A homopurine . homopyrimidine sequence of the c:fos promoter was chosen as a target for a triple helix oligonucleotide. Eight DNA oligonucleotides that ranged from 14 to 31 bp were shown to form a triple helix with three sequences within the c-fos promoter region. Reactive derivatives of homopyrimidine oligonucleotides bearing the 5'-or 3'-terminal DNA alkylation aromatic 2-chloroethylamino group were also synthesized. It was concluded, based on the physical properties of the DNA oligonucleotide complex, that the oligonucleotide forms a colinear triplex with the duplex binding sites. We investigated in detail, using electrophoretic mobility and footprinting protection, whether such oligonucleotide . DNA complexes are of benefit in designing high-affinity probes for a natural DNA sequence in the mouse c-fos gene. Our results demonstrate that four different DNA targets within the c-fos promoter region can form triplex structures with synthetic oligonucleotides in a sequence-specific manner. Moreover, in vitro modifications of the retinoblastoma-gene-product-binding site of the cTfos promoter at position -83 in front of the cAMP/cAMP-responsive element binding site and fos-binding site 3/activator-protein-2-like (FBS3/AP-2-like) site at position -431 by triple helix forming oligonucleotides cause dramatic suppression of ,fox-chloramphenicol acetyltransferase activity in endothelial cells. These results provide a basis for the development of a specific oligonucleotide target forming triplex-DNA complex, and emphasize the importance of a target forming triplex as a basis for control of gene expression and cell proliferation.Keywords: cTfos ; triplex ; promoter ; transcription factor ; gene regulation, Intermolecular DNA triple helix formation offers the opportunity to achieve precise sequence recognition, and has a potential use in gene therapy [I, 21. The formation of a specific complex between two strands of polyuridylic acid and one strand of polyadenylic acid in the presence of divalent cations was first reported in 1957 131. Recent studies have revealed the site-specific formation of short intermolecular triplexes by a wide variety of techniques, which include different kinds of footprintings, affinity cleavage, and NMR [4-1 I]. Chemical and physical evidence indicates that the nucleotide bases of the third strand occupy the major groove of the Watson-Crick target duplex [12, 131. A triple helix in nucleic acid results from specific Hoogsteen-type or reverse Hoogsteen-type hydrogen-bonding interactions between bases in a homopurine strand of a Watson-Crick duplex and an additional third strand. Several DNA triplets have been characterized resulting in two distinct classes of structural motifs in DNA triplexes. In the case of pyrimidine . purine . pyrimidine (Y*RY) triplexes (so-called pyrimidine motif), the third pyrimidine-rich strand runs parallel to the purine strand of the target duplex resulting in the formation of T*AT and C+*GC base triple combinations [4, 6, 111. The requirement for protonation of the th...