Hydrogen bonding is weak in the presence of free water. The stacking of the bases is due to the hydrophobic interactions of the pi electrons and keeps water from the hydrogen bonding of the bases.
Solvents break up hydrophobic interactions, allowing water free access to the hydrogen bonds.
This weakens the hydrogen bonds between the bases by competition with the water. ACN, EtOH and IPA are good solvents to consider including in anion exchange mobile phases. Examples are NaClO 4 and NaBr. A cosmotropic salt increases structure. These salts should be avoided for difficult oligos.