Biomedical subjects
Publications and source records attributed to Kurt V Gothelf.
A cleavable heterobifunctional cross-linker for the reversible conjugation of amines to thiol-modified DNA has been developed and tested. The succinimidyl 2-(vinylsulfonyl)ethyl carbonate (SVEC) was prepared in three steps and tested for its ability to react with amines and thiols. The linker was efficient for binding leucine to a thiol-modified DNA sequence and for releasing the amino acid at pH 11.8.
A general approach to N-arylation and N-alkenylation of all five DNA/RNA nucleobases at the nitrogen atom normally attached to the sugar moiety in DNA or RNA has been developed. Various protected or masked nucleobases engaged readily in the copper-mediated Chan-Lam-Evans-modified Ullmann condensation with a range of different boronic acids at room temperature and were subsequently converted to the corresponding deprotected or unmasked adducts. Different N(3)-protecting groups were examined in the case of thymine, where the benzoyl group afforded the highest yields. A 4-alkylthio-substituted pyrimidin-2(1H)-one served as both a cytosine and a uracil precursor and was N-arylated and N-alkenylated in high yields. Adenine was efficiently and selectively N-arylated and N-alkenylated at the N(9) position by employing a bis-Boc-protected adenine derivative, while a bis-Boc-protected 2-amino-6-chloropurine served as guanine precursor and could also be selectively N(9)-arylated and N(9)-alkenylated.
The synthesis of an elongated linear oligonucleotide-functionalised module (ELOM) is described. The ELOM structure is based on an oligo(phenylene ethynylene) backbone substituted with two decyloxy groups. The two termini constitute two salicylaldehyde moieties acting as chemical cross-linkers. Before incorporation into an oligonucleotide sequence the organic part of the module, the elongated linear module (ELM), is functionalised with a dimethoxytrityl group and a phosphoramidite group. This enables incorporation into the middle of 30-mer oligonucleotide sequences by automated DNA synthesis. The obtained ELOMs were characterised by polyacrylamide gel electrophoresis and MALDI-TOF mass spectrometry. In analogy with previously reported LOM and TOM structures the coupling reactions of the ELOM modules were tested.
DNA sequence-controlled on-and-off switching of a singlet oxygen sensitizer has been developed and demonstrated. The singlet oxygen photosensitizer pyropheophorbide-a (P) was attached to a 15-mer nucleotide sequence. A molecule that could quench the sensitizer, the so-called "black hole quencher 3" (Q), was attached to a complementary nucleotide strand. Upon hybridization of the two conjugates, singlet oxygen production from P was completely shut down. Upon the addition of a third DNA sequence that can displace and release the P-DNA conjugate from the P-Q pair, up to 85% of the singlet oxygen production was recovered. This system is a model for a benign drug that becomes active only in the presence of a specific targeted nucleotide sequence.
A new electrochemical DNA sensor providing detection capabilities down to 100 attomol of target DNA has been developed. The method applies CdS, ZnS, and PbS nanoparticles conjugated with short DNA sequences which are immobilized via hybridization with complementary sequences on a gold surface. When the DNA target is added, it can be identified by ousting the existing hybridization between one of the DNA-nanoparticle conjugates and the surface DNA. The nanoparticles remaining at the surface are detected by stripping voltammetry. The setup is constructed to give a signal-off response with a build-in control signal as only one of two different metal sulfide signaling probes on the surface is removed by hybridization with the DNA target. The competition assay is, in principle, label-free since no labels are required for detection after addition of DNA target. The dissociation of PbS nanoparticles from the surface after addition of the DNA target has been imaged by fluid phase AFM.
The coupling of aptamers with the coding and amplification features of inorganic nanocrystals is shown for the first time to offer a highly sensitive and selective simultaneous bioelectronic detection of several protein targets. This is accomplished in a single-step displacement assay in connection to a self-assembled monolayer of several thiolated aptamers conjugated to proteins carrying different inorganic nanocrystals. Electrochemical stripping detection of the nondisplaced nanocrystal tracers results in a remarkably low (attomole) detection limit, that is, significantly lower than those of existing aptamer biosensors. The new device offers great promise for measuring a large panel of disease markers present at ultralow levels during early stages of the disease progress.
