Use of the nuclease inhibitor aurintricarboxylic acid (ATA) for improved non-viral intratumoral in vivo gene transfer by jet-injection

BACKGROUND: Stability, integrity and retention of the DNA within the targeted tissue is decisive for efficient gene transfer using naked DNA. Pre-clinical and clinical studies require reproducible transfection rates by preventing rapid degradation of naked DNA in the transduced tissue. Tumor tissues contain nuclease activity, which can affect DNA stability if naked DNA is used. Therefore, inhibition of nuclease-mediated DNA degradation by the nuclease inhibitor aurintricarboxylic acid (ATA) might lead to improved gene transfer efficiency in tumor tissues. METHODS: For both, DNA-degradation analysis and in vivo gene transfer experiments, the beta-galactosidase (LacZ)-expressing pCMVbeta and the cytosine deaminase (CD)-expressing pCMV-CD plasmid were used. Influence of the nuclease inhibitor ATA was determined in tumors, in which naked pCMVbeta or pCMV-CD DNA and ATA was co-administered by jet-injection. The nuclease activity and inhibition by ATA was analyzed using the DNase Alert detection system. The influence of ATA on LacZ expression was determined by specific ELISA and its effect on the therapeutic efficacy of CD gene transfer on tumor growth was determined in vivo. RESULTS: The screening of different human mammary and colon carcinoma models revealed strong nuclease activity rapidly degrading naked plasmid DNA. Co-administration of ATA with pCMVbeta or pCMV-CD for in vivo jet-injection of tumors prevented DNA from nuclease degradation associated with either increased LacZ gene expression or improved reduction in tumor growth. CONCLUSIONS: Tumor-associated nuclease activity is a notable hurdle in gene transfer of naked DNA and therefore inhibition of nucleolytic degradation of plasmid DNA facilitates intratumoral gene expression.     

Mechanism of action of polymeric aurintricarboxylic acid, a potent inhibitor of protein--nucleic acid interactions

The mechanism of inhibition of protein--nucleic acid complex formation by polymeric aurintricarboxylic acid (ATA) was investigated by proton magnetic resonance spectroscopy. The approach was the synthesis of totally deuterated ATA, followed by a 100-MHz proton magnetic resonance study of its interaction with bovine pancreatic ribonuclease A (RNase), a model nucleic acid binding protein. The binding of ATA to RNase elicited chemical shift changes and line broadening in the C(2)--H resonances of histidyl residues 12 and 119, both of which are located in the active site, whereas that of histidyl residue 105, which resides on the exterior of the protein structure, is unaffected. (Histidyl residue 48 is not observed under our conditions except at high pH.) The epsilon-methylene protons of the lysyl side chains were also broadened upon the binding of ATA. Polymeric ATA displaces cytidine 2'-monophosphate and cytidine 3'-monophosphate from the active site of the enzyme as revealed by nuclear magnetic resonance spectroscopy. These observations suggest that the mechanism of action of ATA involves competition between the nucleic acid and the polymeric ATA for binding in the active site of the protein. Electron spin resonance spectroscopy reveals that polymeric ATA is a stable free radical, thus accounting for the major line broadening effect upon binding to protein. This finding may provide a powerful means of probing the nucleic acid binding site of proteins by proton magnetic resonance spectroscopy.     

Aurintricarboxylic acid is a potent inhibitor of phosphofructokinase.

Aurintricarboxylic acid (ATA) was found to be a very potent inhibitor of purified rabbit liver phosphofructokinase (PFK), giving 50% inhibition at 0.2 microM. The inhibition was in a manner consistent with interaction at the citrate-inhibitory site of the enzyme. The data suggest that inhibition of PFK by ATA was not due to denaturation of the enzyme or the irreversible binding of inhibitor, since the inhibition could be reversed by addition of allosteric activators of PFK, i.e. fructose 2,6-bisphosphate or AMP. Two other tricarboxylic acids, agaric acid and (-)-hydroxycitrate, were found to inhibit PFK. ATA at much higher concentrations (500 microM) was shown to inhibit fatty acid synthesis from endogenous glycogen in rat hepatocytes; however, protein synthesis was not altered.     

Nucleic acid hybridization using DNA covalently coupled to cellulose.

We describe a method for linking RNA and DNA covalently to finely divided cellulose through a diazotized aryl amine, which reacts primarily with guanine and uracil (thymine) residues of single strands. The high efficiency of coupling and high capacity of the cellulose for nucleic acid make possible a product with as much as 67 mug of nucleic acid per mg of cellulose. The product is especially suitable for hybridization experiments where very low backgrounds are important, and it is stable in 99% formamide at 80 degrees C so that hybridized nucleic acid can be recovered easily. Full length linear Simian Virus 40 (SV40) DNA, produced by cleavage of SV40(I) DNA with S1 nuclease, can be coupled to diazo cellulose with an efficiency of 80-90%, and is effective in hybridization experiments with SV40 DNA, complementary RNA synthesized in vitro from SV40(I) DNA with E. coli RNA polymerase, and the SV40-specific fraction of total RNA from SV40-infected and transformed cells. In these experiments an excess of cellulose-bound DNA was used, and the efficiency of hybridization was about 90% when ribonuclease treatment of the hybrids was omitted.     

