Biomedical subjects

F Eckstein

Publications and source records attributed to F Eckstein.

At least 199 records · Page 11Linked to original sources

PubMed1994

Interactions of 2'-modified azido- and haloanalogs of deoxycytidine 5'-triphosphate with the anaerobic ribonucleotide reductase of Escherichia coli.

The anaerobic Escherichia coli ribonucleotide reductase (class III reductase) responsible for the synthesis of the deoxyribonucleotides required for anaerobic DNA replication contains an oxygen-sensitive glycyl radical (Gly-681) suggesting involvement of radical chemistry in catalysis. The amino acid sequence of this enzyme completely differs from that of earlier described aerobic class I (prototype, aerobic E. coli) and class II (prototype, Lactobacillus leichmanii) reductases that use radical chemistry but employ other means for radical generation. Here, we study the interaction between the anaerobic E. coli reductase with the 5'-triphosphates of 2'-chloro-2'-deoxycytidine, 2'-fluoro-2'-deoxycytidine, and 2'-azido-2'-deoxycytidine (N3CTP), which are mechanism-based inhibitors of class I and II reductases and, on interaction with these enzymes, decompose to base, inorganic di(tri)phosphate and 2'-methylene-3(2H)-furanone. Also, with the anaerobic E. coli reductase, the 2'-substituted nucleotides act as mechanism-based inhibitors and decompose. N3CTP scavenges the glycyl radical of the enzyme similar to the interaction of N3CDP with the tyrosyl radical of class I enzymes. However, we found no evidence for a new transient radical species as is the case with class I enzymes. Our results suggest that the chemistry at the nucleotide level for the reduction of ribose by class III enzymes is similar to the chemistry employed by class I and II enzymes.

Anaerobiosis↗

PubMed1994

Isoguanosine substitution of conserved adenosines in the hammerhead ribozyme.

Isoguanosine has been incorporated into a 34-mer hammerhead ribozyme by the solid-phase phosphoramidite method, using an acetamidine base protecting group. The activity of the hammerhead ribozyme when singly mutated to isoguanosine at the adenosine positions 6, 9, and 13 was 1-2-fold less than the wild-type activity. Mutations to 2-aminopurine ribonucleoside at positions 9 and 13 were 5-fold reduced in activity, but that at position 6 was approximately 30-fold reduced. These results support the view that the 6-amino functions of A6, A9, and A13 are not very important for catalysis. The 2-position of A6 tolerates a carbonyl function but not an amino group, whereas A9 and A13 tolerate both functional groups. The tolerance of a 2-amino group at A9 and A13 makes G(anti)/A(anti) Watson-Crick type base mispairing for G12/A9 and A13/G8 unlikely.

2-Aminopurine↗

PubMed1994

Antisense oligonucleotide inhibition of acetylcholinesterase gene expression induces progenitor cell expansion and suppresses hematopoietic apoptosis ex vivo.

To examine the role of acetylcholinesterase (EC 3.1.1.7) in hematopoietic cell proliferation and differentiation, we administered a 15-mer phosphorothioate oligonucleotide, antisense to the corresponding ACHE gene (AS-ACHE), to primary mouse bone marrow cultures. Within 2 hr of AS-ACHE addition to the culture, ACHE mRNA levels dropped by approximately 90%, as compared with those in cells treated with the "sense" oligomer, S-ACHE. Four days after AS-ACHE treatment, ACHE mRNA increased to levels 10-fold higher than in S-ACHE cultures or in fresh bone marrow. At this later time point, differential PCR display revealed significant differences between cellular mRNA transcripts in bone marrow and those in AS-ACHE- or S-ACHE-treated cultures. These oligonucleotide-triggered effects underlay considerable alterations at the cellular level: AS-ACHE but not S-ACHE increased cell counts, reflecting enhanced proliferation. In the presence of erythropoietin it also enhanced colony counts, reflecting expansion of progenitors. AS-ACHE further suppressed apoptosis-related fragmentation of cellular DNA in the progeny cells, and it diverted hematopoiesis toward production of primitive blasts and macrophages in a dose-dependent manner promoted by erythropoietin. These findings suggest that the hematopoietic role of acetylcholinesterase, anticipated to be inverse to the observed antisense effects, is to reduce proliferation of the multipotent stem cells committed to erythropoiesis and megakaryocytopoiesis and macrophage production and to promote apoptosis in their progeny. Moreover, these findings may explain the tumorigenic association of perturbations in ACHE gene expression with leukemia.

