Single-Cell Biophysics: Measurement, Modulation, and Modeling

Single-Cell Biophysics: Measurement, Modulation, and Modeling

Poster Abstracts

67-POS

Board 34

Threading Moiety Size Determines Locking Mechanism of DNA Threading Intercalators

Thayaparan Paramanathan

1,2

, Andrew Clark

, Fredrik Westerlund

, Per Lincoln

, Ioulia

Rouzina

, Mark C. Williams

Bridgewater State University, Bridgewater, MA, USA,

Northeastern University, Boston, MA,

USA,

Chalmers University of Technology, Gothenburg, Sweden,

The Ohio State University,

Columbus, OH, USA.

Threading intercalators are small molecules that bind to DNA by threading their ancillary motifs

through DNA bases to intercalate a middle planar section between the DNA base pairs. These

dumbbell-shaped molecules exhibit incredibly slow kinetics and high binding affinity compared

to classical intercalators. These properties put them in the class of prospective anti-cancer drugs.

We have been exploring a variety of ruthenium based threading intercalators using optical

tweezers. In an optical tweezers set-up, a single DNA molecule is attached between two

polystyrene beads and manipulated in the presence of various concentrations of intercalators to

characterize their DNA binding properties. These intercalators are introduced to the system at

different concentrations, while a single DNA molecule is held at a constant force. Measurements

of DNA extension as a function of time provide the DNA equilibrium binding affinity and force-

dependent binding kinetics for these molecules, revealing the structural rearrangements required

for intercalation. In this study we explore the binding of a binuclear ruthenium complexes ΔΔ-

[μ-bidppz(bipy)4Ru2]4+ (ΔΔ-B) in order to compare it with a previously studied sister molecule

ΔΔ-P. These molecules have the same middle intercalating dppz component that interacts with

the DNA and only their ancillary side chains, which must thread between the bases, are varied by

size. ΔΔ-P previously showed an unusual locking mechanism, in which DNA must first increase

in length for intercalation to occur, before decreasing in length as equilibrium is approached. The

force dependence of the kinetics for ΔΔ-B suggests that the small reduction in the size of side

chain in results in the elimination of the locking mechanism, fundamentally altering the overall

structural rearrangements required for binding.