Self-assembly of adsorbed organic molecules is a promising route towards functional surface nano-architectures, and our understanding of associated dynamic processes has been significantly advanced by several scanning tunnelling microscopy (STM) investigations. Intramolecular degrees of freedom are widely accepted to influence ordering of complex adsorbates, but although molecular conformation has been identified and even manipulated by STM, the detailed dynamics of spontaneous conformational change in adsorbed molecules has hitherto not been addressed. Molecular surface structures often show important stereochemical effects as, aside from truly chiral molecules, a large class of so-called prochiral molecules become chiral once confined on a surface with an associated loss of symmetry. Here, we investigate a model system in which adsorbed molecules surprisingly switch between enantiomeric forms as they undergo thermally induced conformational changes. The associated kinetic parameters are quantified from time-resolved STM data whereas mechanistic insight is obtained from theoretical modelling. The chiral switching is demonstrated to enable an efficient channel towards formation of extended homochiral surface domains. Our results imply that appropriate prochiral molecules may be induced (for example, by seeding) to assume only one enantiomeric form in surface assemblies, which is of relevance for chiral amplification and asymmetric heterogenous catalysis.
DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.
The presence of water was found to have a significant impact on the conversion of some Hartwig-Buchwald reactions between amides with arylbromides. Seven amidation reactions were studied in a series of experiments containing 0-400 mol % water. When cesium carbonate is used as the base both in dioxane and toluene, water can have a beneficial effect. The experiments have also shown that for some reactions, anhydrous conditions are unnecessary and sometimes can hinder the reaction.
[reaction: see text] Singlet molecular oxygen (a(1)Delta(g)) has been produced and optically monitored in time-resolved experiments upon nonlinear two-photon excitation of photosensitizers that contain triple bonds as an integral part of the chromophore. Both experiments and ab initio computations indicate that the photophysical properties of alkyne-containing sensitizers are similar to those in the alkene-containing analogues. Most importantly, however, in comparison to the analogue that contains double bonds, the sensitizer containing alkyne moieties is more stable against singlet-oxygen-mediated photooxygenation reactions. This increased stability can be advantageous, particularly with respect to two-photon singlet oxygen imaging experiments in which data are collected over comparatively long time periods.
DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.
Mixed self-assembled monolayers of 2-(mercaptooctyl)hydroquinone (QH2) and alkylthiols were formed on gold electrodes in EtOH and the redox process of the hydroquinone moiety of QH2 was characterized by cyclic voltammetry (CV) in 0.1 M H(2)SO(4). The monolayers were formed at a series of QH2:alkylthiol ratios and the QH2:alkylthiol ratio in solution was compared to the electrochemical response from QH2 in the obtained monolayer. Mixed monolayers of QH2 with hexylthiol, dodecylthiol, and octadecylthiol were studied. The length of the alkylthiol is crucial for the electrochemical response from QH2 in the monolayer. The total concentration of thiols during monolayer formation and incubation times were also studied and low concentrations of < 2.5 mM and long incubation times gave rise to lower peak separation, lower peak half widths in the CVs of the mixed monolayers, and lower background current. The stability of a pure QH2 monolayer and a 1:4 QH2:hexylthiol monolayer toward high potentials of up to 1.5 V versus Ag/AgCl was also studied and it was observed that the mixed monolayer is significantly more stable than the pure QH2 monolayer.
The oxidation of tetramethylthiourea (TMTU) at gold electrodes in acetonitrile, leading to dissolution of the electrode, has been studied by electrochemical methods and by an electrochemical quartz crystal microbalance (EQCM). TMTU in acetonitrile readily adsorbs at gold electrodes and an estimated coverage of 5.5 x 10(-10) mol cm(-2) (30 A2 per molecule) was measured electrochemically. Nevertheless, the oxidation of TMTU in solution is a diffusion-controlled process and is strongly influenced by the electrode material, as observed by comparison of gold electrodes with glassy carbon and platinum working electrodes. In the absence of TMTU, EQCM cyclic voltammetry experiments showed dissolution of gold through a 1e- oxidation process at potentials more positive than 1.20 V vs saturated calomel electrode (SCE). Potential step and cyclic voltammetry EQCM experiments performed using gold surfaces in the presence of TMTU revealed TMTU-assisted etching of gold at potentials as low as 0.35 V vs SCE. In the potential region from 0.35 to 1.20 V the current response of TMTU oxidation mimics the response expected for a redox-active species in solution, including the presence of a mass-transfer-limited region, which supports the conclusion that the etching process in this potential region is initiated by the oxidation of TMTU at the gold surface. The current efficiency of the TMTU-assisted etching was found to vary between 12 electrons per gold atom dissolved (e/Au) (E = 0.50 V vs SCE) and 2 e/Au (0.90 V < E < 1.20 V). At potentials <0.90 V the dominant electrochemical process is the formation of TMTU+, whereas at higher potentials the etching of the gold surface by formation of a Au(I)-TMTU+ species becomes equally important. At potentials above 1.20 V the etching is no longer dependent on the diffusion of TMTU and the e/Au value approaches 1.
