Crosslinked duplex DNA nanogels that target specified proteins.

Specific detection of protein biomarkers plays an important role in diagnostics and therapeutics. We have fabricated polymeric nanogels, which can specifically interact with the cancer biomarker thrombin to serve as a model. Two types of 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymers bearing a thrombin-binding oligonucleotide aptamer and its complementary chain were independently synthesized by redox-initiated radical polymerization. These MPC polymers associate in a complimentary fashion due to double strand formation of the oligonucleotides in aqueous media, leading to the spontaneous formation of spherical nanogels. Nanogel formation was confirmed by dynamic light scattering (DLS) and transmittance microscopy. The average size of nanogel particles was 124 ± 2 nm and the nanogels were mono-dispersed (polydispersity index 0.21). Functional intercalators could be stably incorporated into nanogels through the physical interaction between the intercalators and the oligonucleotides. The ethidium bromide (EtBr)-incorporating nanogels were used as detectors for thrombin. The fluorescence intensity of solutions containing the EtBr-incorporating nanogels was decreased with an increase in the concentration of thrombin. The transformation of quadruplex-thrombin structure from complementary double-stranded structures resulted in the decrease in fluorescence intensity. In contrast, the intensity did not change when the nanogels were incubated with albumin. Thrombin is only one such model used to demonstrate this technique; oligonucleotide aptamers can be freely designed to interact with versatile bio-substances. Therefore, aptamer-crosslinked nanogels can be appropriate nanomaterials for disease diagnosis and therapy.

Surface engineering of macrophages with nucleic acid aptamers for the capture of circulating tumor cells.

In order to enhance the interactions between macrophages and cancer cells, thiol-terminated nucleic acid aptamers were immobilized on methacryloyl-functionalised carbohydrates of macrophages. The adhesion of cancer cells on the surface modified macrophages was significantly accelerated.

Stabilization of DNA Structures with Poly(ethylene sodium phosphate).

The structure and stability of biomolecules under molecular crowding conditions are of interest because such information clarifies how biomolecules behave under cell-mimicking conditions. The anionic surfaces of chromatin, which is composed of DNA strands and histone complexes, are concentrated in cell nuclei and thus generate a polyanionic crowding environment. In this study, we designed and synthesized an anionic polymer, poly(ethylene sodium phosphate) (PEP·Na), which has a nucleic acid phosphate backbone and created a cell nucleus-like environment. The effects of molecular crowding with PEP·Na on the thermodynamics of DNA duplexes, triplexes, and G-quadruplexes were systematically studied. Thermodynamic analysis demonstrated that PEP·Na significantly stabilized the DNA structures; e.g., a free energy change at 25 °C for duplex formation decreased from -6.6 to -12.8 kcal/mol with 20 wt % PEP·Na. Thermodynamic parameters further indicated that the factors for the stabilization of the DNA structures were dependent on sodium ion concentration. At lower polymer concentrations, the stabilization was attributed to a shielding of the electrostatic repulsion between DNA strands by the sodium ions of PEP·Na. In contrast, at higher polymer concentrations, the DNA structures were entropically stabilized by volume exclusion, which could be enhanced by electrostatic repulsion between phosphate groups in DNA strands and in PEP·Na. Additionally, increasing PEP·Na concentration resulted in increasing enthalpy of the DNA duplex but decreasing enthalpy of DNA G-quadruplex, indicating that the polymers also promoted dehydration of the DNA strands. Thus, polyanionic crowding affects the thermodynamics of DNA structures via the sodium ions, volume exclusion, and hydration. The stabilization of DNA by the cell nucleus-like polyanionic crowding provides new information regarding DNA structures and allows for modeling reactions in cell nuclei.

Tetramolecular quadruplex stability and assembly.

