Electric birefringence of kilobase-sized DNA molecules

Abstract

Transient electric birefringence has been used to characterize the rotational diffusion of linear, circularly permuted pBR322 and SV40 DNA molecules. The birefringence relaxation times vary with the site of linearization, suggesting that the circularly permuted DNAs have different conformations in solution. The longest relaxation times are observed for DNA sequence isomers linearized at the major bend centers identified by gel electrophoresis 1 1 N.C. Stellwagen, Electrophoresis, 15 (1995) 691. . SV40 sequence isomers linearized at other locations have faster, but approximately equal, terminal relaxation times, suggesting that their free solution conformations are relatively independent of the location of the bend center within the sequence. By contrast, the terminal relaxation times of the various pBR322 sequence isomers vary approximately in accord with their electrophoretic mobilities in large-pore polyacrylamide gels, suggesting that the different mobilities may reflect real conformational differences between the sequence isomers.