# A Flexible Quadruple-Stranded Helicate Demonstrates a Strong Binding Preference for DNA Three-Way Junctions by Induced Fit

## TL;DR

A new flexible molecule binds strongly to DNA three-way junctions by adapting its shape, offering insights into designing drugs that target specific DNA structures.

## Contribution

A flexible quadruple-stranded helicate with induced fit binding to DNA three-way junctions is introduced, contrasting traditional lock-and-key mechanisms.

## Key findings

- The helicate binds 3WJs with high affinity (Kd = 12 nM) compared to 4WJs (Kd > 4 μM).
- Molecular dynamics simulations show the helicate's size and flexibility allow induced fit binding to 3WJs.
- The helicate disrupts a base pair in 3WJs to increase cavity size and stabilize binding.

## Abstract

Nucleic acid junctions are key to many biological functions
from
recombination and repair to viral nucleic acid insertion and are an
attractive, functional biomolecular target. We describe a quadruple-stranded
diplatinum helicate that binds both three-way (3WJ) and four-way DNA
junctions (4WJ). This allows us to probe the relative importance of
size and shape in junction-binder design. Despite the helicate’s
tetragonal symmetry/shape being compatible with the 4WJ, microscale
thermophoresis (MST), isothermal calorimetry (ITC), and gel electrophoresis
competition experiments demonstrate that this metallo-supramolecule
displays a stronger affinity for 3WJs (Kd = 12 nM) than
for 4WJs (Kd > 4 μM) and other DNA structures.
The
experimental findings are supported by molecular dynamics simulations
that reveal the critical role of size. While the open form of the
4WJ is promoted when the helicate is in the cavity, the helicate’s
small size means it is unable to maintain π contacts with all
four junction base-pairs simultaneously. Although the helicate is
slightly too large for the smaller 3WJ cavity, simulations and experiments
show that it can open up the cavity (increasing the junction’s
hydrodynamic radius) by disrupting a base pair. The flexible helicate
also responds to the cavity upon binding by favoring one enantiomer
and allowing the helicate to adopt a stable final structure inside
the 3WJ that is an induced fit of the two dynamic structures (supramolecule
and DNA). This contrasts with previous lock-and-key examples of junction
recognition and opens up new possibilities for how to design DNA and
RNA junction-binding compounds.