Antisense TRPM-2 oligodeoxynucleotides chemosensitize human androgen-independent PC-3 prostate cancer cells both in vitro and in vivo.

Although numerous chemotherapeutic regimens have been evaluated for patients with hormone-refractory prostate cancer, none has improved survival. Testosterone-repressed prostate message-2 (TRPM-2), which is highly up-regulated after androgen withdrawal and during androgen-independent progression in prostate cancer, has been shown to inhibit apoptosis induced by various kinds of stimuli. The objectives in this study were to test whether antisense (AS) oligodeoxynucleotides (ODNs) targeted against TRPM-2 enhance chemosensitivity in human androgen-independent prostate cancer PC-3 cells both in vitro and in vivo. Initially, the potency of 10 AS ODNs targeting various regions of the TRPM-2 mRNA were evaluated, and the AS ODN targeted to the TRPM-2 translation initiation site (AS ODN#2) was found to be the most potent sequence for inhibiting TRPM-2 expression in PC-3 cells. Despite significant dose-dependent and sequence-specific suppression of TRPM-2 expression, AS ODN#2 had no effect on growth of PC-3 cells both in vitro and in vivo. However, pretreatment of PC-3 cells with AS ODN#2 significantly enhanced chemosensitivity of Taxol (paclitaxel) and mitoxantrone in vitro. Characteristic apoptotic DNA laddering and cleavage of poly(ADP-ribose) polymerase were observed after combined treatment with AS ODN#2 plus paclitaxel or mitoxantrone but not with either agent alone. In vivo administration of AS ODN#2 plus either paclitaxel or mitoxantrone significantly decreased PC-3 tumor volume by 80 or 60%, respectively, compared with mismatch control ODN plus either paclitaxel or mitoxantrone. In addition, terminal deoxynucleotidyl transferase-mediated nick end labeling staining revealed increased apoptotic cells in tumors treated with AS ODN#2 plus paclitaxel or mitoxantrone. These findings confirm that TRPM-2 overexpression confers resistance to cytotoxic chemotherapy in prostate cancer cells and illustrates the potential utility of combined treatment with AS TRPM-2 ODN plus chemotherapeutic agents for patients with hormone-refractory prostate cancer.

Purification of antisense oligonucleotides.

Chromatography is an effective tool for obtaining high-purity synthetic oligonucleotides for a variety of end uses, including antisense drug therapy. Reversed-phase and anion-exchange chromatographies are widely used techniques for this application. While selectivity of these techniques can be modified by methods such as ion-pair RP-HPLC or affinity chromatography, these are presently used only at small scales. RP chromatography makes use of terminal hydrophobic-protecting groups to increase retention and selectivity. The main advantages of the RP method are its utility for the purification of a wide variety of modified oligonucleotide structures, its applicability across a range of terminal hydrophobic groups, such as fluorescein, and its ready use from small scale to very large scale with a minimal requirement for process development. AX-HPLC can also give high-purity products at generally higher media capacities. A more extensive method development effort is typically required for the AX-HPLC purification of AO. The AX yield per unit operation can be lower, but the isolated yield of DMT-off desalted oligonucleotide can be equal to or higher than that from RP-HPLC. As additional AO drugs enter and mature in the market, there will be a potential need for ton-scale purification processes. AX provides a way to scale up production on somewhat less expensive equipment with reduced organic solvent requirements.

A case study: oligonucleotide purification from gram to hundred gram scale.

This article describes the purification and scale-up of ISIS 2302, a 20-mer phosphorothioate oligonucleotide by anion-exchange (AX) chromatography. The key operating parameters were optimized at gram scale and further scaled up to hundred gram. SOURCE 30Q, a high efficiency polymeric chromatographic media was used for both the small and large-scale work. High length-based purity and yield were maintained at scale-up. This purification is one of the largest demonstrations of AX purification of phosphorothioate oligonucleotide.

Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au-S bond breaking.

Photothermal release of DNA from gold nanoparticles either by thermolysis of the Au-S bonds used to anchor the oligonucleotides to the nanoparticle or by thermal denaturation has great therapeutic potential, however, both processes have limitations (a decreased particle stability for the former process and a prohibitively slow rate of release for the latter). Here we show that these two mechanisms are not mutually exclusive and can be controlled by adjusting laser power and ionic strength. We show this using two different double-stranded (ds)DNA-nanoparticle conjugates, in which either the anchored sense strand or the complementary antisense strand was labeled with a fluorescent marker. The amounts of release due to the two mechanisms were evaluated using fluorescence spectroscopy and capillary electrophoresis, which showed that irradiation of the decorated particles in 200 mM NaOAc containing 10 mM Mg(OAc)(2) with a pulsed 532 nm laser operating at 100 mW favors denaturation over Au-S cleavage to an extent of more than six-to-one. Due to the use of a pulsed laser, the process occurs on the order of minutes rather than hours, which is typical for continuous wave lasers. These findings encourage continued research toward developing photothermal gene therapeutics.

[Separation of phosphodiester oligodeoxynucleotides and phosphorothioate antisense oligodeoxynucleotides by capillary zone electrophoresis at low pH].