Acetylcholinesterase↗

PubMed1994

AUA-cleaving hammerhead ribozymes: attempted selection for improved cleavage.

In order to find a ribozyme which can cleave the AUA triplet efficiently, the specificities and rates of intermolecular cleavage by the ribozyme of the satellite RNA of the barley yellow dwarf virus have been determined. Although it cleaves the AUA triplet in the plus strand of the viroid RNA, cleavage of AUC and AUU is more efficient, and AUG is essentially not cleaved. Attempts were made to increase cleavage efficiency by in vitro selection with randomization at positions 7, 10.1, and 11.1 in the core region. Fifteen clones were analyzed, two of which showed increased AUA cleavage efficiency. They have a G10.1.C11.1 base pair and a pyrimidine at position 7. This corresponds to the sequence of the consensus hammerhead ribozyme. Attempts to further increase cleavage efficiency by in vitro selection of the consensus hammerhead ribozyme with randomization of the 10 nucleotides in the core region or of the sBYDV ribozyme with 12 core nucleotides randomized were not successful.

Base Sequence↗

PubMed1994

High activity and stability of hammerhead ribozymes containing 2'-modified pyrimidine nucleosides and phosphorothioates.

The influence of chemical modifications on the catalytic activity and stability of a hammerhead ribozyme directed against the long terminal repeat RNA of the human immunodeficiency virus 1 was examined. Previous studies had shown that substitution of all pyrimidine nucleosides by their 2'-fluoro analogs led to an 8-fold decrease in catalytic efficiency in the cleavage reaction compared to the unmodified ribozyme (Heidenreich, O., and Eckstein, F. (1992) J. Biol. Chem. 267, 1904-1909). It is shown here that replacement of the 2'-fluoro-2'-deoxyuridines in the conserved region of this ribozyme, positions 4 and 7, by 2'-amino-2'-deoxyuridines fully restores catalytic activity of the ribozyme. Ribozymes containing these 2'-modifications show an increased stability against RNases present in fetal calf serum and in cell culture supernatant. The stability is increased further by the incorporation of four terminal phosphorothioates as protection against 3'-exonucleases, the degree of which depends on the secondary structure of the ribozyme. Such ribozymes are stable in undiluted fetal calf serum for at least 24 h. The results clearly demonstrate the potential to design stable ribozymes without any loss of catalytic activity.

Animals↗

PubMed1994

Oligonucleotide duplexes containing 2'-amino-2'-deoxycytidines: thermal stability and chemical reactivity.

Thermal stabilities of oligonucleotides containing 2'-amino-2'-deoxycytidines were determined and compared to those of the unmodified oligonucleotides. The presence of the 2'-aminonucleoside destabilized duplexes in a RNA as well as a DNA context at pH 7 as well as at pH 5. The pKa of the 2'-amino group was determined by 13C-NMR spectroscopy to be 6.2. The reactivity of an oligonucleotide containing a 2'-aminonucleoside was exploited for the incorporation of rhodamine by its isothiocyanate derivative.

Amines↗

PubMed1994

The influence of geometry on the stress distribution in joints--a finite element analysis.

