Yen-Ling Chen 1 Yuh-Jyh Jong 2, 3 Jerome Ferrance 4 Jan-Sing Hsien 5 Chi-Jen Shih 6 Chia-Hsien Feng 6 Ming-Tsang Wu 7 Shou-Mei Wu 1, 6 1 Faculty of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan 2 Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 3 Department of Pediatrics, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan 4 Department of Chemistry, University of Virginia, Charlottesville, VA, USA 5 Department of Surgery, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan 6 Faculty of Fragrance and Cosmetics, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan 7 Department of Occupational and Environmental Medicine, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan Received July 8, 2007 Revised August 22, 2007 Accepted September 9, 2007 Research Article Single nucleotide polymorphism detection in the hMSH2 gene using conformation- sensitive CE CE allows for highly reproducible analysis of DNA fragments which can be used to detect DNA mutations including SNPs. We have utilized a simple and direct CE analysis method for SNP analysis called conformation-sensitive CE (CSCE), based on the principle of single nucleotide different to produce conformational changes in the mildly denaturing solvent system. This method was applied to analysis of a mutation in the promoter region of the hMSH2 gene. This gene belongs to the human DNA mismatch repair system, which is responsible for recognizing and repairing mispaired nucleotides, and mutations in the hMSH2 gene are known to cause hereditary non- polyposis colorectal cancer (HNPCC). PCR fragments generated from the promoter region of the hMSH2 gene, displaying either a C/C homozygote, C/T heterozygote, or T/T homozygote genotype, did not require further pretreatment before electrokinetic injection. The CE separation, using a 16Tris-borate-EDTA (TBE) buffer containing 3% w/v hydroxylethyl cellulose (HEC) and 6 M urea, was performed under reverse polarity with a separation temperature of 157C. The genotypes of 204 healthy volun- teers and 13 colorectal cancer patients were determined using CSCE, and the results confirmed by DNA sequencing. While the CSCE separations were shown to be highly reproducible and sensitive for screening large populations, no correlation was observed between cancer patients and this hMSH2 gene polymorphism. Keywords: Conformation-sensitive CE / hMSH2 gene / Single nuclotide polymorphisms DOI 10.1002/elps.200700488 634 Electrophoresis 2008, 29, 634–640 1 Introduction The human MSH2 gene is part of a highly conserved DNA repair system, which recognizes and replaces mispaired nucleotides in dsDNA [1]. A role for hMSH2 in cancer has firmly been established in hereditary nonpolyposis colorectal cancer (HNPCC) [2–9]. HNPCC is a dominantly inherited autosomal disease. Its characteristics are known as Lynch syndrome, classified into two types: Lynch Syndrome I (familial colon cancer) and Lynch Syndrome II, which includes other cancers of the gastrointestinal system or the reproductive system [2]. HNPCC is known to be associated with mutations in six genes including hMSH2, hMLH1, hPMS1, hPMS2, hMLH6, and hMLH3; among these, muta- tions in hMSH2, responsible for recognizing mispaired bases in DNA, are thought to be the main contributor [3]. In fact, the majority of germline mutations associated with col- orectal cancer have been identified in the hMSH2 gene [4]. For this reason, relationships between HNPCC or colorectal cancer and mutations in the hMSH2 gene, mapping to hu- man chromosome 2p22-21, have become important research areas [5]. A number of analytical methods to screen for muta- tions in the hMSH2 gene have already been established. Several studies, such as Yuan et al. [6], analyzed an hMSH2 gene mutation in the exon region using denatured HPLC Correspondence: Professor Shou-Mei Wu, Faculty of Fragrance and Cosmetics, Faculty of Pharmacy, College of Pharmacy, Kaoh- siung Medical University, 100, Shi-chuan 1st Rd., Kaohsiung 807, Taiwan E-mail: shmewu@kmu.edu.tw Fax: 1886-7-3159597 Abbrevations: CSCE, conformation-sensitive capillary electro- phoresis; HEC, hydroxyethylcellulose; HNPCC, hereditary nonpo- lyposis colorectal cancer; HPC, hydroxypropylcellulose; HPMC, hydroxypropylmethylcellulose; LPA, linear polyacrylamide; PEO, poly(ethylene oxide); TBE, Tris-borate-EDTA  2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.electrophoresis-journal.com