Rotational dynamics of short DNAs

Bryant S. Fujimoto; Julia M. Miller; Susan Ribeiro; J. Michael Schurr

doi:10.1117/12.146160

17 June 1993 Rotational dynamics of short DNAs

Bryant S. Fujimoto, Julia M. Miller, Susan Ribeiro, J. Michael Schurr

Proceedings Volume 1922, Laser Study of Macroscopic Biosystems; (1993) https://doi.org/10.1117/12.146160
Event: Laser Spectroscopy of Biomolecules: 4th International Conference on Laser Applications in Life Sciences, 1992, Jyvaskyla, Finland

Abstract

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.

Citation Download Citation

Bryant S. Fujimoto, Julia M. Miller, Susan Ribeiro, and J. Michael Schurr "Rotational dynamics of short DNAs", Proc. SPIE 1922, Laser Study of Macroscopic Biosystems, (17 June 1993); https://doi.org/10.1117/12.146160

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