The incongruity of human joints is a phenomenon which has long been recognized, and recent CT-osteoabsorptiometric findings suggest that this incongruity influences the distribution of stress in joints during their normal physiological use. The finite element method (FEM) was therefore applied to five different geometric configurations consistent with the anatomy of articular surfaces, and a program with variable contact areas (Marc) was used to calculate the stress distribution for loads of 100 to 6,900 N. The assumption of congruity between head and socket results in a "bell-shaped" distribution of stress with a maximum value of 61.5 N/mm2 in the depths of the socket, decreasing towards zero at its edges. In the model with a flatter socket the von Mises stresses are higher (max. 101.3 N/mm2); with a deeper socket, lower (max. 53.0 N/mm2). If the diameter of the head is greater, the stresses build up from the periphery of the socket and move towards its depths as the load increases. The combination of an oversized head and a deeper socket results in the most satisfactory stress distribution (max. 43.2 N/mm2). These results extend previous photoelastic findings with incongruous joint surfaces. The calculated mechanical conditions show a relationship to the location of osteoarthritic changes, and are reflected by the distribution pattern of subchondral bone density. A more satisfactory stress distribution is found with functionally advantageous, incongruous joint surfaces (oversized head and deepened socket) than in the congruous joint, and a better nutritive situation for the articular cartilage seems likely.(ABSTRACT TRUNCATED AT 250 WORDS)

Absorptiometry, Photon↗

PubMed1994

The morphology of articular cartilage assessed by magnetic resonance imaging (MRI). Reproducibility and anatomical correlation.

Quantitative assessment of cartilage volume and thickness in a formalin-alcohol fixed specimen of a human patella was conducted with magnetic resonance imaging (MRI), as it is still unclear whether the morphology of normal and damaged cartilage can be accurately demonstrated with this technique. MR imaging was carried out at 1.0 T (section thickness 2 mm, in-plane-resolution 0.39-0.58 mm) with the following pulse sequences: 1) T1-weighted spin-echo, 2) 3D-MPRAGE, 3) 3D-FISP, 4) 3D-MTC-FISP, 5) 3D-DESS, 6) 3D-FLASH. Following imaging, the patella was sectioned perpendicular to the articular surface at intervals of 2 mm with a diamond band-saw. The volume of its cartilage was determined from the anatomical sections and the MR images, using a Vidas IPS 10 image analysing system (Kontron). Measurements were carried out with and without the low-signal layer in the transitional zone between the articular cartilage and the subchondral bone. If the low-signal layer was included, the volume was overestimated with MRI by 16 to 19%. Without the low-signal layer the volumes were less than those determined from the anatomical sections: T1-SE-18.2%, MPRAGE -22.6%, FISP -17.1%, MTC-FISP -9.5%, DESS -9.3% and FLASH -6.1%. The coefficient of variation for a 6-fold determination of the volume amounted to between 6.2% (T1-SE) and 2.6% (FLASH). The FLASH sequence allowed the most valid and reproducible assessment of the cartilage morphology. The remaining difference from the real volume of the cartilage may be due to the fact that the calcified zone of the cartilage is not delineated by MRI.

Aged↗

PubMed1994

Antisense inhibition of butyrylcholinesterase gene expression predicts adverse hematopoietic consequences to cholinesterase inhibitors.

1. To investigate the possibility that cholinesterase inhibitors may cause adverse hematopoietic effects, we employed antisense oligodeoxynucleotides selectively inhibiting butyrylcholinesterase gene expression (AS-BCHE). Complementary sense (S) oligonucleotides served as controls. 2. In primary bone marrow cell cultures grown with interleukin 3 (IL-3), AS-BCHE but not S-BCHE reduced growth of megakaryocyte colony-forming units (CFU-MK) in a dose-dependent manner at the micromolar range. 3. In cultures grown with IL-3, transferrin, and erythropoietin (Epo), cell counts increased up to twofold, yet colony counts (CFU-GEMM) remained unchanged under AS-BCHE treatment. 4. Electrophoretic measurements of DNA ladder as an apoptotic index revealed that the above oligonucleotide effects were not due to nonspecific induction of programmed cell death. 5. Differential cell counts demonstrated increased myeloidogenesis and reduced levels of early megakaryocytes in CFU-GEMM under AS-BCHE, suggesting requirement of the BuChE protein for megakaryopoiesis. 6. In vivo injection of AS-BCHE reduced BCHE mRNA levels in both young and mature megakaryocytes for as long as 20 days, as shown by in situ hybridization. 7. Ex vivo growth of primary bone marrow cells revealed a twofold reduction in CFU-MK colonies grown from the AS-BCHE- but not the S-BCHE-injected mice, 15 days posttreatment. 8. These findings demonstrate that deficient butyrylcholinesterase expression, and hence interference with this enzyme's activity through treatment with or exposure to cholinesterase inhibitors, may cause hematopoietic differences in treated patients.

