Oligonucleotide-poly-L-ornithine conjugates: binding to complementary DNA and RNA

Maleimide-dimethylfuran exo adducts: effective maleimide protection in the synthesis of oligonucleotide conjugates

The reaction of maleimide-containing compounds with 2,5-dimethylfuran gives a mixture of exo and endo isomers from which the exo cycloadduct can be easily isolated taking advantage of its stability in concentrated aqueous ammonia. Bifunctional compounds incorporating a dimethylfuran-protected maleimide (exo adduct) have been attached to resin-linked oligonucleotide chains. Removal of protecting groups masking oligonucleotide functionalities followed by retro-Diels-Alder maleimide deprotection affords maleimido-oligonucleotides suitable for conjugation, as assessed by their reaction with different thiols.

[Synthesis of polyamine-containing oligonucleotides]

A simple and efficient method of synthesis of polyamine-oligonucleotide conjugates in high yields (up to 95%) was suggested. The terminal phosphate group of deprotected oligonucleotides was selectively activated with the redox pair triphenylphosphine-dipyridyl disulfide in the presence of a nucleophilic catalyst, and the activated oligonucleotide derivative was subjected to the reaction with a polyamine.

Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides

Triplex-forming oligonucleotides (TFOs) are DNA-binding molecules, which offer the potential to selectively modulate gene expression. However, the biological activity of TFOs as potential antigene compounds has been limited by cellular uptake. Here, we investigate the effect of cell-penetrating peptides on the biological activity of TFOs as measured in an assay for gene-targeted mutagenesis. Using the transport peptide derived from the third helix of the homeodomain of antennapedia (Antp), we tested TFO-peptide conjugates compared with unmodified TFOs. TFOs covalently linked to Antp resulted in a 20-fold increase in mutation frequency when compared with 'naked' oligonucleotides. There was no increase above background in mutation frequency when Antp by itself was added to the cells or when Antp was linked to mixed or scrambled sequence control oligonucleotides. In addition, the TFO-peptide conjugates increased the mutation frequency of the target gene, and not the control gene, in a dose-responsive manner. Confocal microscopy using labeled oligonucleotides indicated increased cellular uptake of TFOs when linked to Antp, consistent with the gene-targeting data. These results suggest that peptide conjugation may enhance intranuclear delivery of reagents designed to bind to chromosomal DNA.

The use of synthetic polymers for delivery of therapeutic antisense oligodeoxynucleotides

Developed over the past two decades, the antisense strategy has become a technology of recognised therapeutic potential, and many of the problems raised earlier in its application have been solved to varying extents. However, the adequate delivery of antisense oligodeoxynucleotides to individual cells remains an important and inordinately difficult challenge. Synthetic polymers appeared on this scene in the middle 1980s, and there is a surprisingly large variety used or proposed so far as agents for delivery of oligodeoxynucleotides. After discussing the principles of antisense strategy, certain aspects of the ingestion of macromolecules by cells, and the present situation of delivery procedures, this article analyses in detail the attempts to use synthetic polymers as carrier matrices and or cell membrane permeabilisation agents for delivery of antisense oligodeoxynucleotides. Structural aspects of various polymers, as well as the results, promises and limitations of their use are critically evaluated.

Inhibition of human telomerase by PNA-cationic peptide conjugates

The inhibition of human telomerase has been explored using peptide conjugated derivatives of a PNA pentamer directed at the RNA template of telomerase. It is demonstrated that the presence of cationic peptides at the N-terminus of the PNA results in enhanced inhibition of telomerase activity. Furthermore, inhibition depended on the specificity of PNA recognition.

5'-Peptidyl substituents allow a tuning of the affinity of oligodeoxyribonucleotides for RNA

The affinity of amide-linked 5'-aminoacyl and 5'-dipeptidyl DNA octamers for two RNA undecamers with 3'-overhangs was measured via UV melting analysis. A sequence-dependent increase in melting points was observed. At low ionic strength, two appended lysine residues elevate melting points more than two additional A:U base pairs.

Hybridization properties of oligodeoxynucleotide pairs bridged by polyarginine peptides

The hybridization properties of a series of probes, based on two 9mer oligodeoxynucleotides (designated as I and II) having an appended oligoarginine chain (Rn) to produce peptide-oligonucleotide conjugates or peptide-bridged oligonucleotide pairs (e.g. Rn-I or II-Rn-I), were investigated. For the double-linked probes, we found that the peptide bridge induces the two 9mers to bind complementary single-stranded DNA or RNA targets with substantially enhanced thermal stability. The resulting hybrid with complementary DNA was found to assume a 1:1 complex in the B conformation as judged by UV mixing curves and CD spectroscopy. Complexes of single or double-linked probes with complementary RNA exhibited sensitivity to RNase H digestion. The influence of the identity and chirality of the repeating unit in the bridge, the length of the bridge, the gap size and the salt concentration on the hybridization properties of this new class of oligonucleotide probes was also studied. Our data reveal that these compounds exhibit properties that should prove useful in the development of antisense strategies.

