G-rich oligonucleotides for cancer treatment.

Oligonucleotides with guanosine-rich (G-rich) sequences often have unusual physical and biological properties, including resistance to nucleases, enhanced cellular uptake, and high affinity for particular proteins. Furthermore, we have found that certain G-rich oligonucleotides (GROs) have antiproliferative activity against a range of cancer cells, while having minimal toxic effects on normal cells. We have investigated the mechanism of this activity and studied the relationship between oligonucleotide structural features and biological activity. Our results indicate that the antiproliferative effects of GROs depend on two properties: the ability to form quadruplex structures stabilized by G-quartets and binding affinity for nucleolin protein. Thus, it appears that the antiproliferative GROs are acting as nucleolin aptamers. Because nucleolin is expressed at high levels on the surface of cancer cells, where it mediates the endocytosis of various ligands, it seems likely that nucleolin-dependent uptake of GROs plays a role in their activity. One of the GROs that we have developed, a 26-nucleotide phosphodiester oligodeoxynucleotide now named AS1411 (formerly AGRO100 or GRO26B-OH), is currently being tested as an anticancer agent in Phase II clinical trials.

DNA and RNA-DNA annealing activity associated with the tau subunit of the Escherichia coli DNA polymerase III holoenzyme.

The DNA polymerase III (pol III)holoenzyme is the 10 subunit replicase of Escherichia coli. The 71 kDa tau subunit, encoded by dnaX, dimerizes the core polymerase (alpha epsilon theta) to form pol III'[(alpha epsilon theta)2 tau 2]. tau is also a single-stranded DNA-dependent ATPase and can substitute for the gamma subunit during initiation complex formation. We show here that tau also possesses a DNA-DNA and RNA-DNA annealing activity that is stimulated by Mg2+, but neither requires ATP nor is inhibited by non-hydrolyzable ATP analogs. This suggests the tau may act to stabilize the primer-template interaction during DNA replication.

Renaturation of complementary DNA strands by herpes simplex virus type 1 ICP8.

ICP8, the major single-stranded DNA-binding protein of herpes simplex virus type 1, promotes renaturation of complementary single strands of DNA. This reaction is ATP independent but requires Mg2+. The activity is maximal at pH 7.6 and 80 mM NaCl. The major product of the reaction is double-stranded DNA, and no evidence of large DNA networks is seen. The reaction occurs at subsaturating concentrations of ICP8 but reaches maximal levels with saturating concentrations of ICP8. Finally, the renaturation reaction is second order with respect to DNA concentration. The ability of ICP8 to promote the renaturation of complementary single strands suggests a role for ICP8 in the high level of recombination seen in cells infected with herpes simplex virus type 1.

Retroviral nucleocapsid proteins possess potent nucleic acid strand renaturation activity.

The nucleocapsid protein (NC) is the major genomic RNA binding protein that plays integral roles in the structure and replication of all animal retroviruses. In this report, select biochemical properties of recombinant Mason-Pfizer monkey virus (MPMV) and HIV-1 NCs are compared. Evidence is presented that two types of saturated Zn2 NC-polynucleotide complexes can be formed under conditions of low [NaCl] that differ in apparent site-size (n = 8 vs. n = 14). The formation of one or the other complex appears dependent on the molar ratio of NC to RNA nucleotide with the putative low site-size mode apparently predominating under conditions of protein excess. Both MPMV and HIV-1 NCs kinetically facilitate the renaturation of two complementary DNA strands, suggesting that this is a general property of retroviral NCs. NC proteins increase the second-order rate constant for renaturation of a 149-bp DNA fragment by more than four orders of magnitude over that obtained in the absence of protein at 37 degrees C. The protein-assisted rate is 100-200-fold faster than that obtained at 68 degrees C, 1 M NaCl, solution conditions considered to be optimal for strand renaturation. Provided that sufficient NC is present to coat all strands, the presence of 400-1,000-fold excess nonhomologous DNA does not greatly affect the reaction rate. The HIV-1 NC-mediated renaturation reaction functions stoichiometrically, requiring a saturated strand of DNA nucleotide:NC ratio of about 7-8, rather than 14. Under conditions of less protein, the rate acceleration is not realized. The finding of significant nucleic acid strand renaturation activity may have important implications for various events of reverse transcription particularly in initiation and cDNA strand transfer.

Phosphorylation of topoisomerase II by casein kinase II and protein kinase C: effects on enzyme-mediated DNA cleavage/religation and sensitivity to the antineoplastic drugs etoposide and 4'-(9-acridinylamino)methane-sulfon-m-anisidide.