Characterization and use of the potent ribonuclease inhibitor aurintricarboxylic acid for the isolation of RNA from animal tissues.

Inclusion of aurintricarboxylic acid (ATA) in extraction buffers for the isolation of RNA from animal tissues resulted in high yields (0.5-2.0 mg/g of tissue) of undegraded material as judged by agarose-gel-electrophoretic analyses and Northern-blotting experiments. However, ATA bound to nucleic acids, forming stable complexes, and so we have established methods for spectrophotometric quantification of RNA in these coloured complexes, and for easy removal of sufficient ATA to leave RNA in a consistently hybridizable condition at the end of a purification. The use and subsequent removal of ATA was straightforward and gave satisfactory results for all rat tissues tested.     

Properties of Two Nuclease Genes in NEUROSPORA CRASSA

Two genes, nuc-1 and nuc-2, of Neurospora crassa which were responsible for the nucleic acid digestion, were located on linkage group 1 and 2, respectively. A temperature-sensitive mutant (B1ts-2) was obtained from a nuc-2 mutant. Nuclease mutants showed a reduced activity of nuclease N(3) which was found to be a complex consisting of nuclease N(3) (') and inhibitor molecule. Nuclease N(3), nuclease N(3) (') and inhibitor were partially purified and estimated to have the approximate molecular weights of 38,000, 12,500 and 25,000 respectively. A nuc-1 mutant produced the nuclease N(3) (') altered in thermolability. A nuc-2 mutant and B1ts-2 produced the inhibitor altered in the capacity to inhibit nuclease N(3) (') activity. The inhibitor prepared from B1ts-2 was more thermostable than that from other strains. From these results, it was suggested that the nuc-1 gene is the structural gene for nuclease N(3) (') and the nuc-2 gene that for the inhibitor. A possible involvement of this enzyme-inhibitor complex in the regulation of nuclease activity and synthesis of other proteins was suggested.     

A modified Escherichia coli protein production strain expressing staphylococcal nuclease,capable of auto-hydrolysing host nucleic acid

The large-scale production of recombinant biotherapeutics, particularly recombinant proteins, provides significant process and regulatory challenges to the biotechnology industry in order to meet the regulatory agencies stringent requirements in a cost-effective manner. Host cell derived nucleic acid causes problems from both a process and a regulatory perspective, as high molecular weight chromosomal DNA is responsible both for the viscosity of cell lysates, and it is a source of heterologous DNA sequences whose inclusion in the final product must be prevented. We have constructed a modified Escherichia coli JM107 expression host (JMN), containing a staphylococcal nuclease expression cassette, integrated into the host chromosome at the dif locus. The nuclease is expressed as a fusion to the ompA signal peptide, and is translocated to the periplasm of the cell, protecting the cytoplasmic nucleic acid from any toxic activity. The nuclease is released during cell lysis, where it subsequently acts to hydrolyse host nucleic acid present in the lysate. Results with this strain show that sufficient levels of nuclease activity are produced to completely auto-hydrolyse the host's chromosomal DNA to a size non-visible on 1% agarose gel, generating a markedly lower lysate viscosity. This provides a suitable methodology to remove heterologous DNA sequences early in the product stream and decrease lysate viscosity, improving the efficiency of downstream processing and product yield, whilst avoiding the addition of exogenous nuclease and its prohibitive costs at large-scale.     

Self-quenched covalent fluorescent dye-nucleic acid conjugates as polymeric substrates for enzymatic nuclease assays.

A fluorescent method is described for assessing nuclease activity. The technique is based on the preparation of quenched fluorophore-nucleic acid covalent conjugates and their subsequent dequenching due to degradation by nucleases. The resulting fluorescence increase can be measured by a spectrofluorometer and exhibits subpicogram per milliliter sensitivity level for RNase A and low picogram per milliliter level for DNase I. The method is adaptable for quantitative nuclease inhibitor testing.     