Template-directed ligation of peptides to oligonucleotides

BACKGROUND

Oligonucleotide-peptide conjugates have several applications, including their potential use as therapeutic agents. We developed a strategy for the chemical ligation of unprotected peptides to oligonucleotides in aqueous solution. The two compounds are joined via a stable amide bond in a template-directed reaction.

RESULTS

Peptides, ending in a carboxy-terminal thioester, were converted to thioester-linked oligonucleotide-peptide intermediates. The oligonucleotide portion of the intermediate binds to a complementary oligonucleotide template, placing the peptide in close proximity to an adjacent template-bound oligonucleotide that terminates in a 3' amine. The ensuing reaction results in the efficient formation of an amide-linked oligonucleotide-peptide conjugate.

CONCLUSIONS

An oligonucleotide template can be used to direct the ligation of peptides to oligonucleotides via a highly stable amide linkage. The ligation reaction is sequence-specific, allowing the simultaneous ligation of multiple oligonucleotide-peptide pairs.

Gel shift assay: demonstration of enhanced binding of oligo(delta)-L-ornithine-oligodeoxynucleotide conjugates to complementary DNA and RNA

An increase in melting temperature for DNA:DNA duplexes had been observed previously (Zhu et al. Antisense Res. Dev. 3:349-356, 1993) when an oligo(delta)ornithine moiety was covalently appended to a short oligodeoxynucleotide. We now report the analysis of duplex formation by electrophoretic gel shift analysis. In the particular example studied, an increase in Tm of 4 degrees C was found to correspond to about a fivefold increase in binding constant. A similar enhancement by the appended cationic peptide was observed when the target strand was RNA. The use of a competitive assay format for avoidance of adsorptive loss at low concentrations (< 10(-7)M) of the oligonucleotide-oligo(delta)ornithine conjugate is presented.

Stability and pharmacokinetic characteristics of oligonucleotides modified at terminal linkages in mice

To construct the strategy for delivery systems that can control in vivo disposition of antisense oligonucleotides, we studied the stability and basic pharmacokinetic characteristics of oligonucleotides. Decathymidylic acid (T10), a model oligodeoxynucleotide, and its derivatives, 5'-biotin-T10) and 3'-methoxyethylamine 5'-biotin-T10 (3'M5'B-T10), containing phosphoroamidate modification at 3'- and/or 5'-terminal internucleoside linkages, were synthesized. In phosphate-buffered saline (PBS, pH 7.4) containing 10% mouse serum, unmodified T10 was degraded with a half-life of 45 minutes; the degradation half-lives of 5'B-T10 and 3'M5'B-T10 were 11 and 30 h, respectively. In mouse whole blood, 3'M5'B-T10 was relatively stable, and 45% remained intact after 1 h incubation. After intravenous injection of [3H]3'M5'B-T10 into mice at a dose of 1 mg/kg, the radioactivity was rapidly cleared from plasma with a half-life of 2 minutes and accumulated in the kidney, liver, and gallbladder. About 30% of the dose was excreted in the urine within 60 minutes. A much more rapid degradation of [3H]3'M5'B-T10 was observed in vivo than expected from in vitro experiments: more than 90% of the radioactivity in plasma was degradation product at 2 minutes after injection. These results suggested that enzymatic degradation occurred in some compartments in addition to the blood pool. The apparent urinary excretion clearance of [3H]3'M5'B-T10 was close to that of inulin, whereas the apparent hepatic uptake clearance was much greater than that of inulin and comparable to that of dextran sulfate, which is taken up by the liver by scavenger receptors for polyanions.(ABSTRACT TRUNCATED AT 250 WORDS)

Preparation and physical properties of conjugates of oligodeoxynucleotides with poly(delta)ornithine peptides

Oligodeoxynucleotides (12-mers) having either a 3' aminolinker or both 3' and 5' aminolinker groups were synthesized and then reacted with N-iodoacetoxysuccinimide. Separately, a series of peptides, consisting of cysteine carboxyamide and a varying number of residues of ornithine coupled through their side-chain amino groups, was prepared, leaving on the final Fmoc protecting group. Reaction of each Fmoc-peptide with an activated oligodeoxynucleotide yielded the desired conjugates, which were purified by an Fmoc-on/Fmoc-off two-step reversed-phase HPLC procedure. On hybridization with a complementary unmodified 12-mer oligodeoxynucleotide, it was found that there is a gradual increase in melting temperature with the number of ornithine residues, whereas the appended peptide did not perturb the B form of the duplex.