Phosphorothioates in molecular biology

The antiviral activity of RNA-dye combinations

The results of our previous studies (Jamison et al. 1988, 1989, 1990 a, b, c, d, e) have shown that the ability of intercalative dyes to modulate the antiviral activity of poly r(A-U) is related to the groove through which the dyes intercalate into the poly r(A-U). When poly r(A-U) is combined with the minor groove intercalating dyes or the minor/major groove intercalating dyes, optimum enhancement of antiviral activity is observed at the dye/ribonucleotide ratio predicted by the neighbor exclusion model (usually 1/4 or 1/6). No enhancement is observed when poly r(A-U) is combined with major groove intercalating dyes. When poly r(A-U) is combined with additional intercalative dyes to produce a dye/ribonucleotide ratio of 1/4 and a ribonucleotide concentration of 200 microM, the antiviral activity of poly r(A-U) is enhanced 8- to 20-fold, while 50% effective doses of the poly r(A-U) and the dyes decreases 18- to 347-fold. Interferon neutralization assays demonstrate that the interferon-inducing capability of the dye/poly r(A-U) combinations approximates the sum of the interferon-inducing capabilities of the poly r(A-U) and the dyes employed and suggests that the dyes potentiate the antiviral activity of poly r(A-U) without affecting the amount of interferon induced. Direct viral inactivation studies demonstrate that the dyes, poly r(A-U), and the dye/poly r(A-U) combinations do not inactivate VSV at concentrations near the 50% viral inhibitory dose. Assessment of cytotoxicity by microscope examination of HSF cell morphology and trypan blue exclusion indicates that the dye/poly r(A-U) combinations exhibit antiviral activity at concentrations well below those that induce cyto-toxicity. Several of the dyes and the dye/poly r(A-U) combinations exhibit anti-HIV-1 activity, suggesting that the enhancement phenomenon is not virus-specific nor host cell-specific. The enhancement phenomenon is sensitive to the base sequence of the polynucleotide with dye/poly r(A-U) and dye/poly r(G-C) combinations displaying enhanced antiviral activity, while dye/poly (rI).poly (rC) and dye/poly d(A-T) combinations do not. These results suggest that while intercalation of the dye and interferon induction are necessary for enhanced antiviral activity, neither intercalation nor interferon induction alone is sufficient to potentiate the antiviral activity of polyribonucleotides.

Intracellular delivery of nucleoside monophosphates through a reductase-mediated activation process

On the basis of three different models (namely: ddU, AZT and PMEA), mononucleotide phosphotriester derivatives were designed to be able to liberate the corresponding monophosphate (or phosphonate) inside the cell through a reductase-mediated activation process. It was demonstrated that the use of bis[S-(2-hydroxyethylsulfidyl)-2-thioethyl] esters of ddUMP (11), AZTMP (12) and PMEA (17) resulted in intracellular delivery of the parent monophosphate (or phosphonate). This point was corroborated by observation of an anti-HIV effect of, 11 in various cell lines, for 12 in CEM TK- cells and by the enhanced activity observed for 17. Furthermore, the reported decomposition data in cell extracts fully confirm the validity of this approach and show unambiguously the potential for intracellular reductase-mediated activation of the starting drug.

A circular trans-acting hepatitis delta virus ribozyme

A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozyme sequence-containing exon, is reversed. Trans-cleavage activity of the circular HDV-like ribozyme was comparable to linear permutations of HDV ribozymes containing the same core sequence, and was shown not to be due to linear contaminants in the circular ribozyme preparation. In nuclear and cytoplasmic extracts from HeLa cells, the circular ribozyme had enhanced resistance to nuclease degradation relative to a linear form of the ribozyme, suggesting that circularization may be a viable alternative to chemical modification as a means of stabilizing ribozymes against nuclease degradation.

Exploiting the chemical synthesis of RNA

A number of nucleotide phosphoramidites are now available that permit the chemical synthesis of RNA, modified RNA and RNA-DNA chimeric oligonucleotides. Since the chemical strategy allows the introduction of a particular modification at any given site in a nucleotide polymer, very subtle and specific questions regarding structure-function relationships in RNA may be addressed.

