Sequence-based separation of ssDNA in capillary electrophoresis

Abstract

A series of experiments were designed and performed to understand the separation mechanism. Ribonucleotides including adenosine monophosphate (AMP) and uridine monophosphate (UMP) achieved similar separation to GMP, which confirmed that the separation is not based on specific interactions between self-assembled GMP structures and the DNA. Similar separations also were achieved by using dGMP and GMP with glucose or ribose, indicating that the sugar ring is not the cause of the separation. Replacing GMP with other salts achieved various degrees of separation, and the separation by potassium phosphate was almost as good as GMP. We therefore concluded that the separation mechanism is most likely based on general salt effects.