Nucleic acids chemical modifications

Nucleic acids in the DNA contain a high number of nucleophilic sites that can be attacked by electrophilic intermediates (metabolites) of chemical compounds. DNA adducts formed may cause alterations in the expression of a critical gene in the cell and thus lead to cell death. For example, modification of p53 tumor suppressor gene may inactivate the functions of the p53 protein and render cells sensitive to malignant transformation. Also, formation of RNA adducts may inhibit key cellular events because RNA is essential for protein synthesis. 

Fig. 1 Chemical structures of backbone modifications used in therapeutic nucleic acid analogs. Shown are the unmodified DNA/RNA chemical structures in addition to a selection of first (PS), second (OMe, MOE), and third generation (PNA, LNA, MF) nucleic acid modifications...

Recent developments in DNA/RNA chemical synthesis have allowed us to attach some functional groups covalently to nucleic acids, thus permitting the introduction of a functionality or properties not normally present in the native biomolecule The use of non-nucleosidic linkers is probably the most popular approach for the 5 -terminal modification of chemically synthesized nucleic acid oligonucleotides and a number of such linkers are commercially available. The linker shown in Fig. 2 is designed as a phosphoramidate derivative so that it can be incorporated into the 5 -terminus of the sequence as the last... 

Masuda N, Ohnishi T, Kawamoto S, et al. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res. 1999 27 4436 1443. 

Based on the similarity of formalin-induced chemical modification between nucleic acids and proteins, the efficiency of heating protocols for DNA/RNA extraction has been demonstrated (see Chapter 3 for detail). Basic AR principle including heating condition and pH value of AR solution as well as certain chemicals may play roles to establish optimal protocols. 

Nanoparticle surface modification is of tremendous importance to prevent nanoparticle aggregation prior to injection, decrease the toxicity, and increase the solubility and the biocompatibility in a living system [20]. Imaging studies in mice clearly show that QD surface coatings alter the disposition and pharmacokinetic properties of the nanoparticles. The key factors in surface modifications include the use of proper solvents and chemicals or biomolecules used for the attachment of the drug, targeting ligands, proteins, peptides, nucleic acids etc. for their site-specific biomedical applications. The functionalized or capped nanoparticles should be preferably dispersible in aqueous media. 

The following sections describe the major enzymatic and chemical modification procedures used to label nucleic acids and oligonucleotides. 

The chemical modification of nucleic acids at specific sites within individual nucleotides or within oligonucleotides allows various labels to be incorporated into DNA or RNA probes. This labeling process can produce conjugates having sensitive detection properties for the localization or quantification of oligo binding to a complementary strand using hybridization assays. 

Chemical modification also may be used to label directly an oligonucleotide, eliminating the enzymatic step altogether. The chemical modification of nucleic acids can encompass several... 

Many of the chemical derivatization methods employed in these strategies involve the use of an activation step that produces a reactive intermediary. The activated species then can be used to couple a molecule containing a nucleophile, such as a primary amine or a thiol group. The following sections describe the chemical modification methods suitable for derivatizing individual nucleic acids as well as oligonucleotide polymers. 

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