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PubMed1993

Conformational and nucleic acid binding studies on the synthetic nucleocapsid protein of HIV-1.

A 55 residue peptide corresponding to the nucleocapsid protein of HIV-1 (NCp7) containing two zinc binding domains as well as three truncated peptides were synthesized by Fmoc-based solid phase synthesis using the fragment condensation approach. Circular dichroism (CD) data support a conformational model in trifluoroethanol/buffer solution consisting of two helical segments at the chain ends with two Zn-modules in the center of the molecule. CD titration experiments show that the synthetic protein binds two equivalents of Zn2+ stoichiometrically, and the Zn2+ induced conformational changes are completely reversible by addition of EDTA. NCp7 and its S-acetamidomethylated analog (NCp7-Acm), devoid of the zinc co-ordination centers, exhibit preferential binding to RNA with a Kd = approximately 10(-9) M irrespective of the cysteine modification as determined by filter binding assays. The binding affinity of the NCp7 protein to single-stranded DNA is lower than to RNA. Binding to double-stranded DNA is lower than to ssDNA. The NCp7-Acm protein exhibits reduced single-stranded DNA binding affinity compared to the unmodified protein. Nucleic acid binding analyses with the fragments of NCp7 protein suggest that two basic amino acid stretches are involved in RNA binding of the NCp7.

Amino Acid Sequence↗
PubMed1984

Early and late functions in a bipartite RNA virus: evidence for translational control by competition between viral mRNAs.

It has been shown previously that Drosophila cells infected with black beetle virus synthesize an early viral protein, protein A, a putative element of the viral RNA polymerase. Synthesis of protein A declines sharply by 6 h postinfection, whereas synthesis of viral coat protein alpha continues for at least 14 h. The early shutoff in protein A synthesis occurred despite the presence of equimolar proportions of the mRNAs for proteins A and alpha, RNAs 1 and 2, respectively. We have now been able to mimic this translational discrimination in a cell-free protein-synthesizing system prepared from infected or uninfected Drosophila cells, thus allowing further analysis of the mechanism by which translation of RNA 1 is selectively turned off. The results revealed no evidence for control by virus-encoded proteins or by virus-induced modification of mRNAs by the cell-free system. Rather, with increasing RNA concentration, viral RNA 1 was outcompeted by its genomic partner, RNA 2. This suggests that the early shutoff in intracellular synthesis of protein A is due to decreasing ability of RNA 1 to compete for a rate-controlling translational factor(s) as the concentration of viral RNAs accumulates within the infected cell.

Cell-Free System↗
PubMed1993

Proton NMR studies of manganese ion binding to tRNA-derived acceptor arm duplexes.

Several RNA duplexes corresponding to the acceptor arms of different tRNAs have been analyzed with respect to their divalent metal ion binding capability by means of proton NMR spectroscopy using paramagnetic Mn2+ ions as probes. In particular, the role of GU wobble base pairs has been analyzed with reference to their potential for creating metal ion binding sites. It is shown that both the structural modifications induced by GU pairs in the A-RNA geometry and the sequence context seem to affect the metal ion binding capabilities.

Base Sequence↗
PubMed2006

Antisense treatments for biothreat agents.

Antisense oligomers (ASOs) represent a promising technology to treat viral and bacterial infections, and have already been shown to be successful against a variety of pathogens in cell culture studies and nonhuman primate models of infection. For these reasons, antisense technologies are being pursued as treatments against biothreat agents such as Ebola virus, dengue virus and Bacillus anthracis. Several generations of modified oligonucleotides have been developed to maximize nuclease resistance, target affinity, potency, cell entry, and other pharmacokinetic properties. First-generation ASOs contain phosphorothioate modifications to increase stability through nuclease resistance. Further chemical modifications in second-generation ASOs include 2'-O-methyl and 2'-O-methoxy-ethyl oligos, which increase nuclease resistance and oligo:RNA binding affinities. Third-generation ASOs contain a variety of chemical modifications that enhance stability, affinity and bioavailability. A fourth class of oligonucleotide-based compounds consists of small interfering RNAs, which have recently become widely used for gene knockdown in vitro and in vivo. This review focuses on the third-generation phosphorodiamidate morpholino oligomers, which are nonionic and contain a morpholine ring instead of a ribose, as well as phosphorodiamidate linkages in place of phosphorothioates. Multiple antisense oligomer-based therapeutics are being developed for use against biothreat agents, and antisense drugs will likely become a critical member of our arsenal in the defense against highly pathogenic, emerging or genetically engineered pathogens.

