Table 1

Summary of three- and six-finger protein affinities

ProteinTargetTarget sequences (5′-3′)Kd, nM
B3 (F2)b3 GGA GGG GAC g 4
E2 (F2)e2 GGG GGC GAG g 3
C5 (F2)c5 GGA GGC GGG g 30
E2C-HS1 (F2)e2c-hs1 GGG GCC GGA g 45
E2C-HS1 (Zif)e2c-hs1 GGG GCC GGA g 70
E2C-HS1 (Sp1)e2c-hs1 GGG GCC GGA g 35
E2C-HS2 (F2)e2c-hs2 GCC GCA GTG g 70
E2C-HS2 (Zif)e2c-hs2 GCC GCA GTG g 75
E2C-HS2 (Sp1)e2c-hs2 GCC GCA GTG g 25
E2C (F2)e2c-g GGG GCC GGA GCC GCA GTG g 25
E2C (Zif)e2c-g GGG GCC GGA GCC GCA GTG g 1.6
E2C (Zif)e2c-a GGG GCC GGA GCC GCA GTG a 2.3
E2C (Zif)e2c-muths1 AGT CTG AAT GCC GCA GTG g 200
E2C (Zif)e2c-muths2 GGG GCC GGA AGT CTG AAT g 200
E2C (Sp1)e2c-g GGG GCC GGA GCC GCA GTG G 0.5
E2C (Sp1)e2c-a GGG GCC GGA GCC GCA GTG a 0.75
E2C (Sp1)e2c-muths1 AGT CTG AAT GCC GCA GTG g 65
E2C (Sp1)e2c-muths2 GGG GCC GGA AGT CTG AAT g 100
  • Affinities of three- and six-finger proteins for various target sequences were determined by gel shift analysis. Proteins are named with uppercase letters, DNA target sequences with lowercase letters. F2, finger 2 framework; Zif, Zif268 framework; Sp1, Sp1C framework; mut, mutant; Hs, half-site. With respect to the target site overlap phenomenon, the base following each target sequence is given as a lowercase letter. The affinity of the Zif268-DNA interaction was determined to be 10 nM (unpublished results). Kd values are averaged from two independent experiments, with standard deviations of 50% or less.