Chemical synthesis of DNA oligomers containing cytosine arabinoside

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Abstract
The solid phase phospite triester synthesis of oligodeaxynucleotides containing cytosine arabinoside (araC) is described. A protected araC phosphor-amadite was prepared for the introduction of araC residues at 5' termini and internucleotide positions in DNA oligomers. These oligomers were utilized to demonstrate the formation of correct 3'–5' linkages, to test for alkaline lability at the araC site, and to study the stability of duplexes containing araC-G base pairs. For the introduction of araC residues at 3' terminal positions, a protected derivative of araC was coupled to functionalized silica. This material was used to prepare a test oligomer which was characterized enzymatically.