Animals↗
PubMed2004

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.

The hairpin ribozyme is a minimalist paradigm for studying RNA folding and function. In this enzyme, two domains dock by induced fit to form a catalytic core that mediates a specific backbone cleavage reaction. Here, we have fully dissected its reversible reaction pathway, which comprises two structural transitions (docking/undocking) and a chemistry step (cleavage/ligation), by applying a combination of single-molecule fluorescence resonance energy transfer (FRET) assays, ensemble cleavage assays, and kinetic simulations. This has allowed us to quantify the effects that modifications of essential functional groups remote from the site of catalysis have on the individual rate constants. We find that all ribozyme variants show similar fractionations into effectively noninterchanging molecule subpopulations of distinct undocking rate constants. This leads to heterogeneous cleavage activity as commonly observed for RNA enzymes. A modification at the domain junction additionally leads to heterogeneous docking. Surprisingly, most modifications not only affect docking/undocking but also significantly impact the internal chemistry rate constants over a substantial distance from the site of catalysis. We propose that a network of coupled molecular motions connects distant parts of the RNA with its reaction site, which suggests a previously undescribed analogy between RNA and protein enzymes. Our findings also have broad implications for applications such as the action of drugs and ligands distal to the active site or the engineering of allostery into RNA.

Catalysis↗
PubMed2004

Trinucleotide repeats and neurodegenerative disease.

Major insights have been attained into the molecular pathology of the trinucleotide repeat neurodegenerative diseases over the past decade. Genetic definition has allowed subclassification into translated polyglutamine diseases, which are due to CAG repeat expansions, and a more heterogeneous group in which the trinucleotide repeat remains untranslated. The polyglutamine disorders are due to a toxic gain of function of mutant expanded proteins. Neuronal intranuclear inclusions (NIIs) characteristically occur. Protein misfolding, interference with DNA transcription and RNA processing, activation of apoptosis and dysfunction of cytoplasmic elements have all been invoked in the toxic process. The end result is apoptotic cell death with many aspects of neuronal function being perturbed. Promising progress has been made into arresting and reversing neurodegeneration in both cellular and animal models. The molecular mechanisms underlying the untranslated group remain less clear. Impedance of gene transcription secondary to abnormal DNA structures formed by repeats, modification of chromatin gene packaging and dysfunction at the RNA level have all been suggested as possible pathological mechanisms. These diseases remain irreversible. It is hoped that clarification of the molecular pathogenic mechanisms will provide the tools for future therapeutic intervention.

Animals↗
PubMed2005

Receptor activator of NF-kappaB ligand protein expression in UMR-106 cells is differentially regulated by parathyroid hormone and calcitriol.

Expression of the cytokine, receptor activator of NF-kappaB ligand (RANKL), is stimulated by both parathyroid hormone (PTH) and calcitriol in osteoblasts. Most studies have examined the effects on RANKL mRNA, and less information is available on the protein products. We have determined the effects of PTH, the adenylate cyclase stimulator forskolin, and calcitriol, alone and in combination, on endogenous RANKL protein expression in UMR-106 rat osteoblastic osteosarcoma cells by Western blotting and enzyme immunoassay (EIA). PTH and forskolin dose dependently increased a approximately 52 kDa band in whole cell lysates that was detected by both C- and N-terminal directed RANKL antibodies. Calcitriol treatment produced little or no expression of this approximately 52 kDa band, but markedly increased the expression of a approximately 32 kDa band that was only detected with an antibody directed to the N-terminus of RANKL. An EIA based on RANKL binding to OPG detected a large increase in RANKL expression following calcitriol treatment, and much smaller increases with PTH or forskolin. The combination of PTH and calcitriol or forskolin and calcitriol elicited effects similar to those of PTH and forskolin alone, as detected by both Western blotting and EIA. In contrast to the effects on protein, all agents increased RANKL mRNA expression, with the greatest effects seen with the co-treatments. The results indicate that PTH, likely through effects on cyclic AMP, has a different effect on RANKL processing than calcitriol. The approximately 52 and approximately 32 kDa RANKL products appear to interact differently with OPG, which could affect responses to the agents in target cells.

