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J W Engels

Publications and source records attributed to J W Engels.

At least 19 recordsLinked to original sources
PubMed2005

RNA recognition by fluor-aromatic substituted.

RNA exhibits a higher structural diversity than DNA and is an important molecule in the biology of life. It shows a number of secondary structures such as duplexes, hairpin loops, bulges, internal loops, etc. However, in natural RNA, bases are limited to the four predominant structures U, C, A, and G and so the number of compounds that can be used for investigation of parameters of base stacking, base pairing, and hydrogen bond is limited. We synthesized different fluoromodifications of RNA building blocks: 1'-deoxy-1'-phenyl-beta-D-ribofuranose (B), 1'-deoxy-1'-(4-fluorophenyl)-beta-D-ribofuranose (4 FB), 1'-deoxy-1'-(2,4-difluorophenyl)-beta-D-ribofuranose (2,4 DFB), 1'-deoxy- 1'-(2,4,5-trifluorophenyl)-beta-D-ribofuranose (2,4,5 TFB), 1'-deoxy- 1'-(2,4, 6-trifluorophenyl)-beta-D-ribofuranose, 1'-deoxy- 1'-(pentafluorophenyl)-beta-D-ribofuranose (PFB), 1'-deoxy-1'-(benzimidazol-1-yl)-beta-D-ribofuranose (BI), 1'-deoxy-1'-(4-fluoro-1H-benzimidazol-1-yl)-1-beta-ribofuranose (4 FBI), 1'-deoxy- 1'-(6-fluoro- 1H-benzimidazol-1-yl)-beta-D-ribofuranose (6FBI), 1'-deoxy- 1'-(4, 6-difluoro- 1H-benzimidazol- 1-yl)-beta-D-ribofuranose (4,6 DFBI), 1'-deoxy- 1'-(4-trifluoromnethyl- H-benzimidazol-1-yl)-beta-D-ribofuranose (4 TFM), 1'-deoxy-1'-(5-trifluoromnethyl-1H-benzimidazol-1-yl)-beta-D-ribofuranose (5 TFM), and 1'-deoxy-1'-(6-trifluoromethyl-1H-benzimidazol-1-yl)-beta-D-ribofuranose (6 TFM). These amidites were incorporated and tested in a defined A, U-rich RNA sequence (12-mer, 5-CUU UUCXUU CUU-3' paired with 3'-GAA AAG YAA GAA-5'). Only one position was modified, marked as X and Y, respectively. UV melting profiles of those oligonucleotides were measured.

Base Pairing↗
PubMed2005

Synthesis and purification of fluorinated benzimidazole and benzene nucleoside-5'-triphosphates.

The expression "universal base" is very often used to express hybridization properties and recognition patterns of nucleosides. Their behaviour in biological applications, however, is of great interest regarding, e.g.,' their incorporation by polymerases. The 4,6-difluorobenzimidazole and the 2,4-difluorobenzene nucleoside analogues have proven to be universal bases that do not discriminate between the four natural nucleobases in RNA duplexes. Therefore, we synthesized the corresponding triphosphates to evaluate their behavior in polymerase catalyzed reactions and to investigate their ability to serve as substrates for the T7 RNA polymerase.

Benzene↗
PubMed2001

Synthesis and properties of bile acid phosphoramidites 5'-tethered to antisense oligodeoxynucleotides against HCV.

Recently, we synthesized antisense oligonucleotides (AS-ODNs) directed against the non-coding-region (NCR) and the adjacent core region of the hepatitis C virus (HCV) RNA. Backbone modifications like phosphorothioates, methyl- and benzylphosphonates were introduced three at each end of the sequence. For improvement of liver specific drug targeting and/or hepatocellular uptake efficient AS-ODNs were covalently conjugated to biomolecules such as cholesterol or bile acids. The use of base-labile alkylphosphonates afforded mild conditions for deprotection of bile acid conjugated AS-ODNs. Here, we describe a convenient synthesis of new cholic acid and taurocholic acid phosphoramidites. Derivatization to taurocholic acid was effected directly before phosphitylation reaction, which is the last step of the phosphoramidite synthesis. These building blocks were coupled to the 5'-position of AS-ODNs in the last step of solid-phase synthesis. After mild deprotection, purification and characterization the properties of these modified AS-ODNs like their lipophilicity or their ability to form stable duplices to DNA and RNA were investigated. Enhanced lipophilicity and formation of stable duplices and heteroduplices makes bile acid conjugated AS-ODNs interesting as antiviral antisense therapeutics against HCV.