Modulation of DNA binding of glucocorticoid receptor by aurintricarboxylic acid

Effects of aurintricarboxylic acid (ATA) were examined on the DNA binding properties of rat liver glucocorticoid-receptor complex. The DNA-cellulose binding capacity of the glucocorticoid-receptor complex was completely abolished by a pretreatment of receptor preparation with 0.1-0.5 mM ATA at 4 degrees C. The half-maximal inhibition (i.d.50) in the DNA binding of [3H]triamcinolone acetonide-receptor complex [( 3H]TARc) was observed at 130- and 40 microM ATA depending upon whether the inhibitor was added prior to or following the receptor activation. The entire DNA-cellulose bound [3H]TARc could be extracted in a concentration-dependent manner by incubation with 2-100 microns ATA. The [3H]TARc remained intact under the above conditions, the receptor in both control and ATA-treated preparations sedimented in the same region in salt-containing 5-20% sucrose gradients. The action of ATA appeared to be on the receptor and not on DNA-cellulose. The DNA-binding capacity of ATA-treated receptor preparations could be recovered upon exhaustive dialysis. The treatment with ATA did not appear to change the ionic behavior of heat activated GRc; the receptor in both control and the ATA-treated preparations showed similar elution profiles. Therefore, ATA appears to alter the binding to and dissociation of glucocorticoid-receptor complex from DNA. The use of ATA should offer a good chemical probe for analysis of the DNA binding domain(s) of the glucocorticoid receptor.     

Detection of RNA on northern blots by negative staining with aurintricarboxylic acid.

Aurintricarboxylic acid (ATA) is a well-known inhibitor of RNA and DNA modifying enzymes and was suggested as a potent RNase inhibitor for preparation of RNA (Hallick et al., 1977, Nucleic Acids Res. 4, 3055-3064). We show that ATA is a very useful stain for detecting RNA on Northern blots and slot blots although it did not fully protect purified RNA in concentrated solution against RNase A.     

Caspase-3-dependent and caspase-3-independent pathways leading to chromatin DNA fragmentation in HL-60 cells

Apoptosis induced by etoposide (VP-16) in HL-60 cells was confirmed to be caspase-dependent. It was fully inhibited by the broad-spectrum caspase inhibitor Z-VAD-fmk. However, the caspase-3-specific inhibitor Z-DEVD-fmk only partially inhibited apoptosis. This indicated that a second caspase is required in vivo for full activation of the apoptotic nucease CAD. Aurin tricarboxylic acid (ATA) did not inhibit VP-16-induced apoptosis. In contrast, apoptosis induced by hydroxychloroquine (HCQ) in HL-60 cells was caspase-3 independent and was fully inhibited by ATA. Thus, CAD does not appear to be involved in chromatin DNA degradation in this case. A second apoptotic nuclease is postulated to degrade the DNA, likely endo-exonuclease, an abundant nuclear enzyme that acts on both DNA and RNA and is present in latent form. HCQ, but not VP-16, stimulated DNA degradation (laddering) in isolated nuclei. This indicates that the drug can act directly in the nuclei to trigger activation of the second latent apoptotic nuclease.     

Dual functions of Arabidopsis sulfiredoxin: Acting as a redox-dependent sulfinic acid reductase and as a redox-independent nuclease enzyme

Based on the fact that the amino acid sequence of sulfiredoxin (Srx), already known as a redox-dependent sulfinic acid reductase, showed a high sequence homology with that of ParB, a nuclease enzyme, we examined the nucleic acid binding and hydrolyzing activity of the recombinant Srx in Arabidopsis (AtSrx). We found that AtSrx functions as a nuclease enzyme that can use single-stranded and double-stranded DNAs as substrates. The nuclease activity was enhanced by divalent cations. Particularly, by point-mutating the active site of sulfinate reductase, Cys (72) to Ser (AtSrx-C72S), we demonstrate that the active site of the reductase function of AtSrx is not involved in its nuclease function.     

Adapting capillary gel electrophoresis as a sensitive,high-throughput method to accelerate characterization of nucleic acid metabolic enzymes

Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner.     

Aurintricarboxylic acid translocates across the plasma membrane, inhibits protein tyrosine phosphatase and prevents apoptosis in PC12 cells

Aurintricarboxylic acid (ATA) prevents apoptosis in a diverse range of cell types including PC12 cells. It is known to stimulate tyrosine phosphorylation of signaling proteins including Shc proteins, phosphatidylinositol 3-kinase, phospholipase C-g and mitogen-activated protein kinases (MAPKs). However, it has been unclear how ATA increases the phosphorylation of these proteins as it was believed to be membrane impermeable. We found that ATA translocates across the plasma membrane of PC12 cells and have confirmed that it is a potent inhibitor of protein tyrosine phosphatases (PTP ases). Other PTPase inhibitors also prevented apoptosis independent of ATA. These observations indicate that ATA exerts its anti-apoptotic effect on PC12 cells at least in part by inhibiting certain PTPase(s).     

