Single-strand conformation polymorphism analysis by capillary zone electrophoresis in neutral pH buffer

Sensitivity of single-strand conformation polymorphism (SSCP) analysis of p olymerase chain reaction (PCR) products was reported to be lower in capilla ry zone electrophoresis (CZE) compared to conventional slab gel electrophor esis. We examined the effects of buffer ion type, pH, and temperature in an attempt to improve the mutation detectability in the SSCP-CZE mode. It was noted that, by utilizing short-chain polyacrylamide as sieving media while simultaneously lowering the temperature, there was no improvement of confo rmer detectability. On the contrary, there was a large increment in conform ers' resolution by running samples in a lower-pH buffer system. The effects of different buffering ions and pH values were investigated. By using a ne w buffer system, consisting of 35 mM 2-(N-morpholino)propanesulfonic acid ( MES), 30 mM tris(hydroxymethyl)aminomethane (Tris), 1 mu ethylene diaminete traacetic acid (EDTA), pH 6.8, and keeping constant all the other condition s, such as temperature, sieving, applied voltage, capillary length, and inn er diameter (ID), there was a remarkable improvement in resolution and the sensitivity became comparable to that of slab gel systems.