Bile Acids and Salts↗
PubMed2001

Measurement of 2J(H,C)- and 3J(H,C)-coupling constants by alpha/beta selective HC(C)H-TOCSY.

A new heteronuclear NMR pulse sequence for the measurement of nJ(C,H) coupling constants, the alpha/beta selective HC(C)H-TOCSY, is described. It is shown that the S3E element (Meissner et al., 1997a,b) can be used to obtain spin state selective coherence transfer in molecules, in which adjacent CH moieties are labeled with 13C. Application of the alpha/beta selective HC(C)H-TOCSY to a 10 nt RNA tetraloop 5'-CGCUUUUGCG-3', in which the four uridine residues are 13C labeled in the sugar moiety, allowed measurement of two bond and three bond J(C,H) coupling constants, which provide additional restraints to characterize the sugar ring conformation of RNA in cases of conformational averaging.

Base Sequence↗
PubMed2001

Nonprolyl cis peptide bonds in unfolded proteins cause complex folding kinetics.

Folding of tendamistat, an inhibitor of alpha-amylase, is a fast two-state process accompanied by two minor slow reactions, which were assigned to prolyl isomerization. In a proline-free variant, 5% of the molecules still fold slowly with a rate constant of 2.5 s(-1). This reaction is caused by a slow equilibrium between two populations of unfolded molecules. The time constant for this equilibration process, its sensitivity to LiCl and its temperature dependence identify it as a cis-trans isomerization of nonprolyl peptide bonds. Although nonprolyl peptide bonds have the cis conformation populating only approximately 0.15% in unfolded proteins, their large number generates a significant fraction of slow-folding molecules. This emphasizes that heterogeneous populations in an unfolded protein can induce complex folding kinetics on various time scales.

Amino Acid Substitution↗
PubMed2000

pH-independent triple-helix formation with 6-oxocytidine as cytidine analogue.

The syntheses of six different phosphoramidite building blocks of 6-oxocytosine and 5-allyl-6-oxocytosine as analogues of N(3)-protonated cytosine are described. These compounds have been incorporated into oligonucleotides by standard solid-phase synthesis. Hybridization of 15-mer Hoogsteen strands with target 21-mer duplexes was investigated. Comparison of the triplex-forming abilities of the different building blocks revealed that: i) 5-allyl substitution has a negative influence on triplex stability, ii) a uniform backbone of the Hoogsteen strand stabilizes triplexes relative to mixed backbones; iii) RNA strands with 6-oxocytidine or 5-allyl-6-oxocytidine do not form a triple helix with the DNA target duplex, probably due to backbone torsional constraints; and (iv) a 15-mer DNA sequence with three isolated 2'-deoxy-6-oxocytidines has the highest T(m) of all cytidine analogues investigated in this study. CD experiments provided further evidence for the presence or absence of triplex structures. In the course of these temperature-dependent CD measurements we were able to detect duplex and triplex melting independent from each other at selected wavelengths. This methodology is especially interesting in cases where UV melting curves show only one transition owing to spectral overlap.

Circular Dichroism↗
PubMed2000

Retrovirally expressed anti-HIV ribozymes confer a selective survival advantage on CD4+ T cells in vitro.