The effects of serine phosphorylation on the DNA cleavage/religation equilibrium of topoisomerase II and the sensitivity of the enzyme to antineoplastic drugs were characterized. Both casein kinase II and protein kinase C were used for these studies. Each kinase incorporated a maximum of approximately 1.4 phosphate molecules per homodimer of topoisomerase II. When the enzyme was incubated with both kinases simultaneously, phosphate incorporation increased to approximately 2.6 molecules/homodimer. In the absence of antineoplastic drugs, phosphorylation had only a slight effect on the DNA cleavage/religation equilibrium of topoisomerase II. However, in the presence of etoposide or 4'-(9-acridinylamino)methane-sulfon-m-anisidide, phosphorylation attenuated the ability of drugs to stabilize enzyme-DNA cleavage complexes. Levels of drug-induced DNA cleavage products decreased approximately 33% following phosphorylation of topoisomerase II by casein kinase II, approximately 17% following modification by protein kinase C, and approximately 50% following simultaneous phosphorylation of the enzyme by both kinases. This latter 50% reduction in DNA cleavage products correlated with an approximately 2-fold increase in the apparent first order rate constant for DNA religation mediated by simultaneously modified topoisomerase II. These results strongly suggest that the sensitivity of topoisomerase II toward antineoplastic drugs can be modulated by altering the phosphorylation state of the enzyme.

Renaturation of DNA catalysed by yeast DNA repair and recombination protein RAD10.

The RAD10 gene of Saccharomyces cerevisiae is required for the incision step of excision repair of ultraviolet-damaged DNA, and it functions in mitotic recombination. RAD10 has homology to the human excision repair gene ERCC-1. Here we describe the purification of the protein encoded by RAD10 and show that it is a DNA-binding protein with a strong preference for single-stranded DNA. We also show that RAD10 promotes the renaturation of complementary DNA strands.

Ethidium bromide-mediated renaturation of denatured closed circular DNAs: mechanistic aspects and fractionation of DNA on a molecular weight basis.

When closed circular duplex DNAs are exposed to alkali in the presence of ethidium bromide, from 0 to 100% of the DNA can be recovered as the fully base-paired duplex (native) form upon neutralization of the solutions. The fraction of native DNA depends on the concentration of ethidium bromide, time of incubation, ionic strength and temperature of the solutions before neutralization as well as the molecular weight and superhelix density of the DNA. Limiting ethidium concentrations exist below and above which 0 and 100% of the DNA, respectively, is recovered as native material under a given set of incubation conditions regardless of the length of time of incubation before neutralization. The strong molecular weight dependence of the fraction of DNA recovered in the native form after a given time of pre-neutralization incubation at ethidium concentrations between the limiting values noted above allows larger DNAs to remain fully denatured upon neutralization while smaller DNAs in the same mixture are fully renatured. This permits the rapid fractionation of mixtures of closed duplex DNAs on the basis of molecular weight when a technique for the separation of denatured from fully base-paired DNA is applied to such mixtures. Such a separation has been demonstrated through the marked enrichment of plasmid cloning vector DNA containing cloned inserts in the fractions that remain denatured after neutralization of alkaline solutions of these DNAs containing ethidium bromide.

Xenopus transcription factor A promotes DNA reassociation.

We demonstrate by agarose gel electrophoresis and DNase I footprinting that Xenopus transcription factor A promotes DNA reassociation. This ability of factor A is dependent upon the domain-like structure of the protein. Digestion of factor A by papain results in a protein fragment which promotes DNA reassociation whereas a smaller fragment obtained by trypsin digestion does not. Although factor A requires zinc for specific binding to the 5 S RNA gene, the metal is not required for single-stranded DNA binding or promotion of DNA reassociation by this protein. The factor A-dependent renaturation of the 5 S RNA gene from its individual 32P end-labeled strands results in the proper gene conformation as evidenced by the restoration of the DNase I footprint characteristic of the intragenic control region. Alterations in DNase I cleavage patterns induced by factor A on the individual 5 S DNA strands are distinct from those induced by the protein on the duplex 5 S RNA gene. The ability of factor A to promote DNA reassociation further defines the possible roles of this protein in the formation of active transcription complexes and their maintenance during repeated rounds of transcription.

Circulating DNA in systemic lupus erythematosus. Isolation and characterization.

Immunoprecipitable double-stranded (dsDNA) was previously shown to persist in the circulation of a clinically recognizable subgroup of patients with systemic lupus erythematosus (SLE). Plasma from 10 such patients was subjected to a DNA isolation procedure that used a combination of proteolysis, phenol extraction, and hydroxylapatite adsorption and elution in the presence of urea. The isolated dsDNA was radiolabeled by nick translation and then characterized by isopyknic ultracentrifugation in CsCl under both neutral and alkaline conditions, as well as after digestion with S1-endonuclease. These experiments demonstrated essential identity in nucleotide base composition between the plasma-derived DNA and human genomic DNA. The presence of specific human base sequences in the plasma DNA was demonstrated by finding that authentic human genomic DNA accelerated the renaturation of plasma DNA when compared with the effect of nonhuman, control DNA. The proportion of such sequences in plasma DNA was estimated by attempting to renature the plasma DNA in the presence of human DNA under conditions shown to result in complete renaturation of human DNA in model experiments. In this way, a minimum of 47% of plasma DNA base sequences could be shown also to be present in human genomic DNA. However, an average of 10-20% of the plasma-derived DNA failed to renature under these conditions, a result that was further confirmed by comparing the renaturation of the tritium-labeled plasma DNA specimens, in double-label experiments, with internal controls consisting of 14C-labeled authentic human DNA. Attempts to drive the reaction to completion with human DNA led to a similar conclusion. The relative nonrenaturability of this fraction of plasma DNA did not appear to be attributable to extensive chain breakage, although adequate analysis of this DNA subfraction was limited by reagent availability. It was therefore concluded that, in this group of SLE patients, persistently circulating DNA consisted largely of base sequences also found in human genomic DNA. The additional presence in plasma of a DNA subfraction that differed in its renaturation behavior from human genomic DNA was recognized, although its significance could not be established with certainty.

Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein.

The ability of a nucleic acid helix-destabilizing protein from calf thymus, UP1, to facilitate renaturation of yeast tRNALeu3 and Escherichia coli 5S RNA is shown to be a consequence of the protein's ability to bind stoichiometrically to single-stranded polynucleotide regions. A comparison of the inhibitory effect of different homopolymers on UP1-induced renaturation of tRNALeu3 does not indicate significant base specificity in UP1 binding, and a 3'-5' ribose phosphate polymer devoid of heterocyclic bases inhibits as well as the homopolynucleotides. These inhibition studies also show that UP1 requires polynucleotide segments of at least three phosphate residues to bind. Mg2+ (which is required for the stabilization of native tRNALeu3) dissociates complexes of UP1 with inactive tRNA, and since the RNAs in those complexes lack a substantial amount of secondary structure, it can upon dissociation readily refold into the native structure. A semiquantitative treatment of UP1-RNA interaction is developed that suggests that only a small number (approximately six) of protein molecules are bound to tRNALeu3 in the complex while analysis of the inhibition studies suggests that these UP1 molecules are not bound in a highly cooperative manner.

Toxicity, interstrand cross-links and DNA fragmentation induced by 'activated' cyclophosphamide in yeast.

Treatment of yeast cells with 4-hydroperoxy-cyclophosphamide (4-OOH-CP), the chemically activated form of cyclophosphamide, results in cell killing, induction of DNA interstrand cross-links and DNA fragmentation. Toxicity of 4-OOH-CP is greatly influenced by the cell's capacity of DNA dark-repair: genetic blocking of non-epistatic pathways of DNA repair results in an increase of sensitivity of several orders of magnitude. DNa primary lesions have been measured using a haploid, excision deficient, dTMP-uptaking mutant of S. cerevisiae. In this strain, a significant extent of DNA cross-linking can already be observed at a survival of 88%. At a concentration of 100 nmol/ml 4-OOH-CP, renaturability of DNA increases up to 12 h of drug exposure and drops to lower values upon further incubation. In contrast to the time course of renaturability, DNA double-strand breakage is seen at later stages of drug treatment and continuously increases as a function of incubation time. Whereas inactivation of cells and induction of strand breakage continue upon postincubation of cells, comparable effects are much less pronounced for DNA renaturability.

Comparative study on the effects of cyclophosphamide on yeast in vitro and in the host-mediated assay: DNA damage and biological response.

Cyclophosphamide (CP), whether applied in its chemically activated form as 4-hydroperoxy-cyclophosphamide (4-OOH-CP) in vitro or in the host-mediated assay (HMA) using rats, exhibits toxic and mutagenic effects on excision deficient yeast cells. The expression of these effects is examined during a prolonged postincubation in buffer and compared with the ability of activated CP to induce interstrand cross-links and DNA fragmentation. At comparable doses, we observed a close similarity of biological and biochemical effects in either test system.

Renaturation of alkali-denatured T7 DNA molecules complexed with ethidium bromide.

Free and ethidium bromide (EB) complexed alkali denatured T7 DNA molecules were renatured at 58 and 62 degrees C respectively for 1--3 h. The structures of the renaturation products of the free candidates were as usual showing native like, branched and unrenatured DNA whereas the structures of the ethidium bromide complexed one were somewhat different, showing non-renatured loop-like and entangled regions present inbetween the renatured segments. On the basis of the linear base sequence of T7 DNA, these non-renatured parts are indicative of the inhibition of renaturation by the complexed EB molecules. Mapping of the non-renatured regions showed that they were present at some specific sites, which inturn suggested that the EB-binding has some base sequence specificity.

The effect of sodium bisulfite on the melting profiles of nucleic acids and on their respective nucleosides.

The effect of sodium bisulfite (0.27 M, pH 7) on melting behavior of DNA, yeast RNA and their respective nucleosides was studied. It was found that bisulfite added not only to pyrimidine bases but also to purine bases of nucleic acids and of nucleosides. The addition products were stable at higher temperatures but reverted to parent compounds at room temperature. The only exception was the addition product of uridine which was stable at room temperature and could be isolated by paper chromatography in a 42-62% yield. Heating of DNA solutions in the presence of bisulfite to 95 degrees C caused a 90% loss of absorbance at 260 nm. On cooling, the absorbance was essentially recovered. When compared to the melting behavior of DNA in 0.27 M NaCl or 0.09 M Na2SO4 (same ionic strength), it was found that bisulfite destabilized double helical structure of DNA and that reversible addition of bisulfite did occur much below the melting temperature of DNA observed in the other two solvents.