Nucleic acid scaffolds

The use of DNA hybridization just described opens up a novel, uncomplicated, yet powerful strategy for supramolecular synthesis Many different devices are connected to a distinct sequence codon and are subsequently organized on a suitable template strand. The utilization of appropriate nucleic acid scaffolds should even allow the fabrication of highly complex supramolecular structures by means of a modular construction kit. For approximately 20 years, the work of Seeman and coworkers [8,27] have been engaged in the rational construction of ID, 2D, and 3D DNA frameworks. They use branched DNA... 

Streptavidin-single-stranded DNA covalent conjugates were described as the building blocks for assembling nanostructured scaffolds [31], The amount and type of biotinylated ligands were used to modulate the affinity of duplex formation between solid-phase-bound nucleic acid templates and DNA-streptavidin conjugates. This system has been proposed for the design of fine-tuned sequence detection systems. 

Bifunctional adamantyl, as a hydrophobic central core, can be used to construct peptidic scaffolding [151], as shown in Fig. 27. This is the reason why adamantane is considered one of the best MBBs. This may be considered an effective and practical strategy to substitute different amino acids or DNA segments on the adamantane core (Fig. 28). In other words, one may exploit nucleic acid (DNA or RNA) sequences as linkers and DNA hybridization (DNA probe) to attach to these modules with an adamantane core. Thus a DNA-adamantane-amino acid nanostructure may be produced. 

We have now adjusted our molecular systems to provide a model in which both forces can operate simultaneously. The U-shaped relationship that exists between the imide function and amides of aryl amines creates a hydrogen bonding edge and a planar stacking surface that converge from perpendicular directions as in 44 to provide a microenvironment complementary to nucleic acid components. A large number of aromatic rings can be functionalized with this simple scaffold, and spacers (R) can also be incorporated. The imide function is a mimic of the thymine residues. 

The surface of each layer has two types of single stranded arms (e.g. one 3 — 5 and one 5 — 3 strand) which can bind to other monomers to render 1st-and 2nd-generation dendrimers 25 and 26. Therefore the molecular scaffold grows exponentially with each sequential layer of hybridization. If an oligonucleotide contains a sequence complementary to those at the surface of these networks it should be hybridized. The remaining free sequences from the other type of arms then bind in a standard nucleic acid blot (after they are bound to... 

Nanosized objects perform various functions in the biomedical field. In the human body, nanosized particulate substances behave very differently from larger particles. In 1986, Maeda et al. found that the stained albumin, having a size of several nanometers, naturally accumulates in the region of cancerous tissues, which is now well known as the enhanced permeability and retention (EPR) effect. Many studies in the field of nanoparticles are based on this finding. Another application of nanoparticles is the delivery system using various polyplexes that are composed of carrier molecules and plasmid DNA or nucleic acid drugs such as antisenses and siRNA. In addition, nanofibers are mainly used for biodegradable scaffolds in tissue... 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

The bottom-up synthesis of metallic nanowires was further applied to construct a nanotransistor device.93 The sequence-specific winding of the homologous nucleic acid carried by the RecA-protein into the duplex DNA was used to address the nucleic acid/protein complex on the DNA scaffold (Fig. 12.27). The subsequent association of the anti-RecA antibody to the protein DNA complex, followed by the association of the biotinylated antiantibody, and the linkage of streptavidin-modified carbon nanotube deposited the tubes in the specific domain of the DNA scaffold. The further... 

Abstract Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and these results are discussed with the focus on facile synthetic routes and favorable performance in biological systems. Many of these carbohydrates have been used to develop alternative types of biomaterials for nucleic acid delivery to typical polyplexes, and these novel materials are discussed. Also presented are polymeric vehicles that incorporate copolymerized carbohydrates into polymer backbones based on polyethylenimine and polylysine and their effect on transfection and biocompatibility. Unique scaffolds, such as clusters and polymers based on cyclodextrin (CD), are also discussed, with the focus on recent successes in vivo and in the clinic. These results are presented with the emphasis on the role of carbohydrate and charge on transfection. Use of carbohydrates as molecular recognition ligands for cell-type specific dehvery is also briefly... 

Natural Polysaccharides as Nucleic Acid Delivery Scaffolds.134... 

Srinivasachari S, Fichter KM, Reineke TM (2008) Polycationic [3-cyclodextrin click clusters monodisperse and versatile scaffolds for nucleic acid delivery. J Am Chem Soc 130 4618 1627... 

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