Molecular dynamics calculations of Cy3 and Cy5 cyanine dyes terminally attached to DNA

Zdeněk Chval¹ Ingrid Romancová,² Ondřej Kroutil,^1,2 Miroslav Šíp¹

¹Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, 370 11 České Budějovice, Czech Republic,

²Department of Physics and Biophysics, Faculty of Sciences, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic

Cyanine Cy3 and Cy5 are fluorescent dyes with many applications in nonlinear optics, laser physics and particularly in biomedical imaging and single-molecule spectroscopy.

In this contribution, the structure and dynamics of cyanine Cy3 and Cy5 dyes terminally attached to the 5’-end of the CCACTAGTGG oligonucleotide are studied by molecular dynamics (MD), metadynamics and DFT calculations. Stacking interactions between the distal indole ring and guanine base are characteristic for the structures of the most probable conformers and these are in excellent agreement with the experimental structures for both dyes.¹ Essential dynamics showed that there are two main modes which describe the relative motion of the cyanine dyes with respect the last GC base pair (Figure 1). Unlike for the Cy3 dye, the Cy5-DNA complex shows similar flexibility but due to the longer pentamethine chain the binding motifs with proximal indole ring are not accessible at 298 K.

Figure 1: Alignment of the structures with respect to the last GC base pair (colored by the atom names). Only atoms of the indole rings and polymethine linker are shown for all the structures except A1 for which the side chains and linker atoms are represented by lines.

A) Rotational- translational motion of the Cy3 dye with respect to the GC base pair in the direction A1 (blue) → A2 (red) → A3 (tan) → A4 (green). The change of stacking interactions during the motion: in A1 the distal indole ring is stacked with G, in A2 the Cy3 dye is almost de-stacked, in A3 and A4 the proximal indole ring is stacked with C and G, respectively.

B) Two translational motions of the Cy3 dye with respect to the GC base pair in the directions: (1) A1 (blue) → B1 (pink) → B2 (cyan) with partial de-stacking, and (2) A1 (blue) → C (violet) in which G is replaced by C in the stacking interactions of the distal indole ring of Cy3.

[1] Norman, D.G.; Grainger, R.J.; Uhrin, D.; Lilley, D.M.J. Biochemistry 2000, 39, 6317

This work is supported by the Czech Science Foundation (grant no. P208-12-0622).