HLA-DQα polymorphisms: Oligonucleotide probes characterize the contribution of first and second domains to electrophoretic variants

Abstract Polymorphism is known to exist within the HLA-DQα locus in the human major histocompatibility complex, although such polymorphism may be “silent” in standard HLA typing. However, DQα polymorphism may be functionally significant, either through DQα epitopes functioning directly in the immune response or by affecting tertiary conformation of Ia molecules through differential α/β pairing. We have previously defined a particular DQα polymorphism through reactivity with a monoclonal antibody and restriction fragment length polymorphism pattern. We now characterize this DQα polymorphism through two-dimensional gel electrophoretic analysis and identify a subset of DQα molecules with unique characteristics. Investigation of these allelic variants using synthetic oligonucleotide probe analysis of genomic DNA suggests a localization of the DNA region encoding the DQα5 epitope and suggests possible evolutionary mechanisms accounting for these unique patterns.