Animals↗
PubMed1986

Effects of different amino-group reagents on ribosomal integrity: structural role of lysine residues.

Treatment of 60S subunits from yeast ribosomes with dicarboxylic acid anhydrides (maleic, dimethylmaleic and tetrahydrophtalic), which introduces negatively-charged residues, is accompanied by substantial dissociation of protein components (35-55%). In contrast, acetic anhydride or cyanate, which introduce uncharged groups, cause practically no protein release, even after extensive modification. Therefore, in addition to blocking lysine-RNA interactions, a large change in the electric charge of the proteins appears to be necessary to obtain dissociation. These results seem to indicate that lysine residues are not essential to ribosome integrity, while arginine-RNA interactions should play an important role in the maintenance of ribosomal structure.

Anhydrides↗
PubMed1987

A simple and rapid solid-phase RNA sequencing method.

A simple and rapid solid-phase RNA sequencing method has been developed based on Peattie's direct chemical method. 3'-Terminally labeled RNA was immobilized on DEAE-cellulose sheets and followed by specific modification with dimethyl sulfate, diethylpyrocarbonate, hydroxylamine (at pH 10 for the uridine and pH 5.5 for the cytidine reaction), and cleavage reaction with aniline. RNA fragments were washed from the DEAE-cellulose sheets using salt solutions, precipitated with ethanol, and separated by 15% polyacrylamide gel electrophoresis. Due to the complete removal of the impurities normally present in the solution method, the higher resolution of the sequencing bands and lower background on the autoradiograph make this solid-phase technique more efficient. This solid-phase technique is much faster and more convenient than the original method.

Animals↗
PubMed1976

Modification of the Ehrlich ascites tumor cell nuclear lipids.

The fatty acid composition of Ehrilich ascites tumor cell nuclei was differend when the tumor-bearing mice were fed diets rich in either coconut or sunflower oil. When coconut oil was fed, the monoenoic fatty acid content of many of the nuclear lipids was increased and their polyenoic fatty acid content was reduced as compared with the sunflower oil diet. By contrast, only small changes were produced in the saturated fatty acid contents of the nuclear lipids. The nuclear membrane choline phospholipid, ethanolamine phospholipid and combined serine phospholipid plus inositol phospholipid fractions exhibited statistically significant changes in fatty acid composition, but the sphingomyelins were not altered appreciably by dietary lipid modification. The fatty acid composition of the small quantity of phospholipids associated with the chromatin was much more resistant to diet-induced mosification. Except for sphingomyelin, the fatty acid composition of the chromatin phospholipids was different from that of the corresponding nuclear membrane phospholipids, containing much larger amounts of fatty acids having less than 16 carbon atoms. The fatty acid compositons of the nuclear triaclglycerols and cholesterol esters, which were associated almost entirely with the chromatin, were modified by the dietary lipid modifications. There were no changes in the DNA, RNA or lipid content of these nuclei. Therefore, this experimental system can be used to prepare mamalian nuclei that differ appreciably only in their fatty acyl composition.

Animals↗
PubMed1988

The distribution of two hnRNP-associated proteins defined by a monoclonal antibody is altered in heat-shocked HeLa cells.

