DNA base pairs: are only the frontier atoms relevant

Share

23 April 2024

The conventional view that the strength of hydrogen-bond interactions in DNA base pairs is solely determined by the position and charge of the frontier atoms (i.e., the atoms that directly participate in the hydrogen bond) has been challenged in a recent study by Celine Nieuwland, Célia Fonseca Guerra, and colleagues from the Vrije Universiteit Amsterdam and the University of Barcelona, as published in Physical Chemistry Chemical Physics. Intermolecular hydrogen bonding plays a central role in self-assembly and molecular recognition in supramolecular (bio)chemistry. This motivates the research group of Professor Célia Fonseca Guerra at the Vrije Universiteit Amsterdam to study the bonding mechanisms of this fundamental interaction in order to understand the molecule of our genetic code better and aid the design of new and improved supramolecular systems and materials.

Unexpected

"This project started with a bachelor internship of a Pharmaceutical Sciences student," recalls Nieuwland. "We wanted to assess how altering the position of heteroatoms on the backside of DNA base pairs influences the intermolecular hydrogen-bond strength." Based on a popular model in the scientific community this adjustment would hardly affect the base pair stability as the hydrogen-bond strength would be mainly determined by the frontier atoms, that is the atoms directly involved in the hydrogen bonding. However, the Amsterdam team and their collaborators from the University of Barcelona found that this was not the case.

"Our quantum-chemical analyses revealed that the binding strength of multiple hydrogen-bonded dimers can be systematically tuned by varying the position of heteroatoms on the backside of the monomers although the position and charge of the hydrogen-bond frontier atoms are unaffected," explains Nieuwland. Instead, they uncovered that the relative hydrogen-bond strengths in these systems follow from the charge accumulation in the interacting molecules, extending beyond the frontier atom framework.

A fruitful collaboration

"We found that the strength of the hydrogen-bond interaction is also affected if one induces a change in the charge distribution on the back side of the interacting molecules." This is a manifestation of two effects: electrostatic interactions are not only between frontier atoms but also between distant atoms (i.e., long-range effects), furthermore the strength of intermolecular orbital interactions-and thus the hydrogen-bond strength-is influenced by charge alterations in non-frontier regions of the molecules. Nieuwland concludes: "It is great to see that a bachelor internship and an external collaboration can turn into a very successful project and a contributing publication."

You can read their work, featured on the cover of Physical Chemistry Chemical Physics,here: Phys. Chem. Chem. Phys.2024, 26, 11306. For more information, contact Prof. Dr. Célia Fonseca Guerra ([email protected]).