In which domain is the bottom of the DNA-binding cleft? What type of secondary structure lines the bottom of the cleft? In which domain is the bottom of the DNA-binding cleft? What type of secondary structure lines the bottom of the cleft? The bottom of the cleft is in the fingers domain. It is lined with alpha helices. The bottom of the cleft is in the fingers domain. It is lined with a beta sheet. The bottom of the cleft is in the thumb domain. It is lined with both alpha helices and a beta sheet. The bottom of the cleft is in the palm domain. It is lined with alpha helices. The bottom of the cleft is in the palm domain. It is lined with a beta sheet.