Low pH capillary electrophoresis application to improve capillary electrophoresis-systematic evolution of ligands by exponential enrichment

• A novel low pH CE-SELEX is proposed for interaction validation of proteins and ssDNA library.
• Reverse migration of complex and unbound ssDNA makes complete protein–ssDNA complex collection without ssDNA interference.
• Direct complex collection at cathode is convenient no need to exactly control collection time.
• Larger amount protein–ssDNA complex collection than common CE-SELEX.

In this work, a novel low pH CE-SELEX (LpH-CE-SELEX) as a CE-SELEX variant is proposed. Transferring (Trf), bovine serum albumin (BSA) and cytochrome c (Cyt c) as model protein are incubated with a FAM labeled ssDNA library, respectively. Incubation mixture is separated in low pH CE (pH 2.6), where positively charged protein, protein–ssDNA complex and negatively charged ssDNA library migrate oppositely without EOF driven. Analysis of protein–ssDNA complex under positive voltage and unbound ssDNA library under negative voltage by CE–UV are applied for interactive evaluation. By increasing injection time, larger amount protein–ssDNA complex can be collected conveniently at the cathode end whereas ssDNA migrates to anode. Finally, stability of protein–ssDNA complex in low pH CE separation is discussed.