The fluorescence polarization anisotropies of ethidium intercalated in duplex DNAs containing 12 to 60 bp were measured and analyzed using a theory of deformable rods to obtain their hydrodynamic radii (R_H). The apparent R_H is 10.0 +/- 0.2 angstroms for 12 and 24 bp, but increases to 11.5 - 12.0 angstroms between 40 and 60 bp. This variation in R_H is attributed to the presence of slowly relaxing bends in the DNA. Consequently, the static equilibrium persistence length must be much smaller than the dynamic persistence length (P_d) defined by the dynamic (instantaneous) bending rigidity. We estimate that P_d > 1000 angstroms. R_H of a 48 bp duplex DNA is largely independent of NaCl concentration, which suggests that interionic forces do not much affect the rotational friction. However, R_H depends significantly on the concentrations of other ions, especially Mg²⁺ and Mn²⁺, which are believed to affect the hydration of DNA.

Date Published: 17 June 1993
PDF: 8 pages
Proc. SPIE 1922, Laser Study of Macroscopic Biosystems, (17 June 1993); doi: 10.1117/12.146160

Published in SPIE Proceedings Vol. 1922:
Laser Study of Macroscopic Biosystems
Jouko E. Korppi-Tommola, Editor(s)