Extensive phosphorothioate substitution yields highly active and nuclease-resistant hairpin ribozymes

The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from two independently synthesized oligoribonucleotides. The catalytic proficiency of the two-piece construct (KM = 48 nM, kcat = 2.3 min-1) is nearly identical to that of the one-piece ribozyme. The two-piece ribozyme is essentially unaffected by substitution with thiophosphates 5' to all guanosines, cytidines, and uridines. In contrast, incorporation of multiple adenosine phosphorothioates in the 5' domain of the ribozyme decreases ribozyme activity by a factor of 25. Modification-interference experiments using ribozymes partially substituted with adenosine phosphorothioate suggest that thiophosphates 5' to A7, A9 and A10 interfere with cleavage to a greater extent than substitutions at other sites within the molecule, but the effect is modest. Within the substrate, phosphorothioate substitution does not directly interfere with cleavage, rather, increasing thiophosphate content decreases the stability of the ribozyme-substrate complex. We describe the construction of a hairpin ribozyme containing dinucleotide extensions at its 5' and 3' ends. Full substitution of this molecule with G and C phosphorothioates results in a ribozyme with greatly enhanced stability against cellular ribonucleases without significant loss of catalytic efficiency.

Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates

Oligodeoxynucleotide-containing phosphorothioate backbones have been used to regulate viral as well as cellular gene expression. The studies carried out in tissue culture have shown promising results on the use of oligonucleotide phosphorothioates as antiviral agents and, at present, study is underway to develop these oligonucleotide analogues as chemotherapeutic agents. To analyze and purify oligonucleotide analogues, high-performance liquid chromatography using weak anion exchange column has been described. The separation of oligonucleotide phosphorothioate is found to be length dependent.

Phosphorothioate oligodeoxynucleotides--anti-sense inhibitors of gene expression?

Phosphorothioate (PS) oligodeoxynucleotides are relatively nuclease resistant, water soluble analogs of phosphodiester (PO) oligodeoxynucleotides. These molecules are chiral but still hybridize well to their RNA targets. While considered for use as in vivo anti-sense inhibitors of gene expression, their biology, especially in the anti-viral area, is dominated by non-sequence specific effects. This review discusses both the sequence and non-sequence specific biologic effects of PS oligomers, and attempts to more clearly indicate their ultimate therapeutic potential.

Mutations in the 915 region of Escherichia coli 16S ribosomal RNA reduce the binding of streptomycin to the ribosome

The nine possible single-base substitutions were produced at positions 913 to 915 of the 16S ribosomal RNA of Escherichia coli, a region known to be protected by streptomycin [Moazed, D. and Noller, H.F. (1987) Nature, 327, 389-394]. When the mutations were introduced into the expression vector pKK3535, only two of them (913A----G and 915A----G) permitted recovery of viable transformants. Ribosomes were isolated from the transformed bacteria and were assayed for their response to streptomycin in poly(U)- and MS2 RNA-directed assays. They were resistant to the stimulation of misreading and to the inhibition of protein synthesis by streptomycin, and this correlated with a decreased binding of the drug. These results therefore demonstrate that, in line with the footprinting studies of Moazed and Noller, mutations in the 915 region alter the interaction between the ribosome and streptomycin.

Phosphorothioate-containing RNAs show mRNA activity in the prokaryotic translation systems in vitro

Phosphorothioate-containing RNAs were generated by transcription of coliphage T7 DNA using the Sp diastereomers of ribonucleoside 5'-O-(1-thiotriphosphates) and T7 RNA polymerase. RNAs in which a single nucleotide was substituted by the corresponding nucleoside phosphorothioate functioned as mRNA in the cell-free translation systems prepared from Escherichia coli and from an extreme thermophilic bacterium, Thermus thermophilus. This substitution increased the efficiency of protein synthesis by stabilizing the mRNAs in these systems. As the proportion of substituted nucleotides was increased, their mRNA activity was decreased accordingly. As judged from the analysis by SDS-polyacrylamide gel-electrophoresis, the proteins synthesized using phosphorothioate-containing mRNAs as template were identical to those obtained with unsubstituted mRNAs. However, larger proteins which were barely detectable when unsubstituted mRNA was used were well represented when phosphorothioate-RNA was used instead. The advantages in using the phosphorothioate-mRNAs in the in vitro translation systems are discussed.

