Stability Of Oligodeoxynucleotides Research Articles

Influence of loop permutation on immunostimulatory activities of CpG oligodeoxynucleotides forming monomeric guanine-quadruplex structures

Introduction: Existing research establishes the role of oligodeoxynucleotides (ODNs) containing cytosine-phosphate-guanine motifs (CpG ODNs) as adjuvants to vaccines against infectious diseases. However, the natural structure of ODN with phosphodiester (PD) linkages is prone to degradation by serum DNase, which limits the application of CpG ODNs. We recently engineered a monomeric guanine-quadruplex (G4)-structured CpG ODN (G4 CpG ODN) and determined that the monomeric G4 increased the DNase resistance, intracellular uptake, and cytokine induction of CpG ODN in vitro and in vivo. However, the effect of the primary sequence on G4 conformation and function of G4 CpG ODN is unclear. Methods: Therefore, in this study, we examine the role of loop permutation, a sequential order of three G4 loops, in G4 folding and immunostimulatory properties of G4 CpG ODNs. We explore the impact of loop permutation on the immunostimulatory activity of GD3_2L, a monomeric G4 CpG ODN that we reported previously. We exchanged the sequence of the second loop with the first and third loops of GD3_2L to obtain GD3_1L and GD3_3L, respectively. The structure of the obtained ODNs was determined by circular dichroism and polyacrylamide gel electrophoresis; the thermodynamic stability of ODN was evaluated through UV melting curve analysis. We assessed the immunostimulatory activity by examining the relative messenger RNA (mRNA) levels of cytokines produced in G4 CpG ODN-stimulated mouse macrophage-like RAW264 by reverse transcription-quantitative polymerase chain reaction method. Results: We found that changing the sequential order of CpG motifs from the second to the first loop resulted in a change in G4 conformation from hybrid to parallel and a decrease in the compactness and thermodynamic stability of GD3_2L. Moreover, swapping order between the second and third loop of GD3_2L led to a hybrid G4 structure that is as stable as GD3_2L but possesses a lower cytokine induction. Conclusion: In conclusion, the loop permutation does not always change the topology and structural compactness; instead, it changes the conformation of CpG motifs in the G4 structure, directly affecting the immunostimulatory properties. Our result demonstrates that the loop-transposition-mediated structural compactness decrease can, if exploited, increase the efficacy of immunostimulatory G4 CpG ODN.

Abolishing HIV-1 infectivity using a polypurine tract-specific G-quadruplex-forming oligonucleotide.

BackgroundHIV is primarily transmitted by sexual intercourse and predominantly infects people in Third World countries. Here an important medical need is self-protection for women, particularly in societies where condoms are not widely accepted. Therefore, availability of antiviral microbicides may significantly reduce sexual HIV transmission in such environments.MethodsHere, we investigated structural characteristics and the antiviral activity of the polypurine tract (PPT)-specific ODN A, a 54-mer oligodeoxynucleotide (ODN) that has been previously shown to trigger the destruction of viral RNA genomes by prematurely activating the retroviral RNase H. The stability of ODN A and mutants thereof was tested at various storage conditions. Furthermore, antiviral effects of ODN A were analyzed in various tissue culture HIV-1 infection models. Finally, circular dichroism spectroscopy was employed to gain insight into the structure of ODN A.ResultsWe show here that ODN A is a powerful tool to abolish HIV-1 particle infectivity, as required for a candidate compound in vaginal microbicide applications. We demonstrate that ODN A is not only capable to prematurely activate the retroviral RNase H, but also prevents HIV-1 from entering host cells. ODN A also exhibited extraordinary stability lasting several weeks. Notably, ODN A is biologically active under various storage conditions, as well as in the presence of carboxymethylcellulose CMC (K-Y Jelly), a potential carrier for application as a vaginal microbicide. ODN A’s remarkable thermostability is apparently due to its specific, guanosine-rich sequence. Interestingly, these residues can form G-quadruplexes and may lead to G-based DNA hyperstructures. Importantly, the pronounced antiviral activity of ODN A is maintained in the presence of human semen or semen-derived enhancer of virus infection (SEVI; i.e. amyloid fibrils), both known to enhance HIV infectivity and reduce the efficacy of some antiviral microbicides.ConclusionsSince ODN A efficiently inactivates HIV-1 and also displays high stability and resistance against semen, it combines unique and promising features for its further development as a vaginal microbicide against HIV.

