Revealing the Hydrogen Bonding Interaction of DNA with Unnatural Bases via Plasmonic Antenna Enhanced Infrared Spectroscopy

Li, J., Li, J., Yan, Z., Ding, XL., Xia, XH.,
The journal of physical chemistry letters


The incorporation of unnatural bases in DNA programming can break through the limits of Watson-Crick and Hoogsteen base pairing to expand the diversity of DNA structures. Thus, understanding the interaction between DNA and unnatural bases is of great importance in DNA nanotechnology. Here, we propose an approach of plasmonic antenna enhanced infrared spectroscopy to study the hydrogen bonding interaction between poly(thymine) DNA (poly T DNA) and melamine. The formation of multiple hydrogen bonds between melamine and thymine of poly T DNA is revealed by the appearance of a new infrared (IR) feature of the NH2 deformation vibration at 1680 cm-1. The binding rate constant (kb) and the dissociation rate constant (kd) of the affinity reaction reach 39.70 M-1·s-1 and 4.49 × 10-5 s-1, respectively. This work offers a valuable IR technique to study DNA nanostructures at the molecular level, providing unique physicochemical views of the interaction mechanism between DNA and unnatural bases in DNA programming.

DOI: 10.1021/acs.jpclett.1c02901