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European Biophysics Journal

, Volume 44, Issue 1–2, pp 1–7 | Cite as

Characterizing the interaction between DNA and GelRed fluorescent stain

  • F. A. P. Crisafuli
  • E. B. Ramos
  • M. S. RochaEmail author
Original Paper

Abstract

We have performed single-molecule stretching and dynamic light-scattering (DLS) experiments to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single-molecule stretching show that the persistence length of DNA–GelRed complexes increases as the ligand concentration increases up to a critical concentration, then decreases for higher concentrations. The contour length of the complexes, on the other hand, increases monotonically as a function of GelRed concentration, suggesting that intercalation is the main binding mechanism. To characterize the physical chemistry of the interaction, we used the McGhee–von Hippel binding isotherm to extract physicochemical data for the interaction from the contour length data. Such analysis enabled us to conclude that the GelRed stain is, in fact, a bis-intercalator. In addition, DLS experiments were performed to study the changes of the effective size of the DNA–GelRed complexes, measured as the hydrodynamic radius, as a function of ligand concentration. We observed qualitative agreement between the results obtained from the two techniques by comparing the behavior of the hydrodynamics radius and the radius of gyration, because the latter quantity can be expressed as a function of mechanical properties determined from the stretching experiments.

Keywords

Intercalation Single-molecule stretching Dynamic light scattering Binding isotherm 

Notes

Acknowledgments

This work was supported by the Brazilian agencies: Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). The DLS experiments were performed in the “Laboratório de Microfluídica e Fluidos Complexos (LMFFC)” of Universidade Federal de Viçosa.

Supplementary material

249_2014_995_MOESM1_ESM.pdf (934 kb)
Supplementary material 1 (pdf 934 KB)

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Copyright information

© European Biophysical Societies' Association 2014

Authors and Affiliations

  • F. A. P. Crisafuli
    • 1
  • E. B. Ramos
    • 1
  • M. S. Rocha
    • 1
    Email author
  1. 1.Laboratório de Física Biológica - Departamento de FísicaUniversidade Federal de ViçosaViçosaBrazil

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