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A Jäschke

Publications and source records attributed to A Jäschke.

At least 19 recordsLinked to original sources
PubMed2006

Atomic force microscopy and anodic voltammetry characterization of a 49-mer diels-alderase ribozyme.

Atomic force microscopy and differential pulse voltammetry were used to characterize the interaction of small highly structured ribozymes with two carbon electrode surfaces. The ribozymes spontaneously self-assemble in two-dimensional networks that cover the entire HOPG surface uniformly. The full-length ribozyme was adsorbed to a lesser extent than a truncated RNA sequence, presumably due to the formation of a more compact overall structure. All four nucleobases composing the ribozyme could be detected by anodic voltammetry on glassy carbon electrodes, and no signals corresponding to free nucleobases were found, indicating the integrity of the ribozyme molecules. Mg2+ cations significantly reduced the adsorption of ribozymes to the surfaces, in agreement with the stabilization of this ribozyme's compact, stable, and tightly folded tertiary structure by Mg2+ ions that could prevent the hydrophobic bases from interacting with the HOPG surface. Treatment with Pb2+ ions, on the other hand, resulted in an increased adsorption of the RNA due to well-known hydrolytic cleavage. The observed dependence of anodic peak currents on different folding states of RNA may provide an attractive method to electrochemically monitor structural changes associated with RNA folding, binding, and catalysis.

Absorption↗
PubMed2002

Ribozyme-catalysed carbon-carbon bond formation.

Numerous RNA molecules with new catalytic properties have been isolated from synthetic combinatorial libraries. A broad range of chemical reactions is catalysed, and nucleic acids can accelerate bond formation between small organic substrates. This review focuses on carbon-carbon bond formation accelerated by in vitro selected ribozymes. Mechanistic investigations and structure-function relationships are discussed.

Base Sequence↗
PubMed2001

Artificial ribozymes and deoxyribozymes.

RNA and DNA molecules with catalytic properties have been isolated by in vitro selection from combinatorial nucleic acid libraries. A broad range of chemical reactions is catalyzed and nucleic acids can accelerate bond formation between small organic substrates. The catalytic performance of nucleic acids can be enhanced by the incorporation of additional functional groups.

Evolution, Molecular↗
PubMed2001

Detection of small organic analytes by fluorescing molecular switches.

A sensor system was developed for the determination of theophylline concentrations based on a theophylline-dependent allosteric ribozyme (Soukup, G. A.; Breaker, R. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3584) in combination with an RNA substrate which is double-labeled with a fluorophore and a quencher dye. In the presence of theophylline, a hammerhead ribozyme domain is switched into an active conformation by the action of a theophylline-binding aptamer domain. Upon substrate cleavage, the quencher is removed from the vicinity of the fluorophore, causing an increased fluorescence signal. Real-time analysis of the cleavage reactions both under single and multiple turnover conditions revealed a dependence on the cleavage rate within a range from 0.01 to 2mM theophylline. The structurally similar molecule caffeine, however, had no detectable influence on the fluorescence signal.

Allosteric Site↗
PubMed2001

RNA-catalyzed carbon-carbon bond formation.

RNA molecules with catalytic properties have been isolated by in vitro selection from combinatorial libraries. A broad range of chemical reactions can be catalyzed, and nucleic acids can accelerate bond formation between small organic substrates. The catalytic performance of nucleic acids can be enhanced by incorporation of additional functional groups. This minireview focuses on carbon-carbon bond formation accelerated by in vitro selected ribozymes.

Base Sequence↗
PubMed2000

Multifunctional DNA conjugates for the in vitro selection of new catalysts.

DNA-substrate conjugates are required for the direct in vitro selection of novel DNA catalysts for reactions between two small reactants. Here we describe the introduction of all necessary features into ssDNA by a novel, multifunctional primer containing a flexible PEG spacer, an o-nitrobenzyl moiety allowing for selective photocleavage, and anthracene as a reactant, a fluorescence label and/or an immobilization tag. These components were checked individually and by a mock selection.

