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Denaturing and non-denaturing gel electrophoresis as methods for the detection ofjunctional diversity in rearranged T cell receptor sequences

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Author: Offermans, M.T.C. · Sonneveld, R.D. · Bakker, E. · Deutz-Terlouw, P.P. · Geus, B. de · Rozing, J.
Institution: TNO Preventie en Gezondheid
Source:Journal of Immunological Methods, 1, 181, 101-114
Identifier: 232928
doi: doi:10.1016/0022-1759(94)00334-S
Keywords: Biology · Heteroduplex DNA molecule · Junctional diversity · Nucleic acid gel electrophoresis · T cell heterogeneity · T cell receptor · Animal · Base Sequence · Comparative Study · DNA · Electrophoresis, Polyacrylamide Gel · Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor · Intestinal Mucosa · Male · Mice · Mice, Inbred BALB C · Molecular Sequence Data · Polymorphism (Genetics) · Receptors, Antigen, T-Cell, gamma-delta · RNA · Sensitivity and Specificity · T-Lymphocytes


Two nucleic acid gel electrophoresis techniques were tested as a possible tool for analyzing junctional diversity in rearranged T cell receptor (TcR) sequences in order to define the extent of T cell heterogeneity. For this purpose denaturing gradient gel electrophoresis (DGGE) as well as non-denaturing gel electrophoresis (nDGE) techniques have been studied. Detection of junctional diversity is based on mobility shifts, caused by nucleotide sequence polymorphism, of polymerase chain reaction amplified rearranged TcR sequences. DGGE as well as nDGE procedures are suitable for the detection of junctional diversity in TcR V gene family sequences based on sequence dependent separation. Compared to DGGE, nDGE of DNA is a relatively simple and rapid procedure, with a high separation potential. nDGE permits separation of double stranded (homoduplexes) and/or single stranded DNA molecules of the majority of TcR chain encoding sequences. Formation and detection of unique heteroduplex molecules combined with single stranded DNA molecule analysis in nDGE permits the recognition of the remaining sequences, thus providing additional information on the degree of T cell heterogeneity. In conclusion, these nucleic acid gel electrophoresis techniques allow a direct assessment of the heterogeneity and clonality of T cell populations by the detection of junctional diversity in TcR chain encoding sequences. This analysis can be performed without the need of cell propagation and/or cellular cloning procedures, thereby eliminating the risk of introducing technical artefacts.