To date, a selective advantage of cells expressing anti-HIV ribozymes has not been shown. This study was undertaken to determine whether such a selective advantage can be demonstrated in vitro. A retroviral vector coding for a hairpin ribozyme targeting the HIV 5'LTR and for the low affinity nerve growth factor receptor (LNGF-RDelta) was designed. Since we demonstrated by RT-PCR that the amount of ribozyme transcripts was highly correlated with the level of surface LNGF-RDelta expression, the vector was utilized to assess ribozyme expression by flow cytometry. Transduced Hut78 and primary CD4+ T cells were purified and subsequently mixed with unmodified cells. After HIV challenge the percentage of ribozyme expressing cells in the cell mixture was monitored by flow cytometry. Twenty-one days after HIV infection the proportion of ribozyme expressing CD4+ T cells was 2.6 times higher in comparison to cells with the control vector. CD4+ T cells with a strong ribozyme expression conferred a 7.4-fold selective advantage at day 21 and a 11.7-fold at day 28. For Hut78 cells a selective advantage was detected exclusively for strongly ribozyme expressing cells. As a mechanism underlying the selective advantage an inhibition of HIV induced apoptosis was shown. These results demonstrate that anti-HIV ribozymes are able to confer a selective survival advantage and indicate that the protective effect is dependent on the amount of ribozyme expression. Gene Therapy (2000) 7, 408-416.

Apoptosis↗
PubMed2000

Solid-state transformation of 4, 2'-anhydro-5-(beta-D-arabinofuranosyl)uracil dihydrate to 4, 2'-anhydro-5-(beta-D-arabinofuranosyl)uracil monohydrate.

Crystals of 4,2'-anhydro-5-(beta-D-arabinofuranosyl)uracil, (I), obtained from an aqueous solution, were characterized as the dihydrate, C(9)H(10)N(2)O(5).2H(2)O, (Ia). In air, these crystals slowly transform to the monohydrate, C(9)H(10)N(2)O(5).H(2)O, (Ib), but remain crystalline. The solid-state transformation proceeds with the loss of one water molecule and a rearrangement of hydrogen-bonded layers of molecules. The furanose ring in (I) has an approximate C4'-exo,O4'-endo twist conformation. The central five-membered ring is slightly puckered. The uracil group is planar within experimental uncertainty.

Arabinofuranosyluracil↗
PubMed1999

Comparative inhibitory potential of differently modified antisense oligodeoxynucleotides on hepatitis C virus translation.

BACKGROUND: A completely modified phosphorothioate antisense oligodeoxynucleotide (cS-ODN 4) directed against nucleotides 326-348 of the hepatitis C virus (HCV) 5' non-coding region (NCR) efficiently inhibits viral gene expression. As cS-ODN exerts undesired side-effects in vivo, we synthesized partially modified ODN 4 that contained only six modified nucleotides which are located at the ODN termini or are scattered along the molecule. The tested modifications were polar phosphorothioates (S) and non-polar methyl- (M) or benzylphosphonates (B). RESULTS: In an in vitro translation system, specific inhibition of HCV gene expression by M-ODN 4 or B-ODN 4 was observed if terminally modified ODN were used; the maximal inhibition was 92.3% +/- 1.9% and 87.1% +/- 3.7%, respectively, at 10 microgram mol L-1 concentration. S-ODN 4 specifically suppressed viral translation irrespective of the location of the modifications, resulting in a maximal inhibition of 86.3% +/- 3.3%. For all terminally modified ODNs the therapeutic index was high, with tB-ODN 4 the second best at 3.8. Inhibition correlated with efficient RNase H-associated cleavage of target RNA. In transient co-transfection experiments of HepG2 cells with a reporter gene construct and the ODN, terminally modified B-ODN 4 was the most effective and specific inhibitor. At a concentration of 5 microgram mol L-1 the suppression of HCV translation was 96.3% +/- 0.7%. CONCLUSION: These data demonstrate that terminally modified B-ODN 4 is a potent inhibitor of HCV gene expression in vitro and in HepG2 cell culture and may be valuable for future antiviral treatment.

Animals↗
PubMed1999

Sequence specific hybridization properties of methylphosphonate oligodeoxynucleotides.