Regulation of amino acid transporter ATA2 by ubiquitin ligase Nedd4-2

We report here that ubiquitin ligase Nedd4-2 regulates amino acid transporter ATA2 activity on the cell surface. We first found that a proteasome inhibitor MG132 increased the uptake of alpha-(methylamino)isobutyric acid, a model substrate for amino acid transport system A, in 3T3-L1 adipocytes as well as the preadipocytes. Transient expression of Nedd4-2 in Xenopus oocytes and Chinese hamster ovary cells down-regulated the ATA2 transport activity induced by injected cRNA and transfected cDNA, respectively. Neither the Nedd4-2 mutant with defective catalytic domain nor c-Cbl affected the ATA2 activity significantly. RNA-mediated interference of Nedd4-2 increased the ATA2 activity in the cells, and this was associated with decreased polyubiquitination of ATA2 on the cell surface membrane. Immunofluorescent analysis of Nedd4-2 in the adipocytes stably transfected with the enhanced green fluorescent protein (EGFP)-tagged ATA2 showed the co-localization of Nedd4-2 and EGFP-ATA2 in the plasma membrane but not in the perinuclear ATA2 storage site, supporting the idea that the primary site for the ubiquitination of ATA2 is the plasma membrane. These data suggest that ATA2 on the plasma membrane is subject to polyubiquitination by Nedd4-2 with consequent endocytotic sequestration and proteasomal degradation and that this process is an important determinant of the density of ATA2 functioning on the cell surface.     

DNA transfection of macaque and murine respiratory tissue is greatly enhanced by use of a nuclease inhibitor

Background

Nuclease activity present within respiratory tissues contributes to the rapid clearance of injected DNA and therefore may reduce the transfection activity of directly injected transgenes. Most gene transfer technologies transduce or transfect murine tissues more efficiently than corresponding primate tissues. Therefore, it is prudent to assess the utility of novel gene transfer strategies in both rodent and primate models before proceeding with further development.

Methods

This study analyzed the effects of ATA (a nuclease inhibitor) on the direct transfection of macaque and murine lung tissue; compared the levels of DNase activity in murine, primate, and human lung fluids; and tested the inhibitory activity of ATA on the DNase activity present in these samples. Fluorescent microspheres were used to detect areas of transfection in lung.

Results

Intratracheal administration of a nuclease inhibitor (ATA) with naked DNA (0.5 µg ATA/g body weight) enhanced direct transfection efficacy in macaque lung by over 86‐fold and by over 54‐fold in mouse lung. Hematoxylin and eosin staining showed no apparent tissue toxicity. Moreover, macaque, human, and mouse lung fluids were found to possess similar levels of DNase activity and this activity was inhibited by similar concentrations of ATA. The authors also successfully pioneered the use of carboxylate‐modified microsphere tracers to identify areas of transfection and/or treatment.

Conclusion

This work provides evidence that using direct nuclease inhibitors will enhance lung transfection and that nuclease activity is present in all lung fluids tested, which can be inhibited by the use of direct DNase inhibitors. Copyright © 2002 John Wiley & Sons, Ltd.

     

High molecular weight phosphorus compound in nucleic acid extracts of the slime mold Physarum polycephalum

Orthophosphate labeled with (32)P was added to the growth medium of the plasmodia of Physarum polycephalum. The nucleic acid extracts of such plasmodia contained (32)P that was not removed by nuclease, protease, or amylase. This labeled material was shown to be separable from nucleic acids, could be eluted from a methylated albumin-kieselguhr column at 0.5 m NaCl, was of high molecular weight, and had several characteristics in common with polyphosphate. A fraction of this polyphosphate-like material was also found in extracts of isolated nuclei.     

The problem of nuclease activity in nucleic acid hybridization reactions: Theoretical considerations

The presence of nucleuses during DNA-DNA or DNA-RNA hybridization reactions alters the kinetics of hybrid formation. Unfortunately, while the effect (even of small amounts of nuclease) on the C₀t curve may be large, it may not be readily detectable. The effect of various types of nuclease is shown. As many nucleuses cause a shift in the position rather than a change in shape of the curve, all studies involving nucleic acid hybridization should assay for the presence of nucleases and care must be taken to avoid their presence as contaminants.     

Aurinetricarboxylic acid: a potent inhibitor of glucose-6-phosphate dehydrogenase.

Inhibition by aurinetricarboxylic acid (ATA) of glucose-6-phosphate (G6P) dehydrogenase was "competitive" with respect to G6P and "mixed type" with respect to NADP+. Inhibited enzyme bound two molecules of ATA. Kinetic constants, Km, Ki at varying pH suggested possible binding of the inhibitor by the sulfhydryl of the enzyme; of the several enzymes tested only milk xanthine oxidase and G6P dehydrogenase from bovine adrenal was inhibited by ATA.