Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for the life on Earth. Apart from Watson-Crick binding, Hoogsteen pairing has been found in many structures of nucleic acids.
Methylation of nucleic acids (NAs) is a post-replication or post-transcription mechanism that can modulate the structure and function of a NA without changing its sequence. Methylation of adenine at the N(6) position to form m6A is one of the most important and common epigenetic markers.
This paper describes an investigation of intermolecular H-bonding interactions of methylated derivatives of adenine with its complementary partner, thymine. Adenine derivatives with (di)methylamino groups in positions 2 or 6 have been prepared and their interactions with a thymine derivative have been studied by NMR spectroscopy and DFT calculations.
It has been found that Hoogsteen pairing is preferred for adenine derivatives, which offer two hydrogen-bond sites on both Watson-Crick and Hoogsteen sides of the molecule. Methylation of the N(6) position leads to further stabilization of the Hoogsteen pair.