Investigating Halogen Bonds as Pairing Force in an Artificial DNA Base Pair

The past decades have seen significant expansion of the nucleic acid space with the development of modified artificial base pairs based on natural nucleic acid analogues and even entirely new designed base pairs. This expansion has led to tremendous potential for applications such as site-specific labeling and structural investigations. However, natural nucleic acids rely strongly on hydrogen bonding as the attraction force, which has driven the development of artificial base pairs that adapt this mechanism. To achieve orthogonality with natural bases, unnatural base pairs with alternative attraction forces, such as hydrophobic interactions, have been developed which however can perturb duplex structures. Our work introduces a completely newly designed artificial base pair that leverages halogen bonding (R-Hal···) as a directional hydrogen bonding-like interaction. We report computational studies that led to the development of this novel unnatural base pair and its synthesis. Our results demonstrate the successful acceptance of a bulky iodinated nucleoside triphosphate by KlenTaq DNA polymerase, enabling the selective enzymatic synthesis of a DNA strand containing the dIIPO-doIPP base pair. Our work presents the first demonstration of a novel base pair with halogen bonding potential that is enzymatically incorporated into DNA.