Loopstructures in synthetic oligodeoxynucleotides.

A comparative nuclear magnetic resonance study of the hydrogen-bonded imino protons in a series of synthetic DNA fragments is presented. The fragments ATCCTA(Tn)TAGGAT are in principle capable of forming either a self-complementary hairpin loop structure (monomer form) or an interior loop structure (dimeric form). It has been shown, that for n = 1 only the dimer structure is present in aqueous solution, whereas the exclusive existence of the hairpin loop structure is indicated for n = 3, 4 & 5. Surprisingly, for n = 2 two different structures appear to be present in solution. Concentration studies show that both monomers and dimers exist side by side in this case. Hairpins as well as interior loops form extra "melting sites" in addition to the wellknown fraying phenomenon at the terminus of the double helix.     

Physicochemical properties of phosphorothioate oligodeoxynucleotides.

We have recently shown that phosphorothioate (PS) oligodeoxynucleotide (ODN) analogs, unlike their normal congeners, exhibit significant anti-HIV activity (Matsukura et al., (1987) Proc. Natl. Acad. Sci. USA 84, 7706-7710). We now report the syntheses, melting temperatures (Tm), and nuclease susceptibilities of a series of phosphorothioate ODN analogs. These include all-PS duplexes, duplexes with one normal chain and the other chain either all-PS, or end-capped with several PS groups at both 3' and 5' ends. The DNase susceptibilities of the S-ODNs are much less than the normal phosphodiesters, but by contrast duplexes of poly-rA with S-dT40 are much more susceptible to RNase H digestion. The Tm's for AT base pairs of S-ODNs are significantly depressed relative to normals, while GC base pairs show much less Tm depression. The Tm's of S-dT oligomers with poly-rA are reduced relative to the duplexes with normal dA oligomers. These results have significance for the biological properties of these analogs as anti-message inhibitors of gene expression, and provide a rational basis for the S-dC/G sequences as potential effective anti-AIDS agents.     

Synthesis and characterization of viologen-modified oligodeoxynucleotides.

Several viologen-tagged oligodeoxynucleotides in the form of covalent linkage at the specific site of the phosphorous backbone were synthesized and characterized. Incorporation of viologen molecules was confirmed by the 31P-NMR, 20% PAGE analysis, enzymatic degradation, and uv, ESR spectra of the derived cation radical. The Tm values and CD spectra of the modified strands with their complementary strands indicate that the introduction of the viologen molecule via linker arm causes no significant perturbation in duplex structure.     

Antisense oligodeoxynucleotides: synthesis, biophysical and biological evaluation of oligodeoxynucleotides containing modified pyrimidines.

6-Azathymidine, 6-aza-2'-deoxycytidine, 6-methyl-2'-deoxyuridine, and 5,6-dimethyl-2'-deoxyuridine nucleosides have been converted to phosphoramidite synthons and incorporated into oligodeoxynucleotides (ODNs). ODNs containing from 1 to 5 of these modified pyrimidines were compared with known 2'-deoxyuridine, 5-iodo-2'-deoxyuridine, 5-bromo-2'-deoxyuridine, 5-fluoro-2'-deoxyuridine, 5-bromo-2'-deoxycytidine, and 5-methyl-2'-deoxycytidine nucleoside modifications. Stability in 10% heat inactivated fetal calf serum, binding affinities to RNA and DNA complements, and ability to support RNase H degradation of targeted RNA in DNA-RNA heteroduplexes were measured to determine structure-activity relationships. 6-Azathymidine capped ODNs show an enhanced stability in serum (7- to 12-fold increase over unmodified ODN) while maintaining hybridization properties similar to the unmodified ODNs. A 22-mer ODN having its eight thymine bases replaced by eight 6-azathymines or 5-bromouracils hybridized to a target RNA and did not inhibit RNase H mediated degradation.     

Strategies for administering targeted therapeutic oligodeoxynucleotides.

Antisense or antigene DNA therapy of diseases that are due to aberrant gene expression is an exciting possibility. A variety of synthetic DNA derivatives has been applied in attempts to regulate the expression of many different genes, both in cell culture and in intact organisms (e.g. mice). Realistic design of human oligodeoxynucleotide-based therapeutic strategies requires many aspects of a candidate disease to be considered (including the disease prevalence, the number and nature of genes and mutations involved, and the tissues which must be targeted). For each DNA derivative intended for therapy, methods of targeting, modes of administration, pharmacokinetics, tissue distribution, toxicity, degradation and excretion must all be considered.     

