Base-modified nucleic acids are being evaluated for applications in biotechnology and as therapeutic agents. We found that bicyclic-C (biC), which is a cytosine derivative with a propene attached at the N(4) and C(5) atoms, increases the stability of DNA duplexes. To establish the conformational effects of biC on DNA and to obtain insight into the correlation between the structure and stability of biC-containing DNA duplexes, the crystal structure of [d(CGCGAATT x biC x GCG)](2) has been determined at 2.2 A resolution. The global and local conformations of the present biC-containing duplex and the native duplex are very similar. Only the base stacking interactions at the base pair steps containing the biC residues are significantly changed. This change in stacking area, however, explains the increased stability of biC-containing DNA duplexes.