Modification of Decoy Oligodeoxynucleotides to Achieve the Stability and Therapeutic Efficacy

The decoy oligodeoxynucleotide (ODN) serves as a decoy sequence for a target transcription factor, then inhibiting its binding to the authentic sequence at the promoter, and consequently hinders the gene expression. ODNs should be properly up taken by the cell and tissue, be specific for one nuclear factor, and be stable against intracellular and serum nucleases. Since phosphodiester oligos are easily degradated by nucleases, chemical modification such as phosphorothioation, and structural modification by ligation of the extremities of two single-strand phosphodiester sequence resulting in a dumbbell shaped ODN (Ribbon-type decoy ODN) are performed to increase the stability of ODNs. In combination, phosphorothioation of specific regions in Ribbon-type decoy has further increased its stability, and the introduction of saturated hydrocarbon polymer spacer linking the two double strands also improved the stability and reduced the production cost. The cellular delivery has been optimized by using the biodegradable polymer D,L-lactide-co-glycolide (PLGA) as a carrier to ODN. The nuclear factor-kappa B (NF-κB) is a convergent point of different pathways, with main role in many pathologies, and poses as an ideal target for decoy ODN strategy. Following this we have designed ODN targeting NF-κB, and in this review, we are going to discuss the various modification performed in an attempt to improve the ODN efficacy, and some promising pre-clinical data and clinical trials using NF-κB decoy ODN.

Synthetic Antisense Oligodeoxynucleotides to Transiently Suppress Different Nucleus- and Chloroplast-Encoded Proteins of Higher Plant Chloroplasts

Selective inhibition of gene expression by antisense oligodeoxynucleotides (ODNs) is widely applied in gene function analyses; however, experiments with ODNs in plants are scarce. In this work, we extend the use of ODNs in different plant species, optimizing the uptake, stability, and efficiency of ODNs with a combination of molecular biological and biophysical techniques to transiently inhibit the gene expression of different chloroplast proteins. We targeted the nucleus-encoded phytoene desaturase (pds) gene, encoding a key enzyme in carotenoid biosynthesis, the chlorophyll a/b-binding (cab) protein genes, and the chloroplast-encoded psbA gene, encoding the D1 protein. For pds and psbA, the in vivo stability of ODNs was increased by phosphorothioate modifications. After infiltration of ODNs into juvenile tobacco (Nicotiana benthamiana) leaves, we detected a 25% to 35% reduction in mRNA level and an approximately 5% decrease in both carotenoid content and the variable fluorescence of photosystem II. In detached etiolated wheat (Triticum aestivum) leaves, after 8 h of greening, the mRNA level, carotenoid content, and variable fluorescence were inhibited up to 75%, 25%, and 20%, respectively. Regarding cab, ODN treatments of etiolated wheat leaves resulted in an up to 59% decrease in the amount of chlorophyll b, a 41% decrease of the maximum chlorophyll fluorescence intensity, the cab mRNA level was reduced to 66%, and the protein level was suppressed up to 85% compared with the control. The psbA mRNA and protein levels in Arabidopsis (Arabidopsis thaliana) leaves were inhibited by up to 85% and 72%, respectively. To exploit the potential of ODNs for photosynthetic genes, we propose molecular design combined with fast, noninvasive techniques to test their functional effects.

Study of the Stability of Oligodeoxynucleotide–Doxorubicin Conjugate In Vitro and Its Pharmacokinetics In Vivo by RP‐HPLC

Oligodeoxynucleotide–doxorubicin conjugate is a novel modified oligodeoxynucleotide (ODN) to inhibit the expression of mdr1 gene. The present study was undertaken to determine the stability of the conjugate in vitro and its pharmacokinetics in vivo using a reverse‐phase HPLC assay. The method employed a short C18 reverse phase column combined with a C8 pre‐column and a linear gradient elution with acetonitrile containing 0.1 M aqueous triethylammonium acetate, pH 7.0. Detection was carried out using a UV‐diode array detector at 254 and 480 nm. Minimum sensitivity of ∼0.15 µg/mL in plasma and 0.1 µg/mL in PBS of the conjugate was achieved. After incubation in 10% activated fetal calf serum for 24 hours, 15.8% of the conjugate was degraded. As a comparison however, 97.2% of the control ODN was degraded within the same incubation time. The pharmacokinetics studies show that the half‐lives of the conjugate is about 8 hours, 4 times longer than ODN as a control. Assay validation studies revealed that the method is accurate, reproducible for determination of the conjugate, and can be used for a pharmacokinetic study of the conjugate.

