Studying Pegylated DNA Complexes by Dual Color Fluorescence Fluctuation Spectroscopy

The influence of natural pulmonary surfactant on the efficacy of siRNA-loaded dextran nanogels

AIM

Topical administration of siRNA nanocarriers is a promising approach in the treatment of pulmonary disorders. Pulmonary surfactant, covering the entire alveolar surface of mammalian lungs, will be one of the first interfaces that siRNA nanocarriers encounter upon inhalation therapy. Therefore, it is of outstanding importance to evaluate the impact of pulmonary surfactant on the performance of siRNA nanocarriers.

MATERIALS & METHODS

The effect of natural lung-derived surfactants on the siRNA delivery capacity of dextran nanogels (DEX-NGs) was evaluated in vitro using flow cytometry and confocal microscopy.

RESULTS

Although the interaction with pulmonary surfactant decreases the cellular internalization of siRNA-loaded DEX-NGs significantly, the gene silencing potential of siRNA-loaded DEX-NGs was maintained. On the other hand, cationic lipid-based siRNA nanocarriers (Lipofectamine™ RNAiMAX) were incompatible with pulmonary surfactants.

CONCLUSION

Our data suggest that pulmonary surfactant can enhance the intracellular siRNA delivery by DEX-NGs, thereby possibly providing new therapeutic opportunities.

Condensed multilamellar structure of a complex of DNA with an amphiphilic block copolymer

Deoxyribonucleic acid (DNA) is an attractive building block for self-assembled nanostructures, because the anionic phosphate group and the base moiety allow it to bind with a broad spectrum of organic and inorganic species through ionic and hydrogen bonding. Here we present a hierarchical structure formed by the ionic complex of DNA with an amphiphilic block copolymer comprising a cationic block. Upon the complexation the cationic block chains wrap around DNA for charge matching and the microphase separation between the hydrophobic block and the hydrophilic component yields a multilamellar structure with liquid crystalline ordering of the DNA chains condensed in the hydrophilic microdomains. Each hydrophilic lamellar domain is found to contain two DNA sublayers separated by a thin water gap, with each sublayer comprising two rows of densely packed DNA chains to lower the interfacial free energy for the present system with strong polar-nonpolar repulsion.

Complexation of lipofectamine and cholesterol-modified DNA sequences studied by single-molecule fluorescence techniques

Lipoplex formation for normal and cholesterol-modified oligonucleotides is investigated by fluorescence correlation spectroscopy (FCS). To overcome the problems related to the fitting of autocorrelation curves when fluorescence bursts are present, the baseline fluorescence levels and the fluorescence bursts in the same trace were separately analyzed. This approach was not previously used in FCS studies of lipoplexes and allowed a more detailed characterization of this heterogeneous system. From the baseline levels, the number of free/bound DNA molecules and the presence of tens to hundreds of nanometer-sized lipoplexes were estimated using various mathematical models. Analysis of the fluorescent bursts provided an indication about the sizes of the lipoplexes, the number of DNA molecules in these aggregates, and the relative amount of lipids in each aggregate. An explanation for the higher transfection efficiency previously reported for one of the cholesterol-modified oligonucleotide compounds was found in relation to the formation of large size lipoplexes.

Can we better understand the intracellular behavior of DNA nanoparticles by fluorescence correlation spectroscopy?

The use of non-viral gene carriers to deliver small nucleic acids like antisense oligonucleotides (ODNs) and small interfering RNA (siRNA) remains an attractive but challenging goal in antisense therapy. Indeed, different barriers need to be overcome in the delivery process before a therapeutic effect can be obtained. One promising technique which we have been evaluating to improve our understanding of the intracellular behavior of nucleic acids/carrier complexes is Fluorescence Correlation Spectroscopy (FCS). In particular, we have used FCS for studying the protection of the nucleic acids against enzymatic degradation, and the association and dissociation of the nucleic acids with their carrier, both in buffer and in living cells. In this report, we will review our experience and findings on the use of FCS for that purpose and discuss the strengths and weaknesses of this interesting technique.

Tetrahydrofuran Activates Fluorescence Resonant Energy Transfer from a Cationic Conjugated Polyelectrolyte to Fluorescein-Labeled DNA in Aqueous Media

A cationic water-soluble conjugated polyelectrolyte, poly[9,9-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-2,5-bis(6'-(N,N,N-trimethylammonium)hexyloxyphenylene) tetrabromide], was synthesized. Fluorescence resonant energy transfer (FRET) experiments between the polymer and fluorescein-labeled single-stranded DNA (ssDNA-Fl) were conducted in aqueous buffer and THF/buffer mixtures. Weak fluorescence emission in aqueous buffer was observed upon excitation of the polymer, whereas addition of THF turned on the fluorescence. Fluorescence self-quenching of ssDNA-Fl in the ssDNA-Fl/polymer complexes as well as electron transfer from the polymer to fluorescein may account for the low fluorescence emission in buffer. The improved sensitization of fluorescence by the polymer observed in THF/buffer could be attributed to the weaker binding between the polymer and ssDNA-Fl and a decrease in dielectric constant of the solvent mixture, which disfavors electron transfer. THF-assisted signal sensitization was also observed for the polymer and fluorescein-labeled double-stranded DNA (dsDNA-Fl). These results indicate that the use of cosolvent provides a strategy to improve the detection sensitivity for biosensors based on the optical amplification provided by conjugated polymers.

