Separation of sequence isomeric pyrimidine oligodeoxynucleotides using reversed-phase high-performance liquid chromatography

Studies on the nucleotide arrangement in DNA. Estimation of sequence isomers in pyrimidine deoxyribo-oligonucleotides

The population of pyrimidine deoxyribo-oligonucleotides obtained from DNA may be separated, first, into fractions comprising identical lengths (isotichs) and, subsequently, into the individual components of an isostich fraction varying in the cytidylic and thymidylic acid composition. At a third level of analysis the proportion of components exhibiting the same composition but different sequence may be determined. Selective removal of cytosine and the subsequent analysis for characteristic thymidine derivatives released during an acid-catalyzed beta-elimination reaction allowed estimation of the relative proportion of sequence isomers for pyrimidine isostichs of length two to five.

[Preparative isolation of tetra-, penta- and hexapurine oligonucleotides from partial hydrolysates of depyrimidinated herring sperm DNA]

Herring sperm DNA is chemically degraded to a complex mixture of purine nucleotides. The oligonucleotides are separated from the partial hydrolysates by column chromatography. The resulting mixture of trimer to hexamer purine oligonucleotides is subsequently fractionated on QAE-Sephadex into different mixtures of sequence-isomeric purine oligonucleotides. In a final separation, which uses reversed-phase (Nucleosil C18) high-performance liquid chromatography, these mixtures are separated under isocratic conditions into 35 pure defined purine oligonucleotides with four to six monomer units, 14 defined mixtures of sequence-isomeric purine oligonucleotides and several unidentified products. Purity and sequence of the isolated oligonucleotides are determined by the "fingerprint" method. The results of the high-performance liquid chromatographic and the "fingerprint" methods of the isolated oligonucleotides are discussed.