DNA-directed coupling of organic modules by formation of stable aluminium-salen complexes, makes possible the subsequent reductive cleavage of disulfide linkers and release of the two oligonucleotide chains attached to each building-block.
Rigid linear and tripoidal organic modules based on the oligo(phenylene ethynylene) backbone having salicylaldehyde-derived termini are synthesized. A highly functionalized 5-iodosalicyl aldehyde was prepared and coupled to each ethynyl group of 1,4-diethynylbenzene or 1,3,5-triethynylbenzene in Sonogashira couplings. The two or three termini of the compounds are functionalized for incorporation in linear and branched oligonucleotide strands. For the linear module (LM), the two termini are equipped with amide spacers, and one of these was functionalized with a DMTr (dimethoxytrityl)-protected hydroxy group and the other with a phosphoramidite. One of the tripoidal modules is prepared with DMTr groups in two of its three termini. A tripoidal module is also synthesized with three different groups on its hydroxy termini: a phosphoramidite, a DMTr group, and an Fmoc group. Extended studies have shown that these rigid linear and tripoidal organic modules can be incorporated into short oligonucleotides. Several of these modules can be applied for DNA-directed assembly and covalent coupling into structures of predetermined connectivity. Such structures have potential application for molecular electronics and nanotechnology.
A new strategy for self-assembly and covalent coupling of encoded molecular modules into nanostructures with predetermined connectivity has been developed. The method uses DNA-functionalized oligo(phenylene ethynylene)-derived organic modules for controlling the assembly and covalent coupling of multiple modules. Rigid linear modules (LM) and tripoidal modules (TM) were functionalized with short oligonucleotides at each terminus. They can hybridize and thereby link up modules containing complementary sequences. Each terminus of the oligo(phenylene ethynylene) modules also consists of a salicylaldehyde moiety, which can form metal-salen complexes with other modules. The salicylaldehyde groups of two modules are brought in proximity when their adjoining DNA sequences are complementary, and they selectively form a manganese-salen complex in the presence of ethylenediamine and manganese acetate. The resulting structures consist of a matrix of linear and branched oligo(phenylene ethynylene)s which are linked by conjugated and rigid manganese-salen complexes. These nanostructures are potential conductors for applications in molecular electronics.
A catalytic enantioselective Henry reaction of silyl nitronates with aldehydes has been developed. Different chiral Lewis acids have been tested for the reaction and it has been found that a variety of chiral copper-ligand complexes can catalyze the Henry reaction. The best yield, diastereo- and enantioselectivity of the nitroalcohols formed are obtained by the application of a copper(II)-diphenyl-bisoxazoline complex as the catalyst in the presence of tetrabutylammonium triphenylsilyldifluorosilicate (TBAT). In order to minimize the epimerization of the nitroaldol products they were converted into the corresponding Mosher esters. The reaction proceeds well for different aromatic aldehydes reacting with alkyl nitronates.
A new organic reaction has been discovered in which nitrones react with carbonyl compounds in an aldoltype reaction to give functionalized beta-hydroxynitrones. The alpha-carbon atom of the nitrone undergoes a nucleophilic addition reaction to electron-deficient ketones, such as alpha-ketoesters, alpha,beta-diketones, and trifluoromethyl ketones, to afford the products in moderate to good yields. The scope and potential of the reaction have been investigated and developed. The reaction can also be catalyzed by secondary amines. The use of chiral cyclic amines, such as L-proline leads to optically active beta-hydroxynitrones in moderate yield and with moderate to high enantiomeric excess. The reaction mechanism was studied by kinetic measurements, intermediate and product analysis, and determination of the absolute configuration of the product; based on these investigations a mechanism for the new reaction is proposed.