Sequence specific hybridization properties of methylphosphonate oligodeoxynucleotides.

Methylphosphonate oligodeoxynucleotides (MPO's) with isomerically pure Rp-configurated methylphosphonates (MP's) were synthesized by block coupling of ApT and TpA dinucleoside methylphosphonates (DMP's, p indicating MP-linkage). Oligonucleotide duplexes (20 mers) with these Rp-MP's showed almost the same melting temperatures (Tm) as those with phosphorodiester bonds. Further a dependence of the duplex stability from the nucleosides (bases) adjacent to the MP moiety was observed. For the first time thermodynamic parameters for the duplex to coil transition of isomerically pure MP's were determined from the concentration dependence of the Tm. CD-spectra of the duplexes show structural changes which can be associated with the transition to a compact helix with higher helix winding angle.     

Synthesis of telomere-mimic carbocyclic 5'-nor oligodeoxynucleotides.

Telomere-mimic S-ODNs have been synthesized and examined their effects on the proliferation of human tumor cell lines by XTT assay. Furthermore, the guanosine derivatives of carbocyclic 5'-nor nucleoside were synthesized.     

Antisense pro-drugs: 5'-ester oligodeoxynucleotides.

Oligonucleotides bearing a terminal lipophilic group attached through a biodegradable ester bond should be useful as antisense pro-drugs with improved cellular uptake. The synthesis of 5'-ester oligonucleotides is, however, problematic due to lability of the ester bond during aqueous ammonia treatment that is commonly used for the deprotection of synthetic oligonucleotides. The synthesis of 5'-palmitoyl oligodeoxynucleotides was accomplished in good yield by the use of a combination of base-labile tert-butylphenoxyacetyl amino protecting groups (t-BPA), the oxalyl-CPG anchor group, and ethanolamine (EA) as a deprotecting reagent.     

Utilization of antisense oligodeoxynucleotides with embryonic tissues in culture.

Experimental embryology has long used manipulation of interacting tissues to examine questions of tissue interaction and differentiation. The potential for specific manipulation of gene expression in such tissues has made the utilization of antisense techniques desirable. However, problems with this methodology have discouraged many investigators from using this approach. Selection of target sequences for antisense oligonucleotides, delivery of oligonucleotides into cells or tissues, and the type of modification of the oligonucleotide to be used all present concerns that must be addressed. This paper describes our approach to selection of target sequence and methods of delivery and describes the synthesis of a methoxyethylamidate-modified antisense oligonucleotide that has proved useful in our studies. This approach has enabled us to explore aspects of tissue interaction in the embryonic heart that would have been difficult to explore in a genetic model.     

Arsonate-specific murine T cell clones. IV. Properties of I-E- and I-A-restricted clones

The T cell antigen L-tyrosine-p-azobenzenearsonate is unique in being a simple determinant that can be presented in the context of both I-A and I-E. I-E-restricted T cell clones derived from B10.A(5R) mice were found to fall into three groups: Type I clones recognized antigen only in the context of syngeneic apcs, Type II clones recognized antigen with the same highly specific major histocompatibility complex restriction but in addition proliferated in response to allogeneic stimuli; Type III clones were "degenerate" in their major histocompatibility complex-restricted recognition of antigen and proliferated when antigen-presenting cells bearing Eb beta Ek alpha (syngeneic), Ek beta Ek alpha, or Ed beta Ed alpha were used. These observations allow some conclusions to be drawn about sites on the I-E molecule that may be functionally significant in the presentation of this antigen. By using the B cell hybridoma LK35.2 as target cells, some of these T cell clones act as cytotoxic cells in the Class II-restricted manner predicted from the results of proliferative assays. Class II-restricted cytotoxicity can therefore be controlled by both I-A and I-E mouse Ir gene loci.     

Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides.