Anthracenes↗
PubMed2000

Synthesis, incorporation efficiency, and stability of disulfide bridged functional groups at RNA 5'-ends.

Modified guanosine monophosphates have been employed to introduce various functional groups onto RNA 5'-ends. Applications of modified RNA 5'-ends include the generation of functionalized RNA libraries for in vitro selection of catalytic RNAs, the attachment of photoaffinity-tags for mapping RNA-protein interactions or active sites in catalytic RNAs, or the nonradioactive labeling of RNA molecules with fluorescent groups. While in these and in similar applications a stable linkage is desired, in selection experiments for generating novel catalytic RNAs it is often advantageous that a functional group is introduced reversibly. Here we give a quantitative comparison of the different strategies that can be applied to reversibly attach functional groups via disulfide bonds to RNA 5'-ends. We report the preparation of functional groups with disulfide linkages, their incorporation efficiency into an RNA library, and their stability under various conditions.

Base Sequence↗
PubMed2000

Evolution of DNA and RNA as catalysts for chemical reactions.

In vitro selection from combinatorial nucleic acid libraries has provided new RNA and DNA molecules that have catalytic properties. Catalyzed reactions now go far beyond self-modifying reactions of nucleic acid molecules. The future application of in vitro selected RNA and DNA catalysts in bioorganic synthesis appears promising.

Acylation↗
PubMed1999

A small catalytic RNA motif with Diels-Alderase activity.

BACKGROUND: The 'RNA world' hypothesis requires that RNA be able to catalyze a wide variety of chemical reactions. In vitro selection from combinatorial RNA libraries has been used to identify several catalytic activities, most of which have resulted in a self-modification of RNA at one of its constituents. The formation of carbon-carbon bonds is considered an essential prerequisite for a complex metabolism based on RNA. RESULTS: We describe the selection and characterization of new ribozymes that catalyze carbon-carbon bond formation by Diels-Alder reaction of a biotinylated maleimide with an RNA-tethered anthracene. Secondary structure analysis identified a 49-nucleotide RNA motif that accelerates the reaction about 20,000-fold. The motif has only 11 conserved nucleotides that are present in most of the selected sequences. The ribozyme motif is remarkably adaptable with respect to cofactor and metal-ion requirements. The motif was also re-engineered to give a 38-mer RNA that can act as a 'true' catalyst on short external substrate oligonucleotide-anthracene conjugates. CONCLUSIONS: We have identified a small, highly abundant RNA motif that can solve the complex task of forming two carbon-carbon bonds between two reactants in trans, a catalytic capacity useful for creating prebiotically relevant molecules. This is the smallest and fastest RNA catalyst for carbon-carbon bond formation reported to date.

Algorithms↗
PubMed1998

Human T cell cyclophilin18 binds to thiol-specific antioxidant protein Aop1 and stimulates its activity.

Cyclophilins (CyPs) define a family of proteins binding to the immunosuppressive drug cyclosporin A (CsA). They are evolutionary highly conserved proteins being present in both pro- and eukaryotes and in different subcellular locations. CyPs possess enzymatic activity, namely peptidyl-prolyl cis-trans isomerase (PPIase) activity and are involved in cellular protein folding and protein interactions. Here we describe a novel interaction of human T cell cyclophilin18 (hCyP18). Abundant cytosolic hCyP18 binds to the thiol-specific antioxidant protein Aop1 and stimulates its enzymatic activity. Aop1 belongs to a family of proteins thought to be involved in defense of oxidative stress. The interaction of both proteins seem to be specific, since other PPIases do not have any stimulatory effect on Aop1.

Antioxidants↗
PubMed1997

The effect of paclitaxel on the radiosensitivity of gynecological tumor cells.

