Nucleic acid electrophoresis separation heavily depends upon gel or nongel sieving matrix. Here we propose a metal ion mediated-capillary electrophoresis (MCE-CE) by utilizing the nonspecific interactions of Mg(2+) and Ca(2+) and demonstrate the size, conformation, or sequence based separation and characterization of versatile nucleic acid molecules in free solution. Mg(2+) and Ca(2+) can induce DNA separation at the concentrations as low as 100 and 50 muM, respectively. Noteworthy, the two naturally occurring polymorphisms of one base substitution that may change the secondary folding structure or base stacking can be discriminated by MCM-CE, showing its unique capability of resolving length-identical but conformation-different ssDNA. Benefiting from the achieved separation, we further demonstrate that the folding conformation of oligomers and its change caused by single base substitution can be promptly sensed by online coupled fluorescence polarization. We anticipate that this method will be applicable in length polymorphism analysis, single-strand polymorphism analysis, hybridization analysis, microRNA analysis, and study of protein-nucleic acid interactions and the conformation-function relationship.