A monoclonal antibody obtained after mice were immunized with hnRNP purified from HeLa cells recognizes two polypeptides of Mr 35,000 and 37,000. By immunocytofluorescence, these antigens can be visualized only in cells previously heat shocked at 45 degrees C for 5 or 10 min, although they are present at the same level in unstressed and stressed cells. The signal, which is mostly concentrated in the interchromatin space, where hnRNP fibrils are located, does not accumulate with time and disappears 4 to 5 h after heat shock. Discrimination between the two types of hnRNP substructures, the 30-50 S monoparticles and the nuclear matrix fibrils, based on differential sensitivity to salt or ribonuclease treatment, showed that in unstressed cells the antigens behave as monoparticle proteins. In contrast, in heat-shocked cells, most 35-37K antigens behave as nuclear matrix proteins. Thus, heat shock seems to induce a rapid and reversible switch of these two antigens from hnRNP monoparticles to the nuclear matrix. The data demonstrate that heat shock, which was previously shown not to alter the overall RNA: protein packaging ratio of hnRNP, induces subtle modifications of their substructure. Such modifications might be of importance since heat shock is known for instance to affect pre-mRNA processing.

Antibodies, Monoclonal↗
PubMed2006

Transcription of gonadotropin beta subunit genes involves cross-talk between the transcription factors and co-regulators that mediate actions of the regulatory hormones.

The gonadotropins LH and FSH have distinct temporal patterns of expression as a result of differential regulation by hormones such as GnRH, steroids and activin. This specific regulation is due to diverse sets of transcription factors that are recruited to the promoters of these genes, and recruit specific co-activator complexes which function to stabilize interactions with the general transcription factors and RNA polymerase II, and also to induce covalent modifications of the histone tails at these gene loci. As these molecular mechanisms are elucidated, the nature of nuclear cross-talk between the various hormonally induced pathways is becoming evident, revealing both negative and positive effects of interacting transcription factors and co-regulators. This paper will review current knowledge on the transcriptional regulation of gonadotropin beta subunit gene expression in the chromatin setting, and will present new data pertaining to nuclear cross-talk between the various endocrine-induced pathways regulating gonadotropin gene transcription.

Animals↗
PubMed2026

Next-generation macrophage engineering in cancer therapy: From TAM reprogramming to CAR-macrophages.

Macrophages are central regulators of the tumor microenvironment (TME), shaping immune suppression, angiogenesis, metabolism, and therapeutic resistance in solid cancers. While early strategies sought to deplete tumor-associated macrophages (TAMs) or block monocyte recruitment, limited efficacy and compensatory mechanisms revealed the need for functional reprogramming rather than elimination. Recent advances in viral vectors, CRISPR-Cas genome editing, and RNA-based delivery platforms have enabled precise genetic modification of macrophages, giving rise to chimeric antigen receptor macrophages (CAR-Ms) and related engineered products. Beyond antigen targeting, effective macrophage engineering requires stabilization of pro-inflammatory identity, resistance to tumor-induced repolarization, metabolic reinforcement, and integration of checkpoint modulation pathways. This review synthesizes current strategies across DNA, mRNA, and siRNA-based platforms, highlighting convergent design principles that connect TAM reprogramming with CAR-M development. We discuss reshaping phagocytosis checkpoints, metabolic and transcriptional stabilization, cytokine augmentation, and synthetic receptor architecture, emphasizing combinatorial and context-aware engineering, while proposing new candidate gene targets. Engineered macrophages are thus evolving from simple effector cells into programmable immune coordinators capable of converting immunologically "cold" tumors into inflamed, therapy-responsive niches.

CAR-M↗
PubMed2002

Biosensor detection of triplex formation by modified oligonucleotides.

Due to the instability of DNA oligonucleotides in biological solutions, antisense or antigene therapies aimed at modulation of specific gene expression will most likely require the use of oligonucleotides with modified backbones. Here, we examine the use of a surface plasmon resonance biosensor (BIAcore) to compare triplex-directed binding of modified oligonucleotides targeted to a region of the murine c-myc promoter. We describe optimization of experimental conditions to minimize nonspecific interactions between the oligonucleotides and the sensor chip surface, and the limitations imposed by certain backbones and sequence types. The abilities of pyrimidine oligonucleotides with various modified backbones to form specific triple helices with an immobilized hairpin duplex were readily determined using the biosensor. Modification of the third-strand oligonucleotide with RNA or 2(')-O-methyl RNA was found to enhance triplex formation, whereas phosphorothioate or phosphotriester substitutions abrogated it. A comparison of these results to DNase I footprinting experiments using the same oligonucleotides showed complete agreement between the two sets of data.

