The chemical synthesis ofnucleic acids and related compounds play an essential role innumerous areas of the life sciences. For example, syntheticoligonucleotides are used as primers for polymerase chain reaction(PCR) (e.g. 20mer) and DNA sequencing studies, as well as for thecreation of site-specific mutations. Certain artificialoligonucleotides have demonstrated usefulness as potentialtherapeutic reagents such as antisense molecules and also as probesin various biochemical studies. Recent progress in DNA microarraytechnology has required immobilization of pure syntheticoligonucleotides (50 60mer) on glass surfaces. In addition, basedon the recently completed sequencing of the human genome, genetherapy and gene-based diagnosis have entered the realm ofpossibility, both of which require the use of natural and unnaturaloligonucleotides of high purity.

The development of specialRNA is one of the key discoveries in the field of RNA application.Short double-stranded RNAs (dsRNA), with a general chain length of21-23mer and a two nucleotide 3’-end overhang, mediate specificgene suppression of mammalian cells. Such RNA is also called smallinterfering RNA (siRNA). siRNA guides endonucleolytic cleavage ofthe target RNA at a single site. The RNAi offers astronomicalpotentials for understanding and manipulating human diseases at thecellular level. Among the vast and rapidly exploding field ofsiRNA, some key developments taking place are summarizedas:

Internucleotide-bondformation is important for the synthesis of nucleic acids. Severalmethods have been developed for the syntheses of oligonucleotides,including the phosphodiester method, the phosphotriester method,the phosphate method, the phosphoramidite method, and theH-phosphonate method. An outline of these methods is provided inFig. (1).Among the methods employed for internucleotide-bondformation, the phosphoramidite method is superior in many respects,including coupling efficiency, stability of building blocks, easeof automation, purity of the product, and synthetic applicability.For the synthesis of medium-size (longer than 20mer)oligonucleotides, the average yield of one-base elongation mustexceed 99%. The amidite method meets this requirement.Phosphoramidites are a stable white powder and are easy to handlein a solid-phase synthesizer. The H-phosphonate method has alsobeen applied for the synthesis of relatively long oligomers (morethan 10mer); however, the purity of the final oligomers tends to berather low.

The synthesis cycle for RNAoligonucleotides consists of the same series of reactions as thecycle that is employed for Fast Deprotection DNA monomers. However,the rate of coupling for RNA monomers is slower, compared to thatof DNA monomers (a coupling time of 10 minutes for RNA monomers isrecommended compared to 90 seconds for DNA monomers). With theexception of the monomers and supports, RNA synthesis isaccomplished with the same reagents as DNA synthesis. All RNAphosphoramidites from GenePharma Reagents are diluted with dryacetonitrile. Fast Deprotection CAP A is employed to prevent thetransacylation of guanidite bases, similar to synthesis oftertbutylphenoxyacetyl (TAC) DNA monomers.