Inhibition of sequence-specific protein-DNA interaction and restriction endonuclease cleavage via triplex stabilization by poly(L-lysine)-graft-dextran copolymer

Therapeutic genome mutagenesis using synthetic donor DNA and triplex-forming molecules

Genome mutagenesis can be achieved in a variety of ways, though a select few are suitable for therapeutic settings. Among them, the harnessing of intracellular homologous recombination affords the safety and efficacy profile suitable for such settings. Recombinagenic donor DNA and mutagenic triplex-forming molecules co-opt this natural recombination phenomenon to enable the specific, heritable editing and targeting of the genome. Editing the genome is achieved by designing the sequence-specific recombinagenic donor DNA to have base mismatches, insertions, and deletions that will be incorporated into the genome when it is used as a template for recombination. Targeting the genome is similarly achieved by designing the sequence-specific mutagenic triplex-forming molecules to further recruit the recombination machinery thereby upregulating its activity with the recombinagenic donor DNA. This combination of extracellularly introduced, designed synthetic molecules and intercellularly ubiquitous, evolved natural machinery enables the mutagenesis of chromosomes and engineering of whole genomes with great fidelity while limiting nonspecific interactions. Herein, we demonstrate the harnessing of recombinagenic donor DNA and mutagenic triplex-forming molecular technology for potential therapeutic applications. These demonstrations involve, among others, utilizing this technology to correct genes so that they become physiologically functional, to induce dormant yet functional genes in place of non-functional counterparts, to place induced genes under regulatory elements, and to disrupt genes to abrogate a cellular vulnerability. Ancillary demonstrations of the design and synthesis of this recombinagenic and mutagenic molecular technology as well as their delivery and assayed interaction with duplex DNA reveal a potent technological platform for engineering specific changes into the living genome.

Delivery of rosiglitazone from an injectable triple interpenetrating network hydrogel composed of naturally derived materials

An in situ gelable and biodegradable triple-interpenetrating network (3XN) hydrogel, completely devoid of potentially cytotoxic extraneous small molecule crosslinkers, is formulated from partially oxidized dextran (Odex), teleostean and N-carboxyethyl chitosan (CEC). Both the rheological profile and mechanical strength of the 3XN hydrogel approximate the combined characteristics of the three individual hydrogels composed of the binary partial formulations (i.e., Odex/CEC, Odex/teleostean, and CEC/teleostean). The 3XN hydrogel is considerably more resistant to fibroblast-mediated degradation compared to each partial formulation in cell culture models; this is attributable to the interpenetrating triple-network structure. The presence of teleostean in the 3XN hydrogel imparts cell affinity, constituting an environment amenable to fibroblast growth. in vivo subdermal injection into mouse model shows that the 3XN hydrogel does not induce extensive inflammatory response nor is there any evidence of tissue necrosis, further confirming the non-cytotoxicity of the hydrogel and its degradation byproducts. Importantly, the capability of the 3XN hydrogel to serve as a sustained drug delivery vehicle is confirmed using rosiglitazone as a model drug. The presence of rosiglitazone profoundly changes the cell/tissue interactions with the subdermally injected 3XN hydrogel. Rosiglitazone suppresses both the inflammatory response and tissue repair in a dose-dependent manner and considerably moderated the hydrogel degradation.

Synergistic stabilization of nucleic acid assembly by 2'-O,4'-C-methylene-bridged nucleic acid modification and additions of comb-type cationic copolymers

Stabilization of nucleic acid assemblies, such as duplex and triplex, is quite important for their wide variety of potential applications. Various stabilization methods, including molecular designs of chemically modified nucleotides and hybrid stabilizers, and combinations of different stabilization methods have been developed to increase stability of nucleic acid assemblies. However, combinations of two stabilizing methods have not always yielded desired synergistic effects. In the present study, to propose a strategy for selection of a rational combination of stabilizing methods, we demonstrate synergistic stabilization of triplex by 2'-O,4'-C-methylene-bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide and addition of poly(l-lysine)-graft-dextran copolymer [poly(l-lysine) grafted with hydrophilic dextran side chains]. Each of these methods increased the binding constant for triplex formation by nearly 2 orders of magnitude. However, their kinetic contributions were quite distinct. The copolymer increased the association rate constant, whereas the 2',4'-BNA modification decreased the dissociation rate constant for triplex stabilization. The combination of both stabilizing methods increased the binding constant by nearly 4 orders of magnitude. Kinetic analyses revealed that the successful synergistic stabilization resulted from kinetic complementarity between increased association rate constants by the copolymer and decreased dissociation rate constants by the 2',4'-BNA modification. The stabilizing effect of one stabilization method did not alter that of the other stabilization method. We propose that kinetic analyses of each stabilizing effect permit selection of a rational combination of stabilizing methods for successful synergy in stabilizing nucleic acid assemblies.