Oligodeoxynucleotides (ODNs) may possess biological activity in vivo, and are used for the cancer therapeusis. Synthesized ODNs contains many by-products, and so their purity check and resolution of single-base, i. e., the separation of ODNs differing by one nucleotide in length, become necessary. In this study, capillary zone electrophoresis (CZE) method was developed for the separation of two sets of model compounds of single-stranded oligodeoxynucleotide mixtures (18 - 20 mers), phosphodiester oligodeoxynucleotides (PO-ODNs) and their phosphorothioate modifications (PS-ODNs), with equal sequences differing in a single base. The effects of the CZE operating parameters on the separation were investigated and optimized to further improve the resolution, such as the pH values and the concentrations of running buffer, the varieties and concentrations of additives, the separation voltage as well as the temperature. It was confirmed that the pH value of the buffer played the most important role in the separation, and the urea used as the additive in the system improved significantly the resolution of PS-ODNs. Consequently, the PO-ODNs and PS-ODNs mixtures could be single-based separated on a fused-silica capillary of 50 microm x 49.0 cm (40.7 cm of effective length) under the optimum conditions: the running buffer system of 50 mmol/L NaH2PO4-H3PO4 (pH 2.24)-7 mol/L urea, the pressure injection of 2 kPa x 10 s, the separation voltage of -20 kV, the column temperature of 25 degrees C, and the ultraviolet (UV) detection at 260 nm. The average resolutions for the separation of 18 - 19 mers and 19 - 20 mers of PO-ODNs were 4.68 and 3.20, respectively; and the average resolutions for the separation of 18 - 19 mers and 19 - 20 mers of PS-ODNs were 1.23 and 0.81, respectively. The relative standard deviations of the migration time and the resolution were all less than 5%. This method will be useful for the qualification of PO-ODNs and PS-ODNs samples as they are used in antisense drug development due to the relatively easy operation and good reproducibility of the method in comparing with the capillary gel electrophoresis.

Synthesis of light-activated antisense oligodeoxynucleotide.

The activity of a 20-mer antisense oligodeoxynucleotide (asODN) is transiently blocked by attaching a partially complementary sense strand (sODN) via a heterobifunctional photocleavable linker (PL). The asODN-PL-sODN conjugate forms a DNA hairpin-like structure that is considerably more stable than the corresponding asODN/sODN duplex. In conjugate form, the asODN is prevented from hybridizing to exogenous RNA or DNA molecules. Activity is restored after modest exposure to UV light (lambda approximately 365 nm). Here, we provide a detailed procedure for synthesizing photoactive asODNs in good yields. Synthesis, purification and analysis of the light-activated asODN can be completed within 1-2 weeks.

[Separation and characterization of oligodeoxynucleotide by fast protein liquid chromatography].

The antisense drug synthesized by DNA synthesizer is an oligodeoxynucleotide (ODN). The purity of the drug should be determined effectively. Because the ODNs are molecules with negative charges at pH 12, they can be separated according to the quantity of charges with them on the ion-exchange column. On anion exchange column, MONO-Q, the ODNs ranged from 19 bases to 21 bases can be separated successfully by gradient elution of NaCl solution from 0 mol/L to 1.8 mol/L. The experiment proved that the fast protein liquid chromatography is a very useful tool for the determination of the antisense drug.

Oligonucleotides with 1,5-anhydrohexitol nucleoside building blocks: crystallization and preliminary X-ray studies of h(GTGTACAC).

Hexitol nucleic acids are oligonucleotides built up from natural nucleobases and a phosphorylated 1,5-anhydrohexitol backbone. The anhydrohexitol oligonucleotide h(GTGTACAC) was synthesized using phosphoramidite chemistry and standard protecting groups. Crystals of h(GTGTACAC) were obtained at either 279 or 289 K by the hanging-drop vapour-diffusion technique using a 24-matrix screen for nucleic acid fragments. The crystals diffract beyond 2.0 A resolution and belong to the hexagonal space group P6222 (or P6422) with unit-cell parameters a = 36.42 and c = 63.33 A.

Selection of effective antisense oligodeoxynucleotides with a green fluorescent protein-based assay. Discovery of selective and potent inhibitors of glutathione S-transferase Mu expression.

Antisense oligodeoxynucleotides (AS-ODNs) are frequently used for the down-regulation of protein expression. Because the majority of potential antisense sequences lacks effectiveness, fast screening methods for the selection of effective AS-ODNs are needed. We describe a new cellular screening assay for the evaluation of the potency and specificity of new antisense sequences. Fusion constructs of the gene of interest and the gene encoding the enhanced green fluorescent protein (EGFP) are cotransfected with AS-ODNs to COS-7 cells. Subsequently, cells are analysed for expression of the EGFP fusion protein by flow cytometry. With the assay, we tested the effectiveness of a set of 15 phosphorothioate ODNs against rat glutathione S-transferase Mu1 (GSTM1) and/or Mu2 (GSTM2). We found several AS-ODNs that demonstrated potent, sequence-specific, and concentration-dependent inhibition of fusion protein expression. At 0.5 microm, AS-6 and AS-8 inhibited EGFP-GSTM1 expression by 95 +/- 4% and 81 +/- 6%, respectively. AS-5 and AS-10 were selective for GSTM2 (82 +/- 4% and 85 +/- 0.4% decrease, respectively). AS-2 and AS-3, targeted at homologous regions in GSTM1 and GSTM2, inhibited both isoforms (77-95% decrease). Other AS-ODNs were not effective or displayed non-target-specific inhibition of protein expression. The observed decrease in EGFP expression was accompanied by a decrease in GSTM enzyme activity. As isoform-selective, chemical inhibitors of GSTM and GSTM knock-out mice are presently unavailable, the selected AS-ODNs constitute important tools for the study of the role of GSTM in detoxification of xenobiotics and protection against chemical-induced carcinogenesis.