Analysis of Altered DNA Structures: Cruciform DNA

Palindromic DNA sequences have the potential to form branched structures called cruciforms, in which the interstrand base pairs within the symmetric region are replaced with intrastrand base pairs. Cruciforms can sometimes form in vivo (1 ), and circumstantial evidence suggests that they may serve functional roles in such processes as transcription (1 ) or DNA replication (2 ). In addition, the four-way branch at the base of the cruciform is structurally equivalent to the Holliday junction, an intermediate in homologous DNA recombination (3 ,4 ). Thus, an understanding of the thermodynamics and kinetics of cruciform formation may illuminate a number of processes in nucleic acid metabolism.