Animals↗

PubMed1994

Inhibition of gene expression with ribozymes.

1. Ribozymes can be designed to cleave in trans, i.e. several substrate molecules can be turned over by one molecule of the catalytic RNA. Only small molecular weight ribozymes, or small ribozymes, are discussed in this review with particular emphasis on the hammerhead ribozyme as this has been most widely used for the inhibition of gene expression by cleavage of mRNAs. 2. Cellular delivery of the ribozyme is of crucial importance for the success of inhibition of gene expression by this methodology. Two modes of delivery can be envisaged, endogenous and exogenous delivery. Of the former several variants exist, depending on the vector used. The latter is still in its infancy, even though chemical modification has rendered such ribozymes resistant against degradation by serum nucleases without impairment of catalytic efficiency. 3. Various successful applications of ribozymes for the inhibition of gene expression are discussed, with particular emphasis on HIV1 and cancer targets. These examples demonstrate the promise of this methodology.

Animals↗

PubMed1994

Use of partially phosphorothioated "antisense" oligodeoxynucleotides for sequence-dependent modulation of hematopoiesis in culture.

To distinguish between sequence-dependent effects and non-specific cytotoxicity of phosphorothioate antisense oligonucleotides (AS-oligos), we introduced AS-oligos blocking expression of 2Hs, the Homo sapiens cell division controller cdc2 kinase, its hematopoietically expressed homolog CHED, and the acetylcholine-hydrolyzing enzyme butyrylcholinesterase (BCHE) into primary murine bone marrow (BM) culture. Antisense oligonucleotides were fully phosphorothioated (Ts) or prepared with three phosphorothioate groups at their 3' termini (S3). Each of these oligos could cause reductions in colony counts either as a result of its sequence-dependent biological capacity or due to sequence-independent cytotoxicity. The Ts and S3 forms of the matching sense oligo, S-BCHE, served for comparison. The S3 forms of AS-2Hs, AS-BCHE, and S-BCHE caused more limited drops in colony counts than their Ts counterparts, reflecting lower cytotoxicity. When incubated with electroblotted BM proteins, Ts but not S3 oligos intensively labeled two protein bands. Moreover, 5'-end 32P-labeled (Ts) S-BCHE labeled nuclear proteins in situ in small, mitotic cells, suggesting correlation between oligo-protein interactions and the sequence-independent cytotoxicity of Ts AS-oligos. Extension of the apparently nontoxic AS-CHED by two adenosine residues at the 3' end, creating a potential for intramolecular hydrogen bond formation, resulted in increased toxicity. These findings recommend the use of nonlooped, partially phosphorothioated oligos for the modulation of hematopoiesis.

Animals↗

PubMed1994

Antisense inhibition of acetylcholinesterase gene expression causes transient hematopoietic alterations in vivo.

