Interactions of Binuclear Ruthenium(II) Complexes with Oligonucleotides in Hydrogel Matrix: Enantioselective Threading Intercalation into GC Context
Journal article, 2013

A stretched poly(vinyl alcohol) (PVA) film provides a unique matrix that enables also short DNA oligonucleotide duplex to be oriented and studied by linear dichroism (LD). This matrix further allows controlling DNA secondary structure by proper hydration (A or B form), and such humid films could potentially also mimic the molecular crowding in cellular contexts. However, early attempts to study intercalators and groove binders for probing DNA in PVA failed due to competitive matrix binding. Here we report the successful orientation in PVA of DNA oligonucleotide duplex hairpins with thread-intercalated binuclear complex [μ-(11,11′-bidppz)(phen)4Ru2]4+, and how LD depends on oligonucleotide sequence and metal center chirality. Opposite enantiomers of the ruthenium complex, ΔΔ and ΛΛ, were investigated with respect to enantioselectivity toward GC stretches as long as 22 bp. LD, supported by emission kinetics, reveals that threading intercalation occurs only with ΔΔ whereas ΛΛ remains externally bound, probably in either or both of the grooves of the GC-DNA. Enantioselective binding properties of sterically rigid DNA probes such as the ruthenium complexes could find applications for targeting nucleic acids, e.g., to inhibit transcription in therapeutic context such as treatment of malaria or cancer.



ruthenium(II) complexes

molecular crowding


Piotr Hanczyc

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Per Lincoln

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Bengt Nordén

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Journal of Physical Chemistry B

1520-6106 (ISSN) 1520-5207 (eISSN)

Vol. 117 2947-2954

Areas of Advance

Nanoscience and Nanotechnology

Life Science Engineering

Materials Science

Subject Categories

Physical Chemistry

Biochemistry and Molecular Biology

Polymer Technologies


Nano Technology