BACKGROUND: Paclitaxel, a natural product from Taxus brevifolia, is a microtubule stabilizing agent, which has been shown to block different cells in the G2/M phase of the cell cycle and consequently, to modulate their radioresponsiveness. Our aim was to test the cytotoxic and radiosensitizing potential of paclitaxel, with respect to different gynecological tumors with varying radiosensitivities. MATERIAL AND METHOD: We performed clonogenic assays and flow cytometry on 2 cell lines, MCF-7 (breast) and CaSki (cervix) cells, and on 2 primary ovarian tumor samples (OC-I and OC-II). The cells were irradiated with 200 kV X-rays, radiation doses of up to 8 Gy were applied either as single doses or in 2 Gy fractions. Paclitaxel concentrations varied from 0.07 to 700 nM, incubation times varied from 3 to 120 h. RESULTS: Paclitaxel alone changed the cell cycle distribution of the cells tested and was cytotoxic in a time and concentration dependent manner. When combined with radiation, most schedules resulted in additive effects of the combined treatments. However, for MCF-7 cells, when 7 nM paclitaxel, applied 24 h before irradiation, were combined with fractionated irradiation a supra-additive effect with a SER of 1.2 was found. For CaSki cells, under comparable conditions the SER was 1.13 but the effects were not statistically significant. CONCLUSION: Under specific conditions, paclitaxel exerted a weak radiosensitizing effect on breast and cervical carcinoma cells. A therapeutic gain may be possible on the basis of an optimal paclitaxel/radiation scheduling.

Antineoplastic Agents, Phytogenic↗
PubMed1997

Pancreatic fibrosis in experimental pancreatitis induced by dibutyltin dichloride.

BACKGROUND & AIMS: Regulatory mechanisms in chronic pancreatitis finally resulting in pancreatic fibrosis cannot be studied sufficiently in human pancreas. Results of a new pancreatitis model in rats suitable for investigation of the processes leading to pancreatic fibrosis are presented. METHODS: Experimental pancreatitis was induced by intravenous application of 8 mg/kg body wt dibutyltin dichloride. Pancreatitis was characterized by histology, serum parameters, and immunohistochemistry, detecting inflammatory cells. Gene expression of collagen type I and transforming growth factor beta1 was shown by Northern blot analysis. RESULTS: Dibutyltin dichloride induced an acute edematous pancreatitis within 24 hours. Extensive infiltration with mononuclear cells could be observed after day 7 followed by the development of fibrosis. Parallel to the cell infiltration, an upregulation of messenger RNA-encoding collagen type I and transforming growth factor beta1 could be shown. An active inflammatory process could be shown until the end of the observation period, i.e., 2 months. CONCLUSIONS: The findings suggest that dibutyltin dichloride-induced pancreatitis in rats is suitable to study cellular interactions and mediators involved in the development of pancreatic fibrosis.

Animals↗
PubMed1996

A nuclear RNA-binding cyclophilin in human T cells.

Cyclophilins (CyPs) are binding proteins for the immunosuppressive drug cyclosporin A (CsA). CyPs are evolutionarily highly conserved proteins present in both pro- and eukaryotes as well as in different subcellular locations. CyPs possess enzymatic activity, namely peptidyl-prolyl cis-trans isomerase (PPIase) activity; CyPs are involved in cellular protein folding and protein interactions. To date, only cyclosporins and proteins are known to interact with CyPs. Here we describe a novel nuclear cyclophilin (hCyP33) from human T cells with an additional RNA-binding domain. This combines for the first time RNA binding and protein folding in one protein.

Amino Acid Isomerases↗
PubMed1994

Synthesis and properties of oligodeoxyribonucleotide-polyethylene glycol conjugates.

