Significant improvement of quality for long oligonucleotides by using controlled pore glass with large pores

A key factor influencing the quality of long oligonucleotides is the choice of controlled pore glass (CPG) which is used as a solid support during oligonucleotide synthesis. We studied the influence of CPG pore size on the quality of 75-mer oligonucleotides. Using electrophoresis and HPLC, we demonstrated failure modes that can occur at certain oligo lengths with 1000A pore size, and compared yield and purity of 75-mer oligos using 1000A and larger pore size CPG. We showed that oligonucleotides with much better quality are obtained using CPG with pore sizes of 1400A and larger. We also identified the key characteristics for CPG selection that lead to the best CPG performance.