Process for performing polynucleotide separations

A method for separating a mixture of polynucleotide fragments, said method comprising:

• a) applying a solution of said fragments and counterion reagent to a column, said column containing separation media having a non-polar surface, wherein said separation media have a pore size greater than 30 Angstroms and an average diameter of 1-100 microns, wherein said separation media comprises silica beads;
• b) eluting said fragments with a gradient eluting solvent of increasing organic component concentration, said eluting solvent containing a counterion agent;
• wherein surfaces which are contacted by the solution of the fragments and the eluting solvent are materials which do not trap or release multivalent metal cations therefrom, wherein said multivalent metal cations comprise multivalent metal cations which are capable of interfering with polynucleotide separation.

A method for separating a mixture of polynucleotide fragments, said method comprising:

• a) applying a solution of said fragments and counterion reagent to a column, said column containing separation media having a non-polar surface, wherein said separation media have a pore size greater than 30 Angstroms, wherein said media comprises alkylated silica beads;
• b) eluting said fragments with a gradient eluting solvent of increasing organic component concentration, said eluting solvent containing a counterion agent;
• wherein surfaces which are contacted by the solution of the fragments and the eluting solvent are materials which do not trap or release multivalent metal cations therefrom, wherein said multivalent metal cations comprise multivalent metal cations which are capable of interfering with polynucleotide separation.