CanonicalVHCDR1 nucleotide sequences are conserved in all jawed vertebrates

Abstract

The antlbody combining alte is formed from the complementarlty-determining reglongs (CDR) of the havy and light chalns. Function, in antibodles, meand diverse atructures capable of binding a variety of llgands and the CDR have long been distinguished ad the sites of a high incidence of non-homologous replacement. The present studies show, despite the apparent protein diversity, the exlstence of canonical nucleotide sequences in the heavy chein CDR1. These sequences deduced from human and mouse CDR1, and their presence demonstratred experimentally in all representatives from the gnaghostome vertebrate classes. This unexpected conservation suggests that selection pressur for sequence diversity is counter-balanced by propertles of the encoded amino acids such as capcity for ligand interaction, structural requirements of the encoded amino acids such as capacity for ligand interaction, structural requirements of the CDR loop and perhaps retention of certain lignad-binding sequences. Part of the canonical nucleotlde sequence involves a motif that has been suggested as a hot spot for somatic hypermutation. The assay for the canonical sequence is PCR-based and provides a novel approach to cloning muitigene family members by using the hypervariable portions as target sequence.