Methylphosphonate oligodeoxynucleotides (MPO's) with isomerically pure Rp-configurated methylphosphonates (MP's) were synthesized by block coupling of ApT and TpA dinucleoside methylphosphonates (DMP's, p indicating MP-linkage). Oligonucleotide duplexes (20 mers) with these Rp-MP's showed almost the same melting temperatures (Tm) as those with phosphorodiester bonds. Further a dependence of the duplex stability from the nucleosides (bases) adjacent to the MP moiety was observed. For the first time thermodynamic parameters for the duplex to coil transition of isomerically pure MP's were determined from the concentration dependence of the Tm. CD-spectra of the duplexes show structural changes which can be associated with the transition to a compact helix with higher helix winding angle.

Nucleic Acid Conformation↗
PubMed1998

Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhibitor [C45A/C73A]tendamistat: an NMR study.

Covalent linkages such as disulfide bonds are important for the stabilization of proteins. In the present NMR study we compare the structure and the dynamics of the single disulfide-deficient variant C45A/C73A of the alpha-amylase inhibitor tendamistat and the wild-type protein, which contains two disulfide bonds (C11-C27 and C45-C73). Complete proton assignment was achieved by standard homonuclear 2D techniques for the variant. Chemical shift differences, intra-strand NOE effects and protected amide proton were used to compare the connectivity of the secondary structure elements of variant and wild-type. Dynamic properties of the wild-type protein were studied by 13C(alpha) heteronuclear NOE experiments with carbon in natural abundance. 15N isotope labeling was necessary to obtain the relaxation parameters of the variant, because of sample degradation. The 15N resonance assignment was achieved by a 15N 3D-NOESY-HMQC. Removal of the C45-C73 bond by the C45A/C73A mutation has no influence upon the beta-barrel structure of tendamistat beside very local changes at the mutation site. The relaxation data revealed only subtle differences between variant and wild-type on a subnanosecond time scale. Only the N-terminus and G62 in the connecting loop between the anti-parallel beta-sheets showed an increased mobility. The results are discussed in respect to thermodynamic stability and the secretion efficiency of tendamistat.

Disulfides↗
PubMed1998

Effective reversal of a transformed phenotype by retrovirus-mediated transfer of a ribozyme directed against mutant N-ras.

A hammerhead ribozyme directed against oncogenic N-ras (N13-ras) was introduced into a retroviral vector and its activity evaluated in vitro and in cell lines. The catalytic efficiency of the ribozyme embedded within a 2618 nucleotides in vitro-generated transcript was not significantly affected by the length of non-base pairing flanking sequences. A sensitive assay based on N-ras/luciferase fusion transcripts as a reporter system was used to assess ribozyme activity in mammalian cells. More than 95% reduction in luciferase activity was observed in cells transduced with a retrovirus containing the active form of the ribozyme, whereas no significant reduction was observed with the inactive form of the same ribozyme. In order to assay the activity of the retrovirally encoded ribozyme in a biological setting, the IL-3-dependent cell line TF-1 was transformed with N13-ras. Expression of N13-ras in these cells induced factor-independent colony growth and a dose-dependent proliferative response to erythropoietin (Epo). Retrovirus-mediated expression of the active form of the ribozyme in these cells restored factor-dependent colony growth and abolished the proliferative response to Epo. The reversion of the transformed phenotype correlated with a reduction in the amount of N13-ras mRNA.

Animals↗
PubMed1998

Synthesis and characterization of 2-mercaptoethanesulfonic acid albumin.

Autoimmune patients treated with ifosfamide (CAS 3778-73-2) and mesna (2-mercaptoethanesulfonic acid, CAS 3375-50-6) in some cases suffered from severe allergic reactions that were proposed to be due to mesna linked to serum albumin by a disulfide bond. To prove the existence of the hypothetic mesna albumin adduct in vivo it was synthesized: The free thiol group of albumin (molecular mass determined by MALDI spectroscopy: 67009 Da) was converted to S-phenylsulfonyl albumin and reacted with mesna to albumin mesna (molecular mass: 67159 Da). In an alternative synthesis albumin was incubated with mesna at pH 8, 40 degrees C (molecular mass of the adduct: 67166 Da).