Hematopoietic acetylcholinesterase (ACHE) gene expression and its implication for development were studied by in vivo administration to mice of an antisense phosphorothioate oligonucleotide targetted toward ACHE (AS-ACHE). Hematopoietic alterations were observed by differential cell counts and ACHE mRNA levels determined by quantified RNA polymerase chain reaction (RNA-PCR) and in situ hybridization analyses. In control mice, injected with phosphate-buffered saline and untreated, ACHE mRNA labeling with ACHE [35S]cRNA was about 10-fold higher on megakaryocytes (MK) compared with all other bone marrow cells and increased by 20-fold during MK development, similar to reports for MK actin mRNA. Drastic reductions occurred in the bone marrow lymphocyte and erythroid fractions 12 days following intraperitoneal injection of AS-ACHE (5 micrograms/g weight) into groups of four mice. RNA-PCR revealed over 1000-fold decreases in ACHE mRNA levels in lymph nodes and bone marrow at this time, while actin mRNA levels dropped by 10 and 100-fold in lymph nodes and bone marrow of AS-ACHE treated mice compared with controls. In view of the developmental increase in MK actin, this suggested arrest in MK development as well. By 20 days postinjection, bone marrow actin mRNA was fully restored and the sensitive in situ hybridization technique revealed that ACHE mRNA levels were also restored and reached levels only 2-3-fold lower than in controls in all bone marrow cells of AS-ACHE treated mice. Moreover, lymphocytes and erythroid cells repopulated to levels 25% above normal, and promegakaryocyte and mature MK fractions of the total MK were 3 and 2-fold higher, respectively, than in controls.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetylcholinesterase↗

PubMed1994

[Stress on the ligamentum transversum acetabuli in physiological stress on the hip joint].

We investigated the strain on the transverse acetabular ligament (TAL) and the labrum close to the anterior and posterior horn of the lunate surface using Omega strain gauges [5] while increasing loads were applied to the hip joint. Two fresh hip joint specimens and four specimens fixed in 3.7% formalin were examined. The two components of the joint were disarticulated and soaked in physiological saline and then placed in a material-testing machine (Zwick) in the neutral position of the joint. The strain on the TAL and the labrum was measured at loads of 10 N, 350 N, 700 N, 1050 N, 1400 N, 2100 N and 2800 N. Finally, the contact areas were measured at a load of 350 N using a polyether casting method. Depending on load, the length of the TAL increased by up to about 3.2% at a load of 2800 N, but the length of the labrum increased by only 0.5% at the same load. Following rotation of the femoral head to positions corresponding to 15 degrees extension and 15 degrees and 30 degrees flexion, only slight differences of about 0.2% for the TAL and even less for the labrum were measured. The contact areas are all located in the anterior and posterior horn of the lunate surface. The measured changes in strain on the TAL confirm the widening of the acetabular notch and a subsequent stretching of the TAL as the load on the hip joint increases.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetabulum↗

PubMed1994

Stress distribution in the trochlear notch. A model of bicentric load transmission through joints.

In 16 cadaver humeroulnar joints, the distribution of subchondral mineralisation was assessed by CT osteoabsorptiometry and the position and size of the contact areas by polyether casting under loads of 10 N to 1280 N. Ulnas with separate olecranon and coronoid cartilaginous surfaces showed matching bicentric patterns of mineralisation. Under small loads there were separate contact areas on the olecranon and coronoid surfaces; these areas merged centrally as the load increased. They occupied as little as 9% of the total articular surface at 10 N and up to 73% at 1280 N. Ulnas with continuous cartilaginous surfaces also had density patterns with two maxima but those were less prominent, and in these specimens the separate contact areas merged at lower loads. The findings indicate a physiological incongruity of the articular surfaces which may serve to optimise the distribution of stress.

Aged↗

PubMed1993

Activity of hammerhead ribozymes containing non-nucleotidic linkers.

Hammerhead ribozymes were synthesized in which the tetranucleotide loop II was replaced by non-nucleotidic linkers of 7, 13, 17 and 19 atoms length. Ribozymes with 17 and 19 atom linkers, in combination with a 4 base pair stem II, had catalytic efficiencies which were 2 fold increased to that of the parent ribozyme with a tetranucleotide loop. Ribozymes with these linkers, but in combination with a 2 base pair stem II, showed a 2 fold decrease in catalytic efficiency when compared to the parent ribozyme. Prolonged preincubation in the presence of MgCl2 was required for hexaethylene glycol linker-modified ribozymes to obtain maximum activity and reproducible kinetic data.

Base Sequence↗

PubMed1993

Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity.

