Flexibility and thermal dynamic stability increase of dsDNA induced by Ru(bpy)2dppz2+ based on AFM and HRM technique

Fuchao Jia,Pascal Hébraud,Jing Wang,Xingguo Liang,Bo Liu,Kezhen Han

doi:10.1186/s13065-019-0584-9

Abstract

Ru(bpy)2dppz2+ has been widely used as a probe for exploring the structure of double-stranded DNA (dsDNA). The flexibility change of DNA helix is important in many of its biological functions but not well understood. Here, flexibility change of dsDNA helix caused by intercalation with Ru(bpy)2dppz2+ was investigated using the atomic force microscopy. At first, the interactions between ruthenium complex and dsDNA helix were characterized and the binding site size (p = 2.87 bp) and binding constant (Ka = 5.9 * 107 M−1) were determined by the relative extension of DNA helix using the equation of McGhee and von Hippel. By measuring intercalator-induced DNA elongation and the mean square of end-to-end distance at different molar ratios of Ru(bpy)2dppz2+ to dsDNA, the changes of persistence length under different ruthenium concentrations were determined by the worm-like chain model. We found that the persistence length of dsDNA decreased with increasing Ru(bpy)2dppz2+ concentration, demonstrating that the flexibility of dsDNA obviously enhanced due to the intercalation. Especially, the persistence length changed greatly from 54 to 34 nm on changing the molar ratio of ruthenium to dsDNA from 0 to 0.2. We speculated that the intercalation of dsDNA with Ru(bpy)2dppz2+ resulted in local deformation or bending of the DNA duplex. In addition, the thermal dynamic stability of DNA helix was measured with high resolution melting method which revealed the increase in thermal dynamic stability of DNA helix due to the ruthenium intercalation.

Highlights

Ruthenium complexes have been widely used in “molecular light switch”, deoxyribose nucleic acid (DNA) structure probes and anticancer drugs due to their good photochemical and photophysical properties [1,2,3,4,5]
The distance between two pixels was determined by their position coordinates l =2 +2, and the contour length of each double-strand DNA (dsDNA) was obtained by summation of the distance (Σ l) of all pixels on the DNA skeleton line
Morphology and binding property analysis In order to gain deeper insight into the influence of Ru(bpy)2dppz2+ intercalators on the conformational properties of dsDNA, it is critical to imaging individual DNA molecule on a mica surface under different ratios of Ru(bpy)2dppz2+ to DNA base pairs (Ru/DNAbps)

Summary

Introduction

Ruthenium complexes have been widely used in “molecular light switch”, deoxyribose nucleic acid (DNA) structure probes and anticancer drugs due to their good photochemical and photophysical properties [1,2,3,4,5]. The interaction between them can be regarded as the modification of double-strand DNA (dsDNA) which influence mainly on two aspects: (1) mechanical properties of DNA double strands which often characterized with the persistence length (it is a measure of how far a polymeric chain persists in a given direction), and (2) thermodynamic stability of DNA double strands. These two kinds of properties have great impacts on its overall shape as well as on many of biological functions, such as chromosomal DNA packaging, DNA damage repair, regulation of gene expression, and protein–DNA binding [14,15,16,17,18].

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Conclusion