Albumins↗
PubMed1997

A sequencing method for RNA oligonucleotides based on mass spectrometry.

Synthetic oligoribonucleotides up to 22 bases have been sequenced by observing different kinetics in exonuclease-induced phosphodiester bond hydrolysis and detecting the fragments by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Common mass spectrometric sequencing methods have disadvantages concerning read length, cost, and specialist instrumentation using RNA as the target molecule because uridine and cytidine have similar masses. Now we are in the position to distinguish U and C by different peak intensities. The method proposed has been verified using specific endonucleases and 13C-labeled nucleotides. This new nongel-based and nonlabeling sequencing strategy offers first RNA sequencing data using the advantages of fast and accurate MALDI-TOF-MS. Preparation steps and measurements are performed in less than 1 h.

Animals↗
PubMed1997

Overexpression, purification, and use of a soluble human interleukin-4 receptor alpha-chain/Ig gamma 1 fusion protein for ligand binding studies. Characterization of ligand binding to soluble IL-4 receptor alpha-chain by surface plasmon resonance measurements and by microtiter-plate-based ELISA with biotinylated IL-4.

The pleiotropic cytokine IL-4 transmits cellular signals mainly via the IL-4 receptor complex, with the alpha-chain as the high affinity binding subunit. Here we describe the overexpression of a soluble IL-4R alpha-chain (sIL-4R) as a fusion to immunoglobulin gamma 1 heavy chain, consisting of the H-CH2-CH3 domains, in baby hamster kidney cells. The dimeric fusion protein named sIL-4R:E gamma 1 was purified from culture supernatant by protein-A affinity chromatography, yielding up to 10 mg/l homogenous protein which was highly stable. The antibody-like features of the sIL-4R:E gamma 1 fusion protein allowed immobilization on a biosensor matrix for surface plasmon resonance measurements by direct amine coupling as well as immobilization on microtiter plates coated with protein A for displacement binding. Kinetic parameters (kon and koff) for binding of IL-4 or the antagonistic mutant IL-4(Y124D) to the sIL-4R:E gamma 1 fusion protein on the chip as determined with the BIAcore instrument showed a high affinity binding with KD = 239 +/- 35 pM and KD=148 +/- 33 pM, respectively. The extremely high kon rate and the relatively slow koff rate for both ligands highlighted the limits of the BIAcore technology. The binding affinity as calculated in displacement binding studies with biotinylated IL-4 was similar for IL-4 and IL-4(Y124D) (IC50=1.1nM), thus offering a simple alternative for initial characterization of IL-4 mutants.

Animals↗
PubMed1997

Specific hammerhead ribozyme-mediated cleavage of mutant N-ras mRNA in vitro and ex vivo. Oligoribonucleotides as therapeutic agents.

Two hammerhead ribozymes targeted to point mutations in codon 13 of the N-ras oncogene were synthesized and their catalytic activity and substrate specificity evaluated in vitro and ex vivo. In vitro studies showed that these ribozymes were specific for the oncogenic form of N-ras, since cleavage was observed only in a 849-nucleotide-long transcript containing mutant but not wild-type N-ras sequences. For the ex vivo studies, the ribozymes were 2'-modified to protect them against degradation by nucleases. 2'-Fluoro-2'-deoxyuridine/cytidine-substituted ribozymes were nearly as active as their unmodified counterparts, but had a prolonged stability in cell culture supernatant containing fetal calf serum. The stability of the modified ribozymes increased by introduction of terminal phosphorothioates groups without significant influence in their catalytic efficiency. A sensitive assay based on the use of N-ras/luciferase fusion genes as a reporter system was established to detect ribozyme-mediated cleavage in HeLa cells. A reduction of nearly 60% in luciferase activity was observed in cells expressing mutant but not wild-type N-ras/luciferase fusion transcripts. Moreover, cleavage of N-ras transcripts in HeLa cells was directly confirmed by a semi-quantitative RT-PCR assay.

Genes, ras↗