Title

Viscometry and Atomic Force Microscopy Studies of the Interactions of a Dimeric Cyanine Dye with DNA

ACS Citation

Bordelon, J. A.; Feierabend, K. J.; Siddiqui, S. A.; Wright, L. L.; Petty, J. T. Viscometry and Atomic Force Microscopy Studies of the Interactions of a Dimeric Cyanine Dye with DNA. J. Phys. Chem. B 2002, 106, 4838-4843.

Abstract

The structures of the noncovalent complexes of DNA with a thiazole orange dimer (TOTO) were investigated in solution and when adsorbed to a mica substrate, using viscometry and atomic force microscopy (AFM), respectively. From the viscosity measurements at low TOTO:base pair concentrations, the dye lengthens the DNA helix by two times the base pair spacing, consistent with bisintercalation. Higher concentrations of TOTO cause a significant decrease in the viscosity of the DNA solutions, as also observed for related bifunctional ligands. The conformational changes induced by the dimer are compared to those of the monomer. The contour lengths of the DNA-TOTO complexes adsorbed onto mica were directly measured by AFM. These lengths and the size of the binding site are inconsistent with the bisintercalation binding mode observed in solution, suggesting an alternative mode of binding on mica. The structures of the noncovalent complexes of DNA with a thiazole orange dimer (TOTO) were investigated in solution and when adsorbed to a mica substrate, using viscometry and atomic force microscopy (AFM), respectively. From the viscosity measurements at low TOTO:base pair concentrations, the dye lengthens the DNA helix by two times the base pair spacing, consistent with bisintercalation. Higher concentrations of TOTO cause a significant decrease in the viscosity of the DNA solutions, as also observed for related bifunctional ligands. The conformational changes induced by the dimer are compared to those of the monomer. The contour lengths of the DNA-TOTO complexes adsorbed onto mica were directly measured by AFM. These lengths and the size of the binding site are inconsistent with the bisintercalation binding mode observed in solution, suggesting an alternative mode of binding on mica.

Source Name

Journal of Physical Chemistry B

Publication Date

1-1-2002

Volume

106

Issue

18

Page(s)

9868-9876

Document Type

Citation

Citation Type

Article