Nucleic acids sugar-phosphate backbone

Nucleic acids possess sugar-phosphate backbones, whose net charges do not change over a relatively wide range of pH. Thus, charge densities are nearly constant for different nucleic acids, as their net charge is proportional to the number of residues (i.e. mass). Therefore, the pH of the medium is not as critical in nucleic acid electrophoretic characterization. 

The primary structure of nucleic acids refers to the sequence in which the four nitrogen bases (A, G, C and T in DNA and A, G, C and U) in RNA are attached to sugar phosphate backbone of the nucleotide chain. 

Just as the structure of a protein depends on its sequence of individual amino acids, the structure of a nucleic acid depends on its sequence of individual nucleotides. To carry the analogy further, just as a protein has a polyamide backbone with different side chains attached to it, a nucleic acid has an alternating sugar-phosphate backbone with different amine base side chains attached. 

Phosphodiester Linkage The sugar-phosphate backbone of nucleic acids can be probed at the phosphodiester linkage by 31p NMR spectroscopy. There are only two kinds of phosphodiester linkages in alternating purine-pyrimidine polynucleotides, namely dA dT and dT dA in poly(dA-dT). 

Peptide nucleic acid (PNA) is another analogue of RNA and DNA that has been considered as a potential ancestor of present day nucleic acids. In this molecule the natural sugar-phosphate backbone has been replaced by peptide-like linkages [218]. In recent years, novel syntheses of PNA have been reported mainly focused on their application for antisense and antigene therapies [219]. The physical-chemical properties of PNA make it both... 

Nucleic acids are polymers containing nitrogenous bases attached to sugar-phosphate backbones. The common nitrogenous bases of nucleic acids are the bicyclic purines, adenine and guanine, and the monocyclic pyrimidines, cytosine, uracil, and thymine (Fig. V-l). 

These purines and pyrimidines join to the sugar-phosphate backbones of nucleic acids through repeating /3-linked AT-glycosidic bonds involving the N9 position of purines and the N1 position of pyrimidines. There are two classes of nucleic acids ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). DNA and RNA differ in one of their nitrogenous base components (uracil in RNA, thymine in DNA) and in their sugar (ribose) moiety, as indicated in Fig. V-2. 

The hydrophobic effect stabilizes the three-dimensional structures of macromolecules. In the nucleic acid double helical structures, the hydrophobic bases are stacked along the helix axis and shielded from solvent by the hydrophilic sugar-phosphate backbone, which is heavily hydrated. A comparable scheme is found in many crystal structures of nucleosides and nucleotides, where the bases are stacked... 

The so-called peptide nucleic acids (PNAs) 2.67 (140-142) are examples of the replacement of the entire sugar-phosphate backbone with different functionah-ties that retain biological activity. The chemistry is similar to SP peptide synthesis employing Boc or Fmoc protocols (see Section 2.1). Peptide-ON hybrids, where either one (143) or two (144) of the ON termini are attached to peptide chains, have been reported. Acyclic silicon phosphoramidites 2.68 (145) have also been used for SPS of silicon-containing ON analogues. 

Nucleic acids, both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are linear polymers of four bases linked to a sugar-phosphate backbone as shown in Fig. 2.5a. The differences between DNA and RNA reside in the sugar moiety forming the backbone, and in one of the four bases whereas the sugar in RNA is ribose, it is deoxyribose in DNA both molecules contain bases adenine (A), guanine (G), and cytosine (C)... 

Most synthetic DNA analogs represent logical departures from the natural structure. However, one of the most radical structural modifications of DNA to appear in the literature is peptide nucleic acid (PNA, Fig. 1), in which the sugar-phosphate backbone is abolished entirely in favor of a pseudopeptide. PNA was first reported by Nielsen et al. in 1991... 

A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone... 

For nucleotides, the situation is more complex. Nucleotides dissociate to polyanions in aqueous solution, which can be readily analysed as [M-H] in negative-ion mode. Acidic protons in the sugar-phosphate backbone may be exchanged for mono and divalent cations from solution, e.g., Na, K, Mg ", and NH/. This actually disperses the signal for a particular nucleic acid over several peaks with different m/z. Desalting and/or ion-pairing agents like DMHA may be applied to reduce these problems. 

The subunits of nucleotides are finked together to form a long polymer chain in nucleic acids. The linkages are formed between the phosphate group of one subunit and the sugar group of the next. This matrix forms a sugar-phosphate backbone to the molecule of nucleic acid. 

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