A triplex-forming oligopyrimidine has been attached at its 5'-end to a photoreactive psoralen derivative and used to target a sequence which forms part of the coding region of the human aromatase gene. The 20 base pair sequence is not a perfect triplex target since it contains three pyrimidine interruptions within the purine-rich strand. Despite this, we have detected triplex-directed photoadduct formation at pH 7.0 between the psoralen-linked oligonucleotide and a 30mer duplex representing the aromatase target. Photoadduct formation was found to be sensitive to pH, temperature, cation concentration and the base composition of the third strand. By varying the base sequence of the target duplex around the psoralen intercalation site, we have characterised the site and mode of psoralen intercalation. The attached psoralen has been found to intercalate at the triplex-duplex junction with a strong preference for one orientation. We have shown that the psoralen will bind at the junction even when there is a preferred TpA step at an adjacent site. We have also compared the binding affinity and photoreactivity of oligodeoxyribonucleotides linked to two different psoralen derivatives and found differences in the rate of crosslinking and the extent of crosslink formation. Finally, we have examined oligodeoxyribonucleotides which are attached to psoralen by polymethylene linkers of different lengths.     

Differential distribution of oligodeoxynucleotides in developing organs with epithelial-mesenchymal interactions.

The use of antisense oligodeoxynucleotides (ODNs) to inhibit gene expression is a usefull method for determining protein function and has potential therapeutic applications. However, there is still great variability in the successfull application of antisense technology to individual systems. In order to assess the ability of different cell types to take up ODNs, developing embryonic tissues were cultured in vitro in the presence of fluoresceine labelled, phosphorothioate substituted ODNs. The distribution of ODNs in individual cell populations was assayed by fluorescent microscopy and the tissue sections were counterstained for epithelial basement membrane formation. High intracellular levels of ODNs were observed in all mesenchymal cells of the lung, salivary gland, kidney, ovary and testis. However, a significant decrease in ODN levels was observed with the formation of new epithelium in kidney and gonads, whereas mature epithelial cells in all tissues had no detecable levels of ODNs. The ability to inhibit gene expression in mesenchymal cells, but not in epithelial cells, was consistent with the distribution pattern of labeled ODNs. These results may indicate a general resistance of epithelial cells to take up ODNs in culture and bear directly on the ability of ODNs to affect gene expression in complex organs with epithelial components.     

Loss of genomic imprinting in Drosophila clones.

Genomic imprinting is a process that genetically distinguishes maternal and paternal genomes, and can result in parent-of-origin-dependent monoallelic expression of a gene that is dependent on the parent of origin. As such, an otherwise functional maternally inherited allele may be silenced so that the gene is expressed exclusively from the paternal allele, or vice versa. Once thought to be restricted to mammals, genomic imprinting has been documented in angiosperm plants (J.L. Kermicle. 1970. Genetics, 66: 69-85), zebrafish (C.C. Martin and R. McGowan. 1995. Genet. Res. 65: 21-28), insects, and C. elegans (C.J. Bean, C.E. Schaner, and W.G. Kelly. 2004. Nat. Genet. 36: 100-105.). In each case, it appears to rely on differential chromatin structure. Aberrant imprinting has been implicated in various human cancers and has been detected in a number of cloned mammals, potentially limiting the usefulness of somatic nuclear transfer. Here we show that genomic imprinting associated with a mini-X chromosome is lost in Drosophila melanogaster clones.     

Blockage of AMV reverse transcriptase by antisense oligodeoxynucleotides.

Wild type chicken gizzard caldesmon (756 amino acids) was expressed in a T7 RNA polymerase-based bacterial expression system at a yield of 1 mg pure caldesmon per litre bacterial culture. A mutant composed of amino acids 1-578 was also constructed and expressed. The wild type and mutant caldesmon were purified and compared with native chicken gizzard caldesmon. Native and wild type expressed caldesmon were indistinguishable in assays for inhibition of actin-tropomyosin activation of myosin ATPase, reversal of inhibition by Ca²⁺-calmodulin and binding to actin, actin-tropomyosin, Ca²⁺-calmodulin, tropomyosin and myosin. The mutant missing the C-terminal 178 amino acids had no inhibitory effect and did not bind to actin or Ca²⁺-calmodulin. It bound to tropomyosin with a 5-fold reduced affinity and to myosin with a greater than 10-fold reduced affinity.