The three guanosines of the central core of a hammerhead ribozyme were replaced by 2-aminopurine ribonucleoside, xanthosine, isoguanosine, inosine, and deoxyguanosine. These analogues were incorporated by automated solid-phase synthesis, with the exception of isoguanosine. This was introduced by ligating a donor, which carried the isoguanosine at its 5'-end, and an acceptor oligoribonucleotide by a T4 DNA ligase-catalyzed reaction. Most of these modifications lowered the rate constant of cleavage by the hammerhead ribozyme drastically. Inspection of the possible hydrogen-bonding interactions disturbed by these modifications suggests that there is no G12A9 or A13G8 mismatched base pair in the central region. Increasing the Mg2+ concentration from 10 to 50 mM did not enhance these rates appreciably. This makes it improbable that the guanosines, including their 2'-hydroxyl groups, are involved in the binding of the catalytically active Mg2+. Transition-state destabilizing energies of 0.6-4.7 kcal mol-1 suggest that essentially all guanosines are involved in a hydrogen-bonding network.

Bacteriophage T4↗

PubMed1993

Preliminary crystallographic studies on the D15 5' to 3' exonuclease from phage T5.

The D15 exonuclease from phage T5 has been crystallized from 35% (w/v) ammonium sulfate by the hanging drop vapor diffusion technique. The crystals grow in tetragonal space group P4(1)22 or P4(3)22 with cell dimensions a = b = 79.2 A and c = 138.0 A. The crystals diffract to 2.5 A and are suitable for X-ray structure determination.

Crystallization↗

PubMed1993

Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA.

The ribozyme derived from the intervening sequence of Tetrahymena thermophila pre-rRNA catalyzes a site-specific endonuclease reaction with both RNA and DNA oligonucleotides: CCCUCUAAAAA + G<-->CCCUCU + GAAAAA. However, the RNA substrate (rS) binds approximately 10(4)-fold stronger than the DNA substrate (dS) and once bound reacts approximately 10(4)-fold faster. Here we have investigated the role of individual 2'-hydroxyl groups by comparing the binding and reactivity of "chimeric" oligonucleotide substrates, in which the 2'-substituents of the individual sugar residues have been varied. Chimeric substrates containing a single ribonucleotide at positions -6 to +3 (numbered from the cleavage site) were cleaved faster than dS by factors of 3.5, 3.5, 2.3, 65, 18, 1700, 7.8, 1.7, and 1.4 [(kcat/Km)chimeric S/(kcat/Km)dS]. The sum of the energetic contributions from the individual 2'-hydroxyl groups of 13.3 kcal/mol accounts for the 12.2 kcal/mol greater stabilization for RNA than for DNA in binding and cleavage (i.e., overall transition-state stabilization). This observation and the significant energetic effects from single ribose substitutions at opositions-3 to +1 strongly suggest that local interactions, rather than overall helical differences, largely account for the different binding and reactivity of the DNA and RNA substrates. Each 2'-hydroxyl group was evaluated for its effect on each of three reaction steps leading to the chemical transition state: two binding steps (duplex formation and docking into tertiary interactions) and the chemical cleavage step. The 2'-hydroxyl groups at positions -3 and -2 stabilize docking, and this stabilization is maintained in the chemical step. This "uniform binding" indicates that these interactions contribute to catalysis by positioning the oligonucleotide substrate for reaction. The 2'-hydroxyl at position +1 has a small effect on the binding step and an additional small but significant effect on the chemical step. Thus, the ribozyme, like protein enzymes, can take advantage of interactions away from the site of chemistry to provide stabilization specifically in the transition state. The 2'-hydroxyl at position -1 exerts its large effect nearly exclusively on the chemical step [Herschlag, D., Eckstein, F., & Cech, T.R. (1993) Biochemistry (following paper in this issue)]. The energetic effects of other modifications of the 2'-substituents provide a crude picture of the active site. The 2'-OCH3 substituent at position -3 inhibits the reaction approximately 10-fold relative to 2'-H, suggesting than an unfavorable interaction cannot be avoided by an isoenergetic structural rearrangement.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