Synthesis and stability of oligodeoxynucleotides containing C8-labeled 2'-deoxyadenosine: novel redox nucleobase probes for DNA-mediated charge-transfer studies.

[reaction: see text] An efficient and convenient synthetic strategy to redox-labeled C8-derivatives of 2'-deoxyadenosine is described. The Pd(0) cross-coupling chemistry is amenable to both oxidative and reductive redox probes. The corresponding phosphoramidites of phenothiazine and anthraquinone nucleosides are amenable to automated DNA synthesis. The resulting labeled oligodeoxynucleotide strands form stable B-form duplexes with melting temperatures and CD spectra similar to those of the unlabeled analogues.

Effect of ultrasound on the stability of oligodeoxynucleotides in vitro

In order for oligodeoxynucleotides (ODNs) to be viable candidates for phonophoresis (i.e. ultrasound-enhanced delivery), they must remain stable on exposure to therapeutic ultrasonic waves. We have examined the stability of radiolabelled ODNs as a function of their chemistry (phosphodiester (PO) and phosphorothioate (PS)) and chain length (7-mer and 20-mer) in aqueous solutions at three different pH values (1, 2 and 7) when subjected to ultrasound at an intensity of 1.5 W cm −2 for 30 min. Whereas all ODNs remained stable at pH 1, pH 2 or pH 7 in the absence of ultrasound, significant degradation was observed at pH 1 upon ultrasound treatment. The sensitivity of ultrasound-enhanced ODN degradation at this pH, starting with the most rapidly degradable species first, was 7-mer PO > 20-mer PO > 7-mer PS > 20-mer PS. Interestingly, ODN stability was unaffected by exposure to an equivalent heat-alone application (pH 1 at 44°C) thus indicating that the mechanical, rather than heating, effects of ultrasound are responsible for the observed ODN degradation.

Stability of antisense DNA oligodeoxynucleotide analogs in cellular extracts and sera

Antisense DNA oligodeoxynucleotides can selectively inhibit the expression of i individual (undesirable) genes and thus, have potential in the treatment of cancer and viral diseases. A prerequisite to their use as therapeutic agents is information on the stability of oligodeoxynucleotides, and their structurally modified analogs, in the biological milieu. To this end, degradation of 5' end and internally [ 32P] labelled unmodified DNA oligodeoxynucleotide (D-oligo) and analogs containing phosphorothioate (S-oligo), methylphosphonate (MP-oligo), and novel alternating methylphosphonate and phosphodiester (Alt-MP-oligo) internucleoside linkages was studied in Hela cell nuclear extract, S100 cytoplasmic extract, normal human serum and calf serum at 37°C. Both 5' end and internally labelled D-oligos showed complete degradation within 30 min incubation in human serum at 37°C. In any given medium, the D-oligo was the least stable oligodeoxynucleotide to nuclease degradation whereas the Alt-MP, MP and S-oligos were generally of comparable stability and all relatively more stable than D-oligo. Interestingly, MP and Alt-MP-oligos also exhibited greater resistance to phosphatases in cellular extracts compared to D and S-oligos. Under the conditions of the experiments, increasing degradation for any given oligonucleotide was observed in the order: S100 cytoplasmic extract < nuclear extract < normal human serum < calf serum. In a study involving alpha-MEM cell culture medium containing 10% heat inactivated fetal calf serum (heated to 56°C for 1 hour), the D-oligo was found to be rapidly degraded (degradation evident within 10 mins) whereas degradation products for the S-oligo were observed within 1 hour. In contrast, the Alt-MP oligo remained stable throughout the 3 hour experiment. These results indicated that in cell culture medium containing heat inactivated serum Alt-MP oligo was more stable than D- and S-oligos.