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Published in Chad A. Mirkin, Spherical Nucleic Acids, 2020
Robert Elghanian, James J. Storhoff, Robert C. Mucic, Robert L. Letsinger, Chad A. Mirkin
A “melting curve” obtained at a wavelength of 260 nm on a nanoparticle-DNA aggregate hybridized by the freeze-thaw cycle gave a “melting” temperature (Tm) of 57°C (Fig. 79.3A, black circles), as compared with Tm = 56°C for a solution of free oligonucleotides hybridized in solution at room temperature in the absence of nanoparticles (Fig. 79.3A, red squares). The curve for the Au-nanoparticle/DNA complex is remarkably steep; the temperature range for melting [full width at half maximum (FWHM) = 4°C] is narrow compared with the temperature range for dissociation of the complex formed from the free oligonucleotides (FWHM = 12°C) (Fig. 79.3A, insets [15]). Corresponding sharp transitions at the same temperature but with a drop in absorbance rather than an increase were obtained when the dissociation of the nanoparticle aggregates was observed at 620 and 700 nm. All of the experiments with the nanoparticle conjugates measure changes in the optical properties of the nanoparticles (not the DNA). The oligonucleotides do not absorb at 620 and 700 nm, and the concentration of the target oligonucleotide in the colloid solution is too low to account for the absorbance change at 260 nm.
Biomolecules and Complex Biological Entities
Published in Simona Badilescu, Muthukumaran Packirisamy, BioMEMS, 2016
Simona Badilescu, Muthukumaran Packirisamy
Because of the presence of hydrogen-bond-forming groups in their molecules, there are two types of base pairs. Usually, the bases are identified by the first letter in their names, like A, T, G., C. The possible base pairs are A-T and G-C, as shown in Figure 3.32. Most DNAs exist in the form of a double helix, in which two linear strands are wound around each other, as seen in Figure 3.32. In double-stranded nucleic acids, base pairs are always formed between a purine and a pyrimidine. Thymine (T) is found only in DNA, while uracil (U) is found only in RNA, as seen in Figure 3.33. There is a phosphodiester linkage between the 5’-phosphate group of one nucleotide unit and the 3’-hydroxyl group of the next one. The backbone of nucleic acids is formed of alternating pentose and phosphate residues, which are both hydrophilic, while at near-neutral pH, the bases are hydrophobic. The bases may be regarded as side groups of the backbone, as can be seen in Figure 3.32. Nucleic acids are synthesized in a 5’ to 3’ direction. During the synthesis in cells, the enzymes (DNA and RNA polymerases) add nucleotides to the 3’ end of the previously incorporated base. By convention, a short nucleic acid, with fifty or less nucleotides, is called an oligonucleotide.
Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA Nanotechnology
Published in Peixuan Guo, Kirill A. Afonin, RNA Nanotechnology and Therapeutics, 2022
Peixuan Guo, Farzin Haque, Brent Hallahan, Randall Reif, Hui Li
A major limiting factor of RNA nanotechnology in therapeutic applications is the cost of the nanoparticle construction, especially for RNA nanoparticles that require larger RNAs. RNA oligonucleotides can be prepared by enzymatic transcription or automated solid-phase synthesis. Enzymatic synthesis can produce relatively long transcripts in significant quantities, while commercial non-enzymatic RNA chemical synthesis can only produce RNAs that are 40–80 nt long. The longest chemically synthetic RNA with biological activity is 117-nt long (Guo et al., unpublished data). When it comes to the synthesis of relatively long RNA oligonucleotides, the yield of a RNA oligo decreases greatly as the length of the oligo increases (Reese, 2002; Marshall and Kaiser, 2004).
PEGYLATION: an important approach for novel drug delivery system
Published in Journal of Biomaterials Science, Polymer Edition, 2021
Deepa Yadav, Hitesh Kumar Dewangan
Oligonucleotides are short DNA or RNA molecules, having a wide range of applications. Oligonucleotides formulation is developed for the efficient and safe delivery of drugs. They play an important role in the targeted drug delivery system. When acting as in vivo, having a short half-life due to its low stability for Exo and endonucleases and fast excretion due to their small size. Diffusion into the cell is prevented by their negative charge. Polyethylene glycol is attached to the hydroxyl group of nucleic acid (directly [48] or with the help of space linker [49] be created to enhance the constancy towards enzyme deprivation, extend the plasma permanence. Diffusion into cells is increased through masking the negative charge of oligonucleotides. A PEGylated aptamer, the 28meroligomer aptanib, has already been approved by the Food Drug Administration for the treatment of age-related macular degeneration of the retina. In this formulation, a branched Polyethylene glycol of 40 kDa was attached to the oligonucleotides during a pent amino linker [50].