DNA↗
PubMed1995

A rapid and simple method for the detection of prostate-specific antigen mRNA in archival tissue specimens using a reverse transcription-polymerase chain reaction assay.

OBJECTIVES: Polymerase chain reaction (PCR) amplification of DNA from archival, fixed tissue sources is now performed routinely. In this report, we describe a reproducible technique for mRNA amplification from archival tissues. METHODS: Archival, fixed tissue was treated with a modification of a rapid, acid guanidinium technique. The RNA yielded was reverse transcribed and subjected to 40 cycles of two-step PCR, using a panel of primers designed to encompass relatively short (less than 250 bp) cDNA fragments. PCR products were analyzed by agarose gel electrophoresis followed by ethidium bromide staining. RESULTS: Using fixed, paraffin-embedded specimens of human prostate, we have demonstrated a reproducible pattern of reverse transcription (RT)-PCR products using several different primer sets. Our data suggest that RNA degradation proceeds to fragments approximately 250 bp or shorter in length but that many of these fragments survive intact over extended periods of time and are of suitable quality to serve as a template for RT and subsequent PCR amplification. CONCLUSIONS: We describe a technique that will allow the retrospective analysis of archival tissues for gene expression. These methods are generally applicable to a wide variety of systems. Such a method will make it possible to perform retrospective studies of gene expression in the archival tissues of patients whose eventual clinical course is already known, greatly shortening the time needed for genetic outcome studies in slowly growing tumors, such as prostate cancer.

Base Sequence↗
PubMed2001

Alcoholic myopathy: biochemical mechanisms.

Between one- and two-thirds of all alcohol abusers have impairment of muscle function that may be accompanied by biochemical lesions and/or the presence of a defined myopathy characterised by selective atrophy of Type II fibres. Perturbations in protein metabolism are central to the effects on muscle and account for the reductions in muscle mass and fibre diameter. Ethanol abuse is also associated with abnormalities in carbohydrate (as well as lipid) metabolism in skeletal muscle. Ethanol-mediated insulin resistance is allied with the inhibitory effects of ethanol on insulin-stimulated carbohydrate metabolism. It acutely impairs insulin-stimulated glucose and lipid metabolism, although it is not known whether it has an analogous effect on insulin-stimulated protein synthesis. In alcoholic cirrhosis, insulin resistance occurs with respect to carbohydrate metabolism, although the actions of insulin to suppress protein degradation and stimulate amino acid uptake are unimpaired. In acute alcohol-dosing studies defective rates of protein synthesis occur, particularly in Type II fibre-predominant muscles. The relative amounts of mRNA-encoding contractile proteins do not appear to be adversely affected by chronic alcohol feeding, although subtle changes in muscle protein isoforms may occur. There are also rapid and sustained reductions in total (largely ribosomal) RNA in chronic studies. Loss of RNA appears to be related to increases in the activities of specific muscle RNases in these long-term studies. However, in acute dosing studies (less than 1 day), the reductions in muscle protein synthesis are not due to overt loss of total RNA. These data implicate a role for translational modifications in the initial stages of the myopathy, although changes in transcription and/or protein degradation may also be superimposed. These events have important implications for whole-body metabolism.

Alcoholism↗
PubMed2002

DNA analogues: from supramolecular principles to biological properties.

Mainly driven by the needs of antisense research, a large number of oligonucleotide analogues have been prepared and evaluated over the last 15 years. Besides minor structural modifications of the building blocks of DNA and RNA itself, a considerable effort has been devoted to the de novo design of nucleoside analogues with improved binding properties. A particularly successful concept turned out to be that of conformational restriction. This review focuses on recent advances in this area and tries to summarize scope and limitations of this design principle.

DNA↗