The chemical synthesis of oligonucleotides and the phosphoramidite methodBy Klaus D. LinseThe study of nucleic acids has now become a fruitful and dynamic scientific enterprise. Nucleic acids are of unique importance in biological systems. Genes are made of deoxyribonucleic acid, or DNA, and each gene is a linear segment, or polymer, of a long DNA molecule. A DNA polymer, or DNA oligonucleotide, contains a linear arrangement of subunits called nucleotides. There are four types of nucleotides. Each nucleotide has three components; a phosphate group, a sugar, and a base that contains nitrogen within its structure. The sugar moiety in DNA oligonucleotides is always dexoiribose, and there are four alternative bases: adenine (A), thymine (T), guanine (G), and cytosine (C). Phosphate groups and deoxyribose sugars form the backbone of each DNA support. The bases are joined to the deoxyribose sugar and protrude laterally. Both oligomers, DNA and RNA, consist of phosphodiester-linked nucleotide units at the 5'->3' position, composed of a 2'-deoxy-D-ribose (DNA) or D-ribose (RNA) in their furanose forms and a heteroaromatic nitrogenous base element (A, T, G and C; A, U, G, C) and the resulting oligonucleotide chain is composed of a polar, negatively charged sugar-phosphate backbone and a series of hydrophobic nitrogenous bases. The amphiphilic nature of these polymers dictates the assembly and maintenance of the secondary and tertiary structures that oligonucleotides can form. In the duplex structure of DNA, genetic information is stored as a linear nucleotide code. This code is accessible and replicable. RNA, or ribonucleic acid, is another structurally related essential biopolymer. RNA differs from DNA in having the sugar ribose instead of deoxyribos... center of paper... oligomer, possible truncated breakdown sequences with free 5'hydroxyl ends, byproducts of deprotection, and silicates from hydrolysis of the glass support . Different purification methods can be used to separate the produced oligonucleotide from the contaminating species. Figure 18: Summary of the phosphoamidite oligonucleotide synthesis method. Reference J.C. Biro, B. Benyó, C. Sansom, Á. Szlávecz, G. Fördös, T. Micsik and Z. Benyó; A common periodic table of codons and amino acids. Biochemical and Biophysical Research Communications 306 (2003) 408–415. Oligonucleotides and analogues: a practical approach. Edited by F. Eckstein. Series editors: D. Rickwood and BD Hames. IRL PRESS. Oxford University Press. 1991. Operations Manual. MilliGen/Biosearch Cyclone™ Plus DNA Synthesizer.Winnacker, Ernst L.; From genes to clones: an introduction to genetic technology. VCH, 1987.