Protection of oligonucleotides against enzymatic degradation by pegylated and nonpegylated branched polyethyleneimine

Among the cationic polymers, polyethyleneimine (PEI) is a promising candidate for delivery of oligodeoxynucleotides (ODNs). In this study, we wondered whether pegylation of PEI influences the complexation with ODNs. We especially aimed to investigate whether ODNs are differently protected against enzymatic degradation in PEI and polyethylene glycol-polyethyleneimine (PEG-PEI) polyplexes. Using fluorescence resonance energy transfer combined with fluorescence correlation spectroscopy, we found that PEI/ODN polyplexes remain to protect the ODNs they carry over a prolonged period of time while in PEG-PEI/ODN polyplexes the degradation of the ODNs slowly proceeds. We attribute this to the fact that PEI seems to compact the ODNs more firmly in the polyplexes' core than PEG-PEI, which apparently also results in a better protection against enzymatic degradation. These observations may also influence the efficiency of PEI-based ODN delivery in vivo, where pegylation is an attractive strategy to enhance the stability of the polyplexes in the blood stream.

Optimization of the Molecular Orbital Energies of Conjugated Polymers for Optical Amplification of Fluorescent Sensors

Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents on the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoinduced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the conjugated polymers and C serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C in polymer/ssDNA-C complexes by addition of ssDNA yields insight into C*...C self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C.

Protection of oligonucleotides against nucleases by pegylated and non-pegylated liposomes as studied by fluorescence correlation spectroscopy

Antisense phosphodiester oligonucleotides (ONs), complexed to carriers such as cationic liposomes, inhibit the production of proteins. The biochemical and biophysical phenomena that govern the extent of this inhibition are still not fully understood. Major biological barriers limiting a pronounced antisense effect are the cellular entry and endosomal escape of the ONs containing liposomes, the release of the ONs from the liposomes and the extra- and intracellular degradation of the ONs. In this paper we focus on the latter barrier and evaluate, by fluorescence correlation spectroscopy (FCS), to what extent phosphodiester ONs complexed to DOTAP/DOPE liposomes, are protected against degradation by nucleases. Liposomes studied were either with or without a polyethyleneglycol (PEG) moiety at the surface. Using non-pegylated liposomes the phosphodiester ONs were initially adequately protected when exposed to DNase I. Indeed, in the mechanism for lipoplex formation as suggested by others, the ONs become trapped between lipid bilayers and are therefore shielded from the environment. However, after a few hours the phosphodiester ONs no longer stayed intact. This was explained by a gradual fusion of the lipoplexes in time thereby spontaneously releasing phosphodiester ONs. Using pegylated liposomes, a substantial fraction of the phosphodiester ONs degraded immediately after exposing the complexes to DNase I. Based on experimental evidence we suggest that the presence of the PEG-chains influences lipoplex formation so that the ONs are not trapped between lipid bilayers and therefore remain accessible by the DNase I enzyme.

Towards a better understanding of the dissociation behavior of liposome-oligonucleotide complexes in the cytosol of cells

To obtain real breakthroughs in antisense therapy, it is necessary to understand the cellular behavior of antisense delivery systems. Fluorescence fluctuation spectroscopy (FFS), which measures in time fluorescence fluctuations in the excitation volume of a microscope and which can thus be applied on a cellular scale, shows potential for this purpose. In this study dual color FFS was explored to characterize the complexation (association and dissociation) between Cy5-labeled oligonucleotides (Cy5-ONs) and FITC-labeled cationic liposomes (FITC-liposomes) in respectively buffer, cell lysate and the cytosol of Vero cells. In Hepes buffer the association of the Cy5-ONs to the FITC-liposomes could be clearly observed from the high peaks of Cy5- and FITC-fluorescence, which appeared simultaneously in the excitation volume. This was explained by the fact that in the complexed state many Cy5-ONs and FITC-liposomes are bound to each other and thus move together through the excitation volume thereby resulting in high fluorescence 'FITC/Cy5-peaks'. FFS measurements on FITC-liposome/Cy5-ONs complexes in cell lysate revealed that a minor part of the Cy5-ONs was released from the complexes. The major part of the Cy5-ONs remained in the complexes, which also seemed to aggregate in cell lysate. In agreement with the measurements in cell lysate, after microinjection of FITC-liposome/Cy5-ONs complexes in the cytosol of Vero cells a part of the Cy5-ONs was released (as Cy-ONs were detected by FFS in the nuclei) while the other part remained bound (as Cy5-peaks were frequently observed in the cytosol). As will be explained, the Cy5-peaks could be due both to Cy5-ONs clustered with cytosol components and Cy5-ONs still complexed to FITC-liposomes with quenched FITC-fluorescence.

FRET-FCS as a tool to evaluate the stability of oligonucleotide drugs after intracellular delivery

The intracellular degradation of single-stranded, double-labeled oligonucleotides (ONs) was studied by following the disappearance of Fluorescence Resonance Energy Transfer (FRET) between the rhodamine green and Cy5 fluorophores attached to respectively the 3' and 5' end of the ONs. The green and red fluorescence intensities upon rhodamine green excitation were monitored using the ultra-sensitive detectors of a dual-color Fluorescence Correlation Spectroscopy (FCS) instrument. The ratio of the red to green fluorescence (R/G ratio) as obtained from such FRET-FCS measurements showed to give accurate information on the integrity of the ONs, without the need for additional auto- or cross-correlation analysis of the registered fluorescence intensity fluctuations. Intracellular measurements revealed that most of the 40mer phosphodiester ONs were degraded before they entered the nucleus. For the 20mer phosphodiester ONs, this degradation occurred more slowly, and both intact and degraded ONs entered the nucleus. For the 20mer phosphorothioate ONs, no intracellular degradation was observed during the measured time period. The sensitive detection of the intracellular fluorescence by the FCS setup will be particularly useful in situations where the expected fluorescence is too low to be detected by FRET-imaging as may occur after intracellular delivery of ONs by cationic carriers.