Phosphoramidite chemistry

More recently, it has been shown that DNA oligomers can be synthesized directly on modified semiconductor surfaces using automated methods (196). The silicon surfaces are first modified to give a terminal, protected, hydroxyl group at which automated phosphoramidite chemistry can be performed (Fig. 61). Semiconductor processing methods... 

The use of click chemistry is a promising strategy as a postsynthetic ligation for nucleic acids in order to circumvent the time-consuming synthesis of phosphoramidites as DNA building blocks [31, 32]. This is particularly relevant for several fluorophores that are unstable under the acidic, oxidative, or basic conditions of automated DNA phosphoramidite chemistry and DNA workup. 

Fig. 64. An a-D-GalNAc phosphotriester dendron built using phosphoramidite chemistry (Kratzer and Roy, unpublished data).385...

Applied Biosystems Expression Array System (Foster City, CA) has devised a chemiluminescence-based microarray platform ntilizing 60-mer oligonncleotides which are validated offline by mass spectrometry and are snbseqnently printed onto a derivatized nylon substrate. Agilent Technologies (Palo Alto, CA) also ntilizes 60-mers, which are synthesized in sitn by ink-jet printing nsing phosphoramidite chemistry. 

Spiegelmers are a new class of substance for a wide field of applications, especially drug design. Their functional properties can be compared with the action of monoclonal antibodies. The production of spiegelmers is as simple as the synthesis of other oligonudeotides because standard chemical methods, for example common phosphoramidite chemistry, can be employed. 

By use of the nucleoside Py-dU we prepared a range of pyrene-modified duplexes by phosphoramidite chemistry [29]. The covalently attached pyrene group is located outside the DNA base stack. On excitation intramolecular ET in the Py-dU group represents injection of an excess electron into the DNA base stack. The differences between the prepared DNA duplexes are the bases located next to the Py-dU group. 

Over the last 20 years methods for the chemical synthesis of oligodeoxyribonucleotides and oligoribonucleotides have become available. The use of phosphoramidite chemistry, the introduction of solid-phase synthesis techniques and the possibility of automated synthe.sis has proved to be a powerful stimulus to streamline and simplify chemical procedures.23 ... 

Tor has reported a versatile method for the site-specific incorporation of polypyridine Ru and Os complexes into DNA oligonucleotides using solid-phase phosphoramidite chemistry. Nucleoside phosphoramidites containing a [(bpy)2M(3-ethynyl-l,10-phenanthroline)] " metal center covalently attached to... 

The cyclohexene nucleoside (CeNA) derivative of adenine (55) was incorporated into ODNs using standard phosphoramidite chemistry. Incorporation of (55) into a mixed DNA sequence resulted in a slight decrease in stability opposite a DNA target, but an increase opposite RNA, similar to results found for anhydrohexitol (HNA) derivatives. However, unlike HNA, CeNA was able to activate RNase H activity. The nucleoside (55) forms duplexes with RNA that are more stable than DNAiRNA duplexes. In NMR studies, it was shown that the cyclohexenyl A nucleotide adopts a y-endo conformation in ds-DNA. A CeNA RNA duplex is cleaved by RNase H, with Km and Vmax in the same order as DNAiRNA, but the Kcat is 600-fold lower for CeNA RNA. 

A 35-residue ollgorlbonucleotide constituting the 5 -end of the initiator tRNA from B.subtilis has been synthesised on solid-phase using phosphoramidite chemistry in combination with 2 -0-t-butyldimethylsilyl protection. For the protection of the exocyclic amino functions of the bases the phenoxyacetyl group was used for adenine and guanine whilst acetyl was preferred for cytosine. These comparatively acid labile acyl groups can be removed using relatively mild... 

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