Regulation of gene expression with double-stranded phosphorothioate oligonucleotides

Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappa B consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappa B. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappa B-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects.

Import-defective colicin B derivatives mutated in the TonB box

The pore-forming colicin B is taken up into Escherichia coli by a receptor and TonB-dependent process. The receptor and colicin B both contain a similar amino acid sequence, close to the N-terminal end, termed the TonB box. Point mutations were introduced into the TonB-box region of the colicin B structural gene cba resulting in colicin B derivatives which were partially or totally inactive against E. coli cells. All derivatives still bound to the receptor. An inactive derivative killed cells when translocated across the outer membrane by osmotic shock treatment, and formed pores in planar lipid bilayer membranes identical to the wild-type colicin. Some of the mutations were partially suppressed by mutations in the tonB structural gene. It was concluded that the TonB-box mutations define a region that is involved in the uptake of colicin B across the outer membrane.

Nucleoside inhibitors of rhodopsin kinase

The specificity of the ATP-binding site of rhodopsin kinase was studied with adenosine analogues that are competitive inhibitors. Systematic changes in the ribose ring (position 5') and the purine ring (positions 2, 6, 7, 8, and 9) and determination of the inhibitory properties of these analogues lead to the following conclusions: (1) The N6 nitrogen in the purine ring is essential for binding at the active site, which may explain the marked preference for ATP rather than GTP as substrate. (2) The configuration of the sugar moiety is critical for the binding. (3) Positions 2, 3, and 8 of the purine ring, as well as the polyphosphate chain, play a minor role in substrate recognition by rhodopsin kinase. (4) ATP gamma S is a good substrate for rhodopsin kinase (thus rhodopsin phosphorothioate, a phosphatase-resistant product, can be formed in order to study the role of phosphorylation in rod outer segments). Pyrrolopyrimidine derivatives are very potent inhibitors of rhodopsin kinase. The Ki of one of these, sangivamycin, is 180 nM. Sangivamycin in solution assumes the anti conformation, as determined by nuclear Overhauser measurement. These measurements show that the most potent inhibitors of rhodopsin kinase, sangivamycin and toyocamycin, occur in solution preferentially in the anti conformation. Many nucleotides and nucleosides tested that are not inhibitors are syn, and many that are inhibitors form a mixture of syn and anti. The hypothesis that inhibitors may have a conformation intermediate between syn and anti was strengthened by testing a cyclic nucleoside locked in an anti conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthesis and properties of dithymidine phosphate analogues containing 3'-thiothymidine

Dithymidine-3'-S-phosphorothioate (d(TspT)) has been prepared from a 5'-O-monomethoxytritylthymidine-3'-S-phosphorothioamidite (7) by activation with 5-(p-nitrophenyl)tetrazole in the presence of 3'-O-acetylthymidine. The resulting dinucleoside phosphorothioite is readily oxidised to the corresponding 3'-S-phosphorothioate using either tetrabutylammonium (TBA) periodate or TBA oxone and has been deprotected under standard conditions to yield d(TspT). This dithymidine phosphate analogue is comparatively resistant to hydrolysis by nuclease P1, but the P-S bond is readily cleaved by aqueous solutions of either iodine or silver nitrate. Dithymidine-3'-S-phosphorodithioate (d[Tsp(s)T]) was prepared in an analogous fashion using sulphur to oxidise the intermediate dinucleoside phosphorothioite. Absolute stereochemistry has been assigned to the diastereoisomers of d[Tsp(s)T] by comparing their physical and chemical properties to those of the dinucleoside phosphorothioates.