The C2H2 zinc finger motif found in many transcription factors is thought t
o be for nucleic acid binding and/or dimerization. Nearly 1% of eukaryote g
enes are estimated to encode this motif. We investigated the gene family en
coding this motif in the Mus musculus mRNA by molecular indexing, a techniq
ue used to select a subpopulation of cDNA by ligation of adapters to cDNA f
ragments digested by a class HS restriction enzyme(s). In place of oligo-dT
primers in the original method, a polymerase chain reaction primer designe
d based on the conserved sequence of the C2H2 zinc finger protein stranded
cDNA was made from various mouse tissue mRNAs, digested with FokI and BsmAI
, and joined with adapters. Amplification of the cDNA with an adapter prime
r and zinc finger-specific primer yielded products enriched in zinc finger
protein genes. Fragments were separated by subsequent denaturing polyacryla
mide gel electrophoresis, and characterized by DNA sequencing. Consequently
, 259 C2H2 zinc finger motif sequences were obtained, among which 166 were
novel. Combined with the reported sequences, these mouse motif sequences we
re compared with those of other species such as Saccharomyces cerevisiae an
d Caenorhabditis elegans. Some of the amino acids in the motif sequence sho
wed strong bias among species. Most of the novel sequences were supposed to
be DNA-binding according to the surface potential of predicted tertiary st
ructures. (C) 2001 Elsevier Science B.V. All rights reserved.