Methods for oligonucleotide synthesis

Abstract

Improved methods for solution-phase synthesis of purified short-chain oligonucleotide coupling units, such as dimers, trimers, and tetramers, suitable for use in solution-phase or solid-phase oligonucleotide synthesis are provided. In one embodiment, there is provided methods of preparing a coupled oligonucleotide, YZ, comprising: (a) providing first nucleotidic segments, Y, in solution, each of the first segments comprising one, two, three, four, six or eight nucleosides, and each of said first segments having a reactive functional group, a, which is a phosphoramidite group; (b) providing a plurality of second nucleotidic segments, Z, in solution, each of said first segments comprising one, two, three, four, six or eight nucleosides, each of said second segments having two non-identical reactive functional groups, b and c, which are a secondary alcohol group and a primary alcohol group, respectively; and (c) reacting said first and second segments in solution to produce a first linkage isomer, YZ-b, which retains a residual secondary alcohol group, b, and a non-identical second linkage isomer, YZ-c, which retains a residual primary alcohol group, c; and (d) reacting a mixture of said YZ linkage isomers, or derivatives thereof, with a selective capping reagent, in solution, whereby said residual secondary alcohol group, b, of said YZ-b linkage isomer remains selectively unchanged, and the residual primary alcohol group, c, of said YZ-c linkage isomer is selectively capped.