Macronuclear proteins from the hypotrichous ciliate Stylonychia lemnae were isolated, separated on SDS-PAGE and electroblotted onto nitrocellulose filters. Filter binding assays with 32P-labeled macronuclear DNA and the synthetic telomere sequence (C4A4/G4T4) in combination with competition experiments revealed strong preference of a protein with a molecular mass of approx. 40 kDa to the terminal sequence of macronuclear gene-sized molecules.