Guanine quadruplexes (G4) are unusual four-stranded nucleic acid structures formed by G-rich DNA/RNA. Beyond their likely biological relevance, the self-assembly, stability, and rigidity of these structures are also interesting for nanotechnology and biotechnology applications. Therefore, efforts are carried out to understand the rules that govern stability and folding of G-quadruplexes. We focus this chapter on tetramolecular conformations which are simple tractable models. We report here the experimental parameters, molecules, and modifications that affect thermal stability and/or association kinetics of these structures. Some chemical modifications which facilitate tetramolecular quadruplex formation and can be useful for nano- or biotechnology are also described.

The role of cationic comb-type copolymers in chaperoning DNA annealing.

G-rich oligonucleotides tend to fall into kinetically trapped unstable structures because of their conformational polymorphism. Nucleic acid chaperones accelerate association of nucleic acids assemblies into the thermodynamically most stable conformations by decreasing the energy barrier for breakage or re-assembly of base pairings. Here, we report that an artificial nucleic acid chaperone, a cationic comb-type copolymer, promotes tetramolecular quadruplex assembly from mixtures of two different G-rich sequences, 5'-TGGGGT-3' (TG(4)T) and 5'-TGGGGGT-3' (TG(5)T). A 1:1 mixture of TG(4)T and TG(5)T mainly gave [TG(4)T▪(TG(5)T)(3)], [(TG(4)T)(2)▪(TG(5)T)(2)] and [(TG(4)T)(3)▪TG(5)T] heteroquadruplexes when the mixture was annealed by cooling from 90 °C to 4 °C at 1.0 °C/min. At a cooling rate of 0.01 °C/min the mixture mostly assembled into [TG(4)T](4) and [TG(5)T](4) homoquadruplexes, indicating that homoquadruplexes were thermodynamically more stable than heteroquadruplexes. In the presence of the copolymer, mainly homoquadruplexes were obtained at cooling rate of 1 °C/min, suggesting that the copolymer promoted formation of the thermodynamically most stable structures. We also showed that the copolymer facilitated the recombination of heteroquadruplexes to homoquadruplexes even at 20-30 °C, implying that the copolymer can promote thermodynamically preferred quadruplex assembly from oligonucleotides trapped in metastable structures. These results show that the copolymer works as a DNA annealer that induces proper assembly of stable DNA structures from heterogeneous kinetically trapped mixtures of structures.

A mirror-image tetramolecular DNA quadruplex.

L-DNA, the mirror image of natural DNA forms structures of opposite chirality. We demonstrate here that a short guanine rich L-DNA strand forms a tetramolecular quadruplex with the same properties as a D-DNA strand of identical sequence, besides an inverted circular dichroism spectra. L- and D-strands self exclude when mixed together, showing that the controlled parallel self-assembly of different G-rich strands can be obtained through L-DNA use.

DNA assembly and re-assembly activated by cationic comb-type copolymer.

Guanine-rich oligonucleotides, such as TG(4)T and TG(5)T, assemble into a tetramolecular quadruplexes with layers of G-quartets stabilized by coordination to monovalent cations. Association rates of the quadruplexes are extremely slow, likely owing to electrostatic repulsion among the four strands. We have shown that comb-type copolymers with a polycation backbone and abundant hydrophilic graft chains form water-soluble polyelectrolyte complexes with DNA and promote DNA hybridization. Here, we report the effect of cationic comb-type copolymers on the kinetics of tetramolecular quadruplex formation. The copolymer significantly increased the association rate of tetramolecular quadruplexes without altering kinetic effects of metal cations in quadruplex formation. Dissociation rates of the quadruplexes were also accelerated by the copolymer suggesting that the copolymer has chaperone-like activity that reduces the energy barriers associated with dissociation and re-assembly of base pairs. This hypothesis was further supported by the observation that the copolymer activated the strand exchange reaction between the quadruplex and a constituting single-stranded.

Cationic comb-type copolymer as a nucleic acid chaperone for DNA quadruplex.

