The chemical synthesis of oligonucleotides and the phosphoramidite methodBy Klaus D. LinseThe study of nucleic acids has now become a successful and dynamic scientific enterprise. Nucleic acids are uniquely important 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 in its structure. The sugar moiety in DNA oligonucleotides is always dexoyribose 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 carrier. The bases are joined with deoxyribose sugar and protrude over the side. Both oligomers, DNA and RNA, consist of 5'->3' phosphodiester-linked nucleotide units that are composed of a 2'-deoxy-D-ribose (DNA) or a D -ribose (RNA) in their furanose and heteroaromatic forms. nucleobase (A, T, G, and C; A, U, G, C), and the resulting oligonucleotide chain is composed of a negatively charged polar sugar-phosphate backbone and a set of hydrophobic nucleobases. The amphiphilic nature of these polymers dictates the assembly and maintenance of the secondary and tertiary structures that the oligonucleotides can form. In the duplex structure of DNA, genetic information is stored as a linear nucleotide code. This code is accessible and replicated. RNA, or ribonucleic acid, is another structurally related essential biopolymer. RNA differs from DNA in that it contains the sugar ribose in place of deoxyribos... middle of paper ...... oligomeric, possible truncated failure sequences with free 5' hydroxyl ends, sub- deprotection products and silicates resulting from the hydrolysis of the glass support. Different purification methods can be used to separate the product oligonucleotide from the contaminating species. Figure 18: summary of the method for synthesizing phosphoamidite oligonucleotides. 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. PRESS IRL. Oxford University Press. 1991. User manual. MilliGen/Biosearch Cyclone™ Plus DNA Synthesizer. Winnacker, Ernst L.; From genes to clones: introduction to genetic engineering. VCH, 1987.