometry of oligo(vinyl acetates) with isopropylol or (1-hydroxyethyl)-2-oxyisopropanyl end groups

Poly(vinyl acetates) with either isopropylol or (1-hydroxyethyl)-2-oxyisopropanyl end groups were analysed by tandem mass spectrometry using a quadrupole-time-of-flight (Q-TOF) instrument. Random scission along the polymer backbone was not observed. Instead the initial scissions were derived from the cleavage of end-group species. The resultant macrocations were subject to further elimination reactions that eventually produced polyene macrocations. A smaller fraction of the initial macrocations also reacted by loss of ketene and this reaction produced macrocations containing vinyl alcohol units.     

Continuous flow in open microfluidics using controlled evaporation

This paper presents a method for programming the flow rate of liquids inside open microfluidic networks (MFNs). A MFN comprises a number of independent flow paths, each of which starts with an open filling port, has a sealed microchannel in which assays can be performed, and an open capillary pump (CP). The MFN is placed over Peltier elements and its flow paths initially fill owing to capillary forces when liquids are added to the filling ports. A cooling Peltier element underneath the filling ports dynamically prevents evaporation in all filling ports using the ambient temperature and relative humidity as inputs. Another Peltier element underneath the CPs heats the pumps thereby inducing evaporation in the CPs and setting the flow rate in the microchannels. This method achieves flow rates in the microchannels ranging from approximately 1.2 nL s(-1) to approximately 30 pL s(-1), and is able to keep 90% of a 0.6 microL solution placed in an open filling port for 60 min. This simple and efficient method should be applicable to numerous assays or chemical reactions that require small and precise flow of liquids and reagents inside microfluidics.     

The use of 1H NMR microscopy to study proton-exchange membrane fuel cells.

To understand proton-exchange membrane fuel cells (PEMFCs) better, researchers have used several techniques to visualize their internal operation. This Concept outlines the advantages of using 1H NMR microscopy, that is, magnetic resonance imaging, to monitor the distribution of water in a working PEMFC. We describe what a PEMFC is, how it operates, and why monitoring water distribution in a fuel cell is important. We will focus on our experience in constructing PEMFCs, and demonstrate how 1H NMR microscopy is used to observe the water distribution throughout an operating hydrogen PEMFC. Research in this area is briefly reviewed, followed by some comments regarding challenges and anticipated future developments.     

Computation of the physio-chemical properties and data mining of large molecular collections

Very large data sets of molecules screened against a broad range of targets have become available due to the advent of combinatorial chemistry. This information has led to the realization that ADME (absorption, distribution, metabolism, and excretion) and toxicity issues are important to consider prior to library synthesis. Furthermore, these large data sets provide a unique and important source of information regarding what types of molecular shapes may interact with specific receptor or target classes. Thus, the requirement for rapid and accurate data mining tools became paramount. To address these issues Pharmacopeia, Inc. formed a computational research group, The Center for Informatics and Drug Discovery (CIDD).* In this review we cover the work done by this group to address both in silico ADME modeling and data mining issues faced by Pharmacopeia because of the availability of a large and diverse collection (over 6 million discrete compounds) of drug-like molecules. In particular, in the data mining arena we discuss rapid docking tools and how we employ them, and we describe a novel data mining tool based on a ID representation of a molecule followed by a molecular sequence alignment step. For the ADME area we discuss the development and application of absorption, blood-brain barrier (BBB) and solubility models. Finally, we summarize the impact the tools and approaches might have on the drug discovery process.     

Simultaneous multichannel mass-specific detection for high-performance liquid chromatography using an array detector sector-field mass spectrometer

The use of a separation step, such as liquid chromatography, prior to inductively coupled plasma mass spectrometry (ICP–MS) has become a common tool for highly selective and sensitive analyses. This type of coupling has several benefits including the ability to perform speciation analysis or to remove isobaric interferences. Several limitations of conventional instruments result from the necessity to scan or pulse the mass spectrometer to obtain a complete mass spectrum. When the instrument is operated in such a non-continuous manner, duty cycle is reduced, resulting in poorer absolute limits of detection. Additionally, with scanning instruments, spectral skew can be introduced into the measurement, limiting quantitation accuracy. To address these shortcomings, a high-performance liquid chromatograph has been coupled to an ICP–MS capable of continuous sample introduction and simultaneous multimass detection. These features have been realized with a novel detector array, the focal plane camera. Instrument performance has been tested for both speciation analysis and for the elimination of isobaric interferences. Absolute limits of detection in the sub picogram to tens of picograms regime are obtainable, while the added mass dimension introduced by simultaneous detection dramatically increases chromatographic peak capacity.     

Enantioselective epoxidation of alkenes catalyzed by 2-fluoro-N-carbethoxytropinone and related tropinone derivatives

Several alpha-substituted N-carbethoxytropinones have been evaluated as catalysts for asymmetric epoxidation of alkenes with Oxone, via a dioxirane intermediate. alpha-Fluoro-N-carbethoxytropinone (2) has been studied in detail and is an efficient catalyst which does not suffer from Baeyer-Villiger decomposition and can be used in relatively low loadings. This ketone was prepared in enantiomerically pure form using chiral base desymmetrization of N-carbethoxytropinone. Asymmetric epoxidation catalyzed by 2 affords epoxides with up to 83% ee. Among other derivatives tested, the alpha-acetoxy derivative 7 affords the highest enantioselectivities.