A biomimetic alternative to poly(ethylene glycol) as an antifouling coating: resistance to nonspecific protein adsorption of poly(L-lysine)-graft-dextran

Poly( L-lysine)- graft-dextran (PLL- g-dex), graft copolymers with dextran side chains grafted onto a poly( L-lysine) backbone, previously shown to be effective as stabilizers of DNA triple helices and as carriers of functional genes to target cells or tissues, were employed in this work to prevent nonspecific adsorption of proteins, as determined by means of optical waveguide lightmode spectroscopy. PLL- g-dex copolymers readily adsorb from aqueous solution onto negatively charged oxide surfaces and significantly reduce nonspecific protein adsorption onto bare silica-titania surfaces. While effective and equivalent surface adsorption and antifouling properties were observed for PLL- g-dex copolymers in a variety of architectures, nanotribological analysis by atomic force microscopy was able to distinguish between the different brush densities produced.

Non-cytotoxic, in situ gelable hydrogels composed of N-carboxyethyl chitosan and oxidized dextran

A series of in situ gelable hydrogels were prepared from oxidized dextran (Odex) and N-carboxyethyl chitosan (CEC) without any extraneous crosslinking agent. The gelation readily took place at physiological pH and body temperature. The gelation process was monitored rheologically, and the effect of the oxidation degree of dextran on the gelation process was investigated. The higher the oxidation degree of Odex, the faster the gelation. A highly porous hydrogel structure was revealed under scanning electron microscopy (SEM). Swelling and degradation of the Odex/CEC hydrogels in PBS showed that both swelling and degradation were related to the crosslinking density of the hydrogels. In particular, the hydrogels underwent fast mass loss in the first 2 weeks, followed by a more moderate degradation. The results of long-term cell viability tests revealed that the hydrogels were non-cytotoxic. Mouse fibroblasts were encapsulated in the hydrogels and cell viability was at least 95% within 3 days following encapsulation. Furthermore, cells entrapped inside the hydrogel assumed round shape initially but they gradually adapted to the new environment and spread-out to assume more spiny shapes. Additionally, the results from applying the Odex/CEC system to mice full-thickness transcutaneous wound models suggested that it was capable of enhancing wound healing.

Inducing the replacement of PNA in DNA.PNA duplexes by DNA

The uncharged DNA-analogue peptide nucleic acid (PNA) can invade into dsDNA by displacing the non-complementary DNA strand. The formed strand displacement complexes can create a sterical hindrance to block access of enzymes such as nucleases and polymerases. Due to the high stability of DNA.PNA duplexes it is usually not possible to displace the PNA strand by ssDNA or ssRNA. We herein report that the polycationic, comb-type copolymer alphaPLL-g-Dex can induce such a replacement of PNA in DNA.PNA duplexes by ssDNA. The influence of the copolymer on strand exchange highly depends on the nature of the oligonucleotides. Acceleration has only been observed when both the starting duplex and the single-stranded exchanger strand were negatively charged. The presented approach should allow the withdrawal of PNA induced sterical hindrance of DNA by rehybridisation with ssDNA.

Rheological characterization of in situ crosslinkable hydrogels formulated from oxidized dextran and N-carboxyethyl chitosan

The gelation kinetics of an in situ gelable hydrogel formulated from oxidized dextran (Odex) and N-carboxyethyl chitosan (CEC) was investigated rheologically. Both Schiff base mediated chemical and physical crosslinking account for its rapid gelation (30-600 s) between 5 and 37 degrees C. The correlation between gelation kinetics and hydrogel properties with Odex/CEC concentration, their feed ratio, and temperature were elucidated. The gelation time determined from crossing over of storage moduli (G') and loss moduli (G' ') was in good agreement with that deduced from frequency sweeping tests according to the Winter-Chambon power law. The power law exponents for a 2% (w/v) Odex/CEC solution (ratio 5:5) at the gel point was 0.61, which is in excellent agreement with the value predicted from percolation theory (2/3). Temperature dependence of gelation time for the same hydrogel formulation is well-described by an Arrhenius plot with its apparent activation energy calculated at 51.9 kJ/mol.