The intermolecular DNA quadruplex is attractive materials for design of nanomolecular constructs and machines. This folding kinetics is, however, slow, hampering its application to these materials. We have reported that the cationic comb-type copolymer accelerated duplex and triplex formation. In this study, the effect of the copolymer on the intermolecular quadruplex folding was investigated. The copolymer was found to accelerate the association of intermolecular quadruplex by three-orders. Furthermore, the copolymer induced the strand exchange reaction between intermolecular quadruplex and its single-stranded counterparts. We suggested that the copolymer acts as a nucleic acid chaperone for the intermolecular quadruplex.

Poly (L-lysine)-graft-dextran acts as a nucleic acid chaperone for tetramolecular quadruplex formation.

DNA sequence 5'-TGGGGT-3'; TG(4)T takes an intermolecular quadruplex structure which composed of four TG(4)T strands associated together by four layers of G-quartets with parallel strand orientation. Interestingly, its association rate is considerably slow, hampering its application of DNA nanobiotechnology. We have reported that the cationic comb-type copolymer seemingly promoted the nucleation step of DNA hybridization to accelerate duplex and triplex formation. Then, we presumed that the copolymer also influenced kinetics of the quadruplex formation. In this study, the effect of the copolymer on the intermolecular quadruplex folding was investigated. The copolymer was found to accelerate both the association and dissociation of tetramolecular quadruplex. We concluded that PLL-g-Dex acts as a nucleic acid chaperone for tetramolecular quadruplex formation.

Polymer brush-stabilized polyplex for a siRNA carrier with long circulatory half-life.

Delivery systems of small interfering RNA (siRNA) are the key to siRNA therapeutic application. In this study, we prepared and evaluated a series of cationic comb-type copolymers (CCCs) possessing a polycationic backbone (less than 30 weight (wt) %) and abundant water-soluble side chains (more than 70 wt.%) as a siRNA carrier with prolonged blood circulation time. Markedly, the CCC with the higher side chain content (10 wt.% PLL and 90 wt.% PEG) showed stronger interaction with siRNA than that with the lower content (30 wt.% PLL and 70 wt.% PEG), suggesting that highly dense PEG brush reinforces interpolyelectrolyte complex between the PLL backbone and siRNA. The siRNA complexed with the CCC was resistant to nucleases in 90% plasma for 24 h in vitro. The CCC having the higher side chain content increased circulation time of siRNA in mouse bloodstream by 100-fold. Surprisingly, even when the CCC and siRNA were separately injected into mouse at 20 min interval, blood circulation of post-injected siRNA was significantly increased. These results imply that the CCC has higher selectivity in its ionic interaction with siRNA than other anionic substances in blood stream. To our knowledge, this is the first example of a polyplex carrier that prolongs blood circulation time of unmodified siRNA without resource-consuming preparation process.

Spectroscopic investigation of cationic comb-type copolymers/DNA interaction: interpolyelectrolyte complex enhancement synchronized with DNA hybridization.

We have demonstrated that cationic comb-type copolymers consisting of a polycation backbone and abundant grafts of water-soluble polymers stabilize DNA hybrids. Furthermore, the copolymers were found to accelerate strand exchange reaction between a double-stranded DNA and its complementary single-stranded DNA. In this article, we investigated the effects of PLL-g-Dex on base pairs of a self-complementary DNA octamer, d(GGAATTCC). The soluble interpolyelectrolyte complex (IPEC) between the DNA and copolymer allowed us to characterize the complex by using spectroscopic methods under physiological ionic condition. Chemical shifts of nucleobase proton signals were not changed by PLL-g-Dex. Furthermore, the copolymer slightly changed the von't Hoff DeltaH accompanying the helix-coil transition of the octamer. These results indicated that the base pairs of the duplex DNA in the IPEC were not perturbed by the polycationic copolymer. It was obviously shown by temperature dependencies of proton and phosphorus NMR spectra that DNA/copolymer interaction was considerably enhanced in response to ds DNA formation. An increase in the density and total number of DNA negative charges upon hybrid formation likely caused the higher affinity of the copolymer with the ds form over that of the copolymer with the ss form. The IPEC formation of CCCs with DNA, however, seems highly sensitive to the coil-helix transition of the DNA.