Chemical Synthesis of Polynucleotides

Remember, both DNA and RNA polymers possess a 3, 5 -phosphodiester backbone. Two potentially reactive species that require protection so that the desired bond formation will occur are hydroxyl functions on the sugar and exocyclic amino functions (if present) on the base. Once this is achieved, then supposedly the desired bond formation can occur  

Of course, as with peptide bond formation, work must be done and so an activation process is necessary. A phosphodiester synthesis would not be possible by merely mixing phosphoric acid with the appropriately protected nucleosides. Finally, as will be discussed later, it may even be desirable to consider protection of the phosphate function. While this is not necessary (and was not done in the initial nucleotide synthesis), it is advantageous and is presently the most accepted protocol. 

Protection of the amino function of adenine, guanine, or cytosine may be necessary to prevent phosphoramidate formation during a phosphorylation. In rarer cases (especially with guanine) it may also serve the purpose of introducing hydrophobicity in an otherwise too polar nucleoside. 

Once acylated, the amino function is rendered chemically unreactive or nonnucleophilic. However, the amino acyl function often have to be introduced in a two-step procedure acylation of the entire nucleoside followed by selective deacylation of the sugar. Further, the glycosidic linkage of the JV-acyl derivative is usually more susceptible to hydrolysis. Typical 

The synthesis of iV-benzoyl guanosine is similar except that the hydroxide is replaced by methoxide. However, JV-benzoyl cytidine may be prepared by direct benzoylation of the base under conditions which do not affect 

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The Letsinger-Caruthers synthesis is unrelated to the biochemical one except in the area of efficiency. Because phosphites are so reactive, they would be totally unsuitable for the genetic tape itself, but because they are so reactive, they are ideally suited as intermediates in the chemical synthesis of polynucleotides. One can accomplish the needed condensation reactions with phosphites under strictly anhydrous conditions with very weakly acidic catalysts, and then stabilize the product by a mild oxidation of the phosphite to the desired phosphate with iodine. 

Polynucleotides possess a great many reactive groups (see Figure 29-1), which must be protected before a conventional chemical synthesis of polynucleotides via the sugar-phosphate polycondensation reaction can be performed. Consequently, an enzymatic synthesis is generally preferred. 

Chemical Synthesis of Oligonucleotides and Polynucleotides of Defined Sequences.—... 

Weber, H. and Khorana, H. G. (1968) Studies on polynucleotides. CIV. Total synthesis of the strac-tural gene for an alanine transfer ribonucleic acid for yeast. Chemical synthesis of an icosadeoxyribo-nucleotide corresponding to the nucleotide sequence 21-40. J. Molec. Biol. 72,219 (and accompanying papers). 

Whereas most of the work discussed so far in this essay has dealt with the synthesis of well-defined biochemical species supporting the theory of chemical evolution as first proposed by A. I. Oparin, one of Oparin s major concerns has been to develop a hypothesis of precellular evolution and to experimentally demonstrate that specific biochemical reactions can occur within simulated precellular entities (coacervates). In an elegant experiment, using polynucleotide phosphorylase in coacervate droplets and the appropriate substrate in the external medium, he showed a continuous uptake of the substrate, a rapid internal synthesis of polynucleotides and a continuous release of phosphate to the external environment. His more recent concepts on evolution of probionts and the origin of cells were presented at the 4th International Conference on the Origin of Life held in Barcelona, Spain, in 1973. Experimental models involving microspheres made of polymers of amino acids have been developed by S. W. Fox and coworkers > and other investigators. 

Nucleic acids are the molecules of the genetic apparatus. They direct protein biosynthesis in the body and are the raw materials of genetic technology (see Genetic engineering). Most often polynucleotides are synthesized microbiologicaHy, or at least enzymatically, but chemical synthesis is possible. 

Some six hundred structures of naturally occurring carbogenic molecules appe on the pages which follow, together with the name of each compound and references to the original literature of successful chemical synthesis. Thus, Part Three of this book is effectively a key to the literature of chemical synthesis as applied to the complex molecules of nature. The survey does not include oligomeric or polymeric structures, such as peptides, proteins, carbohydrates and polynucleotides, which fall outside the scope of this book because they can be assembled by repetitive procedures. 

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