Pools of oligonucleotide conjugates consisting of 10-400 different molecular species were synthesized. The conjugates contained a varying number of ethylene glycol units attached to 3'-terminal, 5'-terminal and internal positions of the oligonucleotides. Conjugate synthesis was performed by phosphoramidite solid phase chemistry using suitably protected polyethylene glycol phosphoramidites and PEG-derivatized solid supports containing polydisperse PEGs of various molecular weight ranges. The pools were analyzed and fractionated by chromatographic and electrophoretic techniques, and the composition of isolated conjugates was revealed by matrix-assisted laser desorption/ionization mass spectrometry. The number and attachment sites of coupled ethylene glycol units greatly influence the hydrophobicity of the conjugates, as well as their electrophoretic mobilities. Conjugation had little effect on the hybridization behavior of oligonucleotide conjugates with unmodified complementary oligonucleotide strands. Melting temperatures were between 67 and 73 degrees C, depending on the size and number of coupled PEG chains, compared to 68 degrees C for the unmodified duplex. Conjugates with PEG coupled to both 3'- and 5'-terminal positions showed a more than 10-fold increase in exonuclease stability.

Base Sequence↗
PubMed1994

Hybridization-based affinity partitioning of nucleic acids using PEG-coupled oligonucleotides.

Polyethylene glycol (PEG)-coupled oligonucleotides are partitioned in an aqueous two-phase system PEG/dextran. The affinity of the oligonucleotide for the PEG-rich phase increases proportionally to the length of the coupled PEG polymer. After hybridization, the PEG-coupled oligonucleotide is able to force a complementary nucleic acid strand into the PEG-rich phase. This property can be used for the sequence-specific isolation of nucleic acids through hybridization-based affinity partitioning. The dependence of the partition coefficient in this system on various parameters is described. The application of this principle to multistage chromatographic separations is demonstrated.

Base Sequence↗
PubMed1992

Inclusion and fractionated release of nucleic acids using microcapsules made from plant cells.

The encapsulation and fractionated release of nucleic acids on vesicular packing (VP) materials have been investigated. The earlier described dependence of the permeation of nucleic acid molecules through the vesicle membranes on the salt concentration is a necessary precondition for both encapsulation and fractionation. Encapsulation is achieved by applying a suitable sample onto a VP column that has been equilibrated with a high-salt buffer. In that buffer the sample molecules are permeable. Immediately after sample application, elution is started with a low-salt buffer, from which the sample molecules are excluded. At the front between the two buffers the permeability changes, and some of the sample molecules distributed inside the vesicles cannot pass through the membranes. These encapsulated molecules can be released by increasing the salt concentration in the eluent. If the encapsulated nucleic acid sample is polydisperse, a stepwise or linear increase in the salt concentration leads to a fractionated release. The fractions obtained differ in their molecular size composition.

Base Sequence↗
PubMedDate not supplied

Libraries of multifunctional RNA conjugates for the selection of new RNA catalysts.

An in vitro selection system was developed for the selection of RNA molecules catalyzing bimolecular reactions between small reactants. The system is based on the direct selection protocol and involves libraries of multifunctional RNA conjugates rather than unmodified RNA transcripts. For the preparation of RNA conjugate libraries, a dinucleotide analog has been designed and synthesized containing a poly(ethylene glycol) linker with an embedded photocleavage site and a terminal attachment site for coupling potential reactants. Reactants are first coupled to the dinucleotide analog by activated ester chemistry and then ligated to the 3'-ends of enzymatically prepared RNA pool molecules, giving libraries of complex conjugates. Species that become attached to biotin on incubation with a biotinylated partner are isolated using streptavidin-derivatized matrices and then subjected to a photocleavage step. Selective cleavage of the linker releases only those RNA species in which reaction has taken place at the linker-coupled reactant, while products with the biotin attached to internal positions of the RNA part remain immobilized. Efficient photocleavage is achieved by laser irradiation at 355 nm, and the released RNAs are intact and amplifiable by reverse transcription. All steps are shown to be compatible with the overall selection procedure, as was shown by performing a model selection cycle. Besides allowing a broader scope of reaction types to be selected for, the strategy relieves the RNA from the requirement to possess substrate properties as well as catalytic activity, and the use of a cleavable linker will suppress the selection of catalysts for side reactions.

Photolysis↗