Synergistic stabilization of nucleic acid assembly by oligo-N3'-->P5' phosphoramidate modification and additions of comb-type cationic copolymers

Synergic stabilization of DNA triplexes by oligo-N3'-->P5' phosphoramidate (PN) modification and additions of comb-type cationic copolymers was demonstrated. The combination of the copolymer and the PN modification increased triplex K(a) about 4 orders of magnitude. Kinetic analysis revealed that observed stabilization resulted from kinetic complimentarity between increased association rates by the copolymer and decreased dissociation rates by the PN modification of triplex forming oligonucleotides. No countering interference between these stabilizing effects was observed. We propose that kinetic analyses of stabilizing effects permit selection of a rational combination of stabilizing methods for successful synergy in stabilizing complex formation.

Synthesis of poly(L-lactide) end-capped with lactose residue

The synthesis of poly(L-lactide) (polyLA) end-capped with lactose residue was studied from the standpoint of development of a new bioabsorbable material. After the hydroxyl group of t-butoxycarbonyl(Boc)-aminoethanol was converted to Boc-aminoethanol-OK by using potassium/naphthalene, L-lactide was polymerized in tetrahydrofuran using Boc-aminoethanol-OK as an initiator at room temperature to prepare polyLA-NHBoc. Subsequently, the removal of the Boc group in terminal Boc-aminoethanol residue was performed by treatment of formic acid to obtain the amino group end-capped polyLA (polyLA-NH(2)) as a reactive polyLA derivative. The coupling reactions of lactose with polyLA-NH(2) were investigated by two methods; the synthetic method through reductive amination of lactose with polyLA-NH(2) in the presence of sodium cyanoborohydride as a reducing agent did not give high degree of substitution of end-capped lactose residue per polyLA molecule, whereas the synthetic method through the ester interchange reaction of lactonolactone with polyLA-NH(2) gave Lac-polyLA perfectly end-capped with lactose residue.

DNA strand exchange stimulated by spontaneous complex formation with cationic comb-type copolymer

Cationic comb-type copolymers (CCCs) composed of a polycation backbone and water-soluble side chains accelerate by 4-5 orders the DNA strand exchange reaction (SER) between double helical DNA and its homologous single-strand DNA. The accelerating effect is considered due to alleviation of counterion association during transitional intermediate formation in sequential displacement pathway. CCCs stabilize not only matured hybrids but also the nucleation complex to accelerate hybridization.

Design of polymer materials enhancing nucleotide hybridization for anti-gene technology

Stabilization of nucleotide hybridization is considered important for improving gene therapy using oligonucleotides. We have designed comb-type copolymer consisting of polycation backbone (polylysine) and hydrophilic side chains as a stabilizer for double and triple helical DNAs. The copolymer considerably increased the thermal stability of triple helical structure but did not affect the reversible transition between triple helical and single-stranded DNA. An in vitro electrophoretic mobility shift assay revealed that the copolymer remarkably increased association constants of both Hoogsteen and reverse Hoogsteen-type triple helix formation. Moreover the triple helix-stabilizing efficiency of the copolymer was significantly higher than that of other oligocations like spermine and spermidine. Not only being good DNA triple helix stabilizer, it has also been shown to accelerate DNA strand exchange reactions between double helical DNA and its complementary oligonucleotides. From these, we conclude that this copolymer is capable of either 'stabilizing' or 'activating' DNA hybrids, and may useful for gene targeting employing oligonucleotides.

Comb-type cationic copolymer expedites DNA strand exchange while stabilizing DNA duplex

The accelerating effect of cationic substances on the DNA strand exchange reaction between a 20 bp DNA duplex and its complementary single strand was studied. A polycationic comb-type copolymer, that consists of a poly(L-lysine) backbone and a dextran graft chain (PLL-g-Dex) and known to stabilize triplex DNA, expedites the strand exchange reaction under physiological relevant conditions. Electrostatically a small excess of the copolymer let to a 300-1500-fold increase in the DNA strand exchange while large excess of spermine or cetyltrimethylammonium bromide, a cationic detergent known to promote markedly hybridization of complementary DNA strands, shows only a slight effect. The efficacy of the copolymer was not affected by a 10 mM Mg2+ concentration. Notably the copolymer promotes the strand exchange reaction while it stabilizes double-stranded DNA. The stabilization of strand exchange intermediates consisting of the parent duplex and the single strand by the copolymer is believed to be responsible for the observed acceleration behavior.