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^^ DEEPER LOOK

Peptide Nucleic Acids (PNAs) Are Synthetic Mimics of DNA and RNA

Synthetic chemists have invented analogs of DNA (and RNA) in which the sugar-phosphate backbone is replaced by a peptide backbone, creating a polymer appropriately termed a peptide nucleic acid, or PNA. The PNA peptide backbone was designed so that the space between successive bases was the same as in natural DNA (see figure). PNA consists of repeating units of N-(2-aminoethyl)-glycine residues linked by peptide bonds; the bases are attached to this backbone through methylene carbonyl linkages. This chemistry provides six bonds along the backbone between bases and three bonds between the backbone and each base, just like natural DNA. PNA oligomers interact with DNA (and RNA) through specific base-pairing interactions, just as would be expected for a pair of complementary oligonucleotides. PNAs are resistant to nucleases and also are poor substrates for proteases. PNAs thus show great promise as specific diagnostic probes for unique DNA or RNA nucleotide sequences. PNAs also have potential application as antisense drugs (see problem 5 in the end-of-chapter problems).

Buchardt, O., et al., 1993. Peptide nucleic acids and their potential applications in biotechnology. Trends in Biotechnology 11:384-386.

11.7 • Hydrolysis of Nucleic Acids

Most reactions of nucleic acid hydrolysis break bonds in the polynucleotide backbone. Such reactions are important because they can be used to manipulate these polymeric molecules. For example, hydrolysis of polynucleotides generates smaller fragments whose nucleotide sequence can be more easily determined.

Hydrolysis by Acid or Base

RNA is relatively resistant to the effects of dilute acid, but gentle treatment of DNA with 1 mM HCl leads to hydrolysis of purine glycosidic bonds and the loss of purine bases from the DNA. The glycosidic bonds between pyrimidine bases and 2'-deoxyribose are not affected, and, in this case, the polynucleotide's sugar-phosphate backbone remains intact. The purine-free polynucleotide product is called apurinic acid.

DNA is not susceptible to alkaline hydrolysis. On the other hand, RNA is alkali labile and is readily hydrolyzed by dilute sodium hydroxide. Cleavage is random in RNA, and the ultimate products are a mixture of nucleoside 2'- and 3'-monophosphates. These products provide a clue to the reaction mechanism (Figure 11.29). Abstraction of the 2'-OH hydrogen by hydroxyl anion leaves a 2'-O~ that carries out a nucleophilic attack on the 8+ phosphorus atom of the phosphate moiety, resulting in cleavage of the 5'-phosphodiester bond and formation of a cyclic 2',3'-phosphate. This cyclic 2',3'-phosphodiester is unstable and decomposes randomly to either a 2'- or 3'-phosphate ester. DNA